1	CL0001	EGF	\N	EGF superfamily	Finn RD, Bateman A	anon	Members of this clan all belong to the EGF superfamily.  This particular superfamily is characterised as having least 6 cysteines residues.\	\	\	\	   These cysteine form disulphide bonds, in the order 1-3, 2-4, 5-6, which are essential for the stability of  the EGF fold.    These disulphide bonds are stacked in a ladder-like arrangement.  The Laminin EGF family is distinguished by having an an additional disulphide bond.  The function of the domains within  this family remains unclear, but they are though to largely  perform a structural role.  More often than not, there domains are arranged a tandem repeats in extracellular proteins.	2008-09-03 15:50:29	2004-03-17 16:02:08	26	325	6259	696	88541	1
3	CL0003	SAM	\N	Sterile Alpha Motif (SAM) domain	Finn RD	anon	SAM domains are found in a diverse set of proteins, which include  scaffolding proteins, transcription regulators, translational  regulators tyrosine kinases and serine/threonine kinases [1-3].   SAM domains are found in all eukaryotes and some bacteria [3] .   Structures of SAM domains reveal a common five helical structure.  The SAM domain is involved in a variety of functions. The most widespread function is in domain-domain interactions.   The SAM domain performs domain-domain interactions using multifarious  arrangements of the SAM domain.  More recently, the SAM domain within  the Smaug protein has been demonstrated to bind to the Nanos 3' UTR translation control element (Rfam:RF00161) [3]. This clan currently only represents the diverse SAM domain family and does not contain the more divergent SAM/Pointed family (Pfam:PF02198).	2008-09-03 15:50:29	2004-03-17 16:21:50	20	126	742	467	11010	1
4	CL0004	Concanavalin	\N	Concanavalin-like lectin/glucanase superfamily	Bateman A	anon	This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.	2008-09-03 15:50:29	2004-03-17 16:44:11	19	1631	2750	3131	34755	1
5	CL0005	Kazal	\N	Kazal like domain	Finn RD	anon	Kazal domains are found in both serine protease inhibitors and extracellular regions of agrins. The structure of the Kazal domain is a small alpha/beta fold. Typically the Kazal domain consists of 2 short-helices and a  3-stranded anti-parallel sheet.  The fold is contains several disulphide bonds. 	2008-09-03 15:50:29	2004-03-17 17:00:11	26	106	337	450	6552	1
6	CL0006	C1	\N	Protein kinase C, C1 domain	Finn RD	anon	The members of this clan are all variations of the protein kinase C1 domain that is characterised by a rich cysteine and histidine content.  The C1 domain is the N-terminal region of conservation found in protein kinase C domains.  This domain is involved in binding many ligands, which include diacylglycerol, phorbol  esters and zinc [1].	2008-09-03 15:50:29	2004-03-17 17:47:56	19	30	728	396	10495	1
7	CL0007	KH	\N	K-Homology (KH) domain Superfamily	Finn RD	anon	The KH domain is thought to be the second most prevalent RNA  binding motif in proteins.  The motif is characterised by a  conserved GXXXGXXG in the middle of the domain.  Structures of KH reveal that the KH domain is arranged as either a  beta-alpha-alpha-beta-beta (mini-KH domain) or  beta-alpha-alpha-beta-beta-alpha (maxi-KH domain).  The secondary elements are separated by at least four loop segments. The second loop is located between beta-1 and al  The KH domain can be found either as single or multiple copies.  The KH domain usually binds RNA as a multimer.	2008-09-03 15:50:29	2004-03-17 17:58:30	17	312	491	5344	38636	1
9	CL0009	ENTH_VHS	\N	ENTH/ANTH/VHS superfamily	Bateman A, McMahon H	anon	This clan includes the related ENTH and ANTH domains as well as the VHS domain. The ENTH domain is approximately 150 residues in length and is a solenoid of alpha-helices. The various ENTH domains have various lipid specificities but the key feature that distinguishes it functionally from ANTH domains is its ability to bend membranes. It does  this by folding an additional N-terminal helix on lipid binding. The ANTH domain is approximately 300 residues in length and is a PtdIns(4,5)P2 binding domain. It has no membrane bending properties. The VHS (Vps-27, Hrs and STAM) domain is a 140 residue long domain present in the very NH2-terminus of at least 60 proteins. Based on their functional characteristics and on recent data on the involvement of VHS in cargo recognition in trans-Golgi, VHS domains are considered to have a general membrane targeting/cargo recognition role in vesicular trafficking [5].	2008-09-03 15:50:29	2004-03-18 10:53:33	19	75	85	345	4028	1
