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