10	CL0010	SH3	\N	Src homology-3 domain	Finn RD	anon	Src homology-3 (SH3) domains are comprised of about 60 amino acids, performing either an assembly or regulatory role.\	       For example, SH3 domains in the Grb2 adaptor protein  are essential for protein-protein interactions and\	\	      signal transduction in the p21 Ras-dependent growth factor signaling pathway.  Alternatively, SH3 performs a regulatory role in the Src family of tyrosine kinases. SH3 domains bind a variety of peptide ligands, many of which  contain a PxxP motif.  This PxxP motif is flanked by different specificity elements [1].   Structures of SH3 domains, both free and ligand complexed, have provided insights into the mechanism of ligand recognition. The SH3 fold consists of two anti-parallel beta sheets that lie  at right angles to each other.  Within the fold, there are two variable loops, referred to as RT and n-Src loops.  When SH3 binds to its ligand, the proline rich ligand adopts a PPII helix conformation, with the PPII helix structure recognised by a pair of grooves on the surface of the SH3 domain that  bind turns of the helix.  The SH3 grooves  are formed by a series of nearly parallel, well-conserved aromatic residues [1].	2008-09-03 15:50:29	2004-03-18 11:12:55	20	564	2030	4044	40209	1
11	CL0011	Ig	\N	Immunoglobulin superfamily	Bateman A, Finn RD	anon	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases.  Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The superfamily can be divided into discrete structural sets, by the presence or absence of beta-strands in the structure and the  length of the domains [1]. Proteins containing domains of the C1 and V-sets are mostly molecules of the vertebrate immune system. Proteins of the C2-set are mainly lymphocyte antigens, this differs from the composition of the C2-set as originally proposed [1]. The I-set is intermediate in structure between the C1 and V-sets and is found widely in cell surface proteins as well as intracellular muscle proteins.	2008-09-03 15:50:29	2004-03-18 16:23:40	25	3370	4292	3474	136715	1
12	CL0012	Histone	\N	Histone superfamily	Bateman A	anon	Members of this clan all possess a histone fold. Generally proteins in this clan are DNA binding.	2008-09-03 15:50:29	2004-04-19 14:28:04	17	742	154	9904	23976	1
13	CL0013	Beta-lactamase	\N	Serine beta-lactamase-like superfamily	Finn RD, Bateman A	anon	This superfamily contains proteins that have a beta-lactamase fold.  This includes beta-lactamases as well as Dala-Dala carboxypeptidases and glutaminases.	2008-09-03 15:50:29	2004-04-19 15:42:28	17	961	303	5474	58501	1
14	CL0014	Glutaminase_I	\N	Class-I Glutamine amidotransferase superfamily	Bateman A	anon	Most members of this clan are glutaminase enzymes. This superfamily is shown to be related in [1]. The clan also contains the DJ-1/PfpI family that includes the peptidase PfpI that has a catalytic Cys-His-Glu triad that differs from the class I GAT Cys-His-Glu triad.	2008-09-03 15:50:29	2004-04-28 09:27:01	21	334	418	7216	67224	1
15	CL0015	MFS	\N	Major Facilitator Superfamily	Bateman A	anon	The major facilitator superfamily (MFS) is one of the two largest families of membrane transporters found on Earth [1]. It is present ubiquitously in bacteria, archaea, and eukarya and includes members that can function by solute uniport, solute/cation symport, solute/cation antiport and/or solute/solute antiport with inwardly and/or outwardly directed polarity [1]. All permeases of the MFS possess either 12 or 14 transmembrane helices [1].	2008-09-03 15:50:29	2004-04-30 16:48:27	19	22	846	6356	249360	1
16	CL0016	PKinase	\N	Protein kinase superfamily	Studholme DJ	anon	This superfamily includes the Serine/Threonine- and Tyrosine- protein kinases as well as related kinases that act on non-protein substrates.	2008-09-03 15:50:29	2004-06-11 14:28:37	21	3279	6514	9586	173964	1
18	CL0018	bZIP	\N	bZIP-like leucine zipper	Studholme DJ	anon	This family of eukaryotic transcription factors contain a basic region adjacent to a leucine zipper.	2008-09-03 15:50:29	2004-06-16 18:30:26	14	321	111	611	8901	1
20	CL0020	TPR		Tetratrico peptide repeat superfamily	Studholme DJ	anon	Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.	2008-09-03 15:50:29	2004-06-21 18:12:39	24	947	20914	6771	404043	1
21	CL0021	OB	\N	OB fold	Studholme DJ, Bateman A	anon	The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands [1].	2008-09-03 15:50:29	2004-06-22 18:31:10	17	1592	988	7656	210543	1
22	CL0022	LRR		Leucine Rich Repeat	Studholme DJ	anon	Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.  This Pfam entry contains Leucine Rich Repeats not recognised by the Pfam:PF00560 model.	2008-09-03 15:50:29	2004-06-23 16:13:12	31	250	9511	3145	175606	1
23	CL0023	P-loop_NTPase	AAA;	P-loop containing nucleoside triphosphate hydrolase superfamily	Studholme DJ	anon	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	2008-09-03 15:50:29	2004-06-23 17:05:20	33	5523	12211	50680	1511292	1
25	CL0025	His_Kinase_A		His Kinase A (phospho-acceptor) domain	Studholme DJ	anon	This is the dimerisation and phospho-acceptor domain of a sub-family of histidine kinases. It shares sequence similarity with Pfam:PF00512 and Pfam:PF07536. It is usually found adjacent to a C-terminal ATPase domain (Pfam:PF02518). This domain is found in a wide range of Bacteria and also several Archaea.  It comprises one of the fundamental units of the two-component signal transduction system [2-7].	2008-09-03 15:50:29	2004-06-29 14:19:46	13	497	5781	7648	242300	1
26	CL0026	CU_oxidase	\N	Multicopper oxidase-like domain	Studholme DJ, Finn RD	anon	Many of the proteins in this family contain multiple similar  copies of this plastocyanin-like domain.	2008-09-03 15:50:29	2004-06-29 16:37:59	19	1015	245	19953	63536	1
27	CL0027	RdRP	\N	RNA dependent RNA polymerase	Bateman A	anon	This clan represents the replicative  RNA dependent RNA polymerase. from a variety of RNA viruses [1].	2008-09-03 15:50:29	2004-08-26 14:33:23	14	852	1801	12549	220781	1
28	CL0028	AB_hydrolase		Alpha/Beta hydrolase fold	Bateman A	anon	This catalytic domain is found in a very wide range of enzymes.	2008-09-03 15:50:29	2004-08-29 17:32:06	21	1989	2396	7428	180167	1
29	CL0029	Cupin		Cupin fold	Bateman A	anon	This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.	2008-09-03 15:50:29	2004-09-06 15:03:53	19	945	1162	6529	112082	1
30	CL0030	Ion_channel	\N	Ion channel (VIC) superfamily	Bateman A	anon	This superfamily contains a diverse range of ion channels that share a pair of transmembrane helices in common. This clan is classified as the VIC (Voltage-gated Ion Channel) superfamily in TCDB.	2008-09-03 15:50:29	2004-09-08 16:21:26	15	718	809	5250	44250	1
31	CL0031	Phosphatase	\N	Phosphatase superfamily	Bateman A	anon	This family includes tyrosine and dual specificity phosphatase enzymes.	2008-09-03 15:50:29	2004-10-26 13:53:48	12	480	558	2966	20482	1
32	CL0032	Dim_A_B_barrel	\N	Dimeric alpha/beta barrel superfamily	Bateman A	anon	This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel.  The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases.	2008-09-03 15:50:29	2004-10-26 16:31:17	14	510	186	4601	39476	1
33	CL0033	POZ	\N	POZ domain superfamily	Bateman A	anon	The POZ domain is found in a variety of transcription factors.  POZ domains are also found in the tetramerisation domain of voltage gated K+ channels. In general these domains mediate homo-oligomerisation.	2008-09-03 15:50:29	2004-10-27 13:52:11	13	223	1167	1178	26677	1
34	CL0034	Amidohydrolase	\N	Amidohydrolase superfamily	Bateman A	anon	This family includes a large family of metal dependent amidohydrolase enzymes [1].	2008-09-03 15:50:29	2004-10-27 17:19:50	14	704	479	5687	79783	1
35	CL0035	Peptidase_MH	\N	Peptidase clan MH/MC/MF	Bateman A	anon	This clan contains peptidases belonging to MEROPS clan MH, MC and MF.  We also include Nicastrin that is part of the gamma secretase complex and not known to be a peptidase.	2008-09-03 15:50:29	2004-10-28 13:48:22	15	680	539	5405	63766	1
36	CL0036	TIM_barrel		Common phosphate binding-site TIM barrel superfamily	Bateman A	anon	This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].	2008-09-03 15:50:29	2004-10-28 15:12:01	23	3964	973	10099	253453	1
37	CL0037	Lysozyme	\N	Lysozyme-like superfamily	Bateman A	anon	Barley chitinase, bacterial chitosanase, and lysozymes from phage and animals all hydrolyse related polysaccharides. The proteins little amino-acid similarity, but have a structurally invariant core consisting of two helices and a three-stranded beta-sheet which form the substrate-binding and catalytic cleft [1].	2008-09-03 15:50:29	2004-10-28 15:30:21	13	1502	527	5612	33680	1
39	CL0039	HUP	PP-loop; PP-ATPase;	HUP - HIGH-signature proteins, UspA, and PP-ATPase.	Bateman A, Anantharaman V	anon	The HUP class contains the HIGH-signature proteins, UspA superfamily and the PP-ATPase superfamily [1]. The HIGH superfamily has the HIGH Nucleotidyl transferases and the class I tRNA synthetases both of  which have the HIGH and the KMSKS motif [1],[2]. The PP-loop ATPase  named after the ATP PyroPhosphatase domain, was initially  identified as a conserved amino acid sequence motif in four distinct groups of enzymes that catalyse the hydrolysis of the alpha-beta phosphate bond of ATP, namely GMP synthetases, argininosuccinate synthetases, asparagine synthetases, and ATP sulfurylases [3]. The USPA superfamily  contains USPA, ETFP and Photolyases [1]	2008-09-03 15:50:29	2004-10-29 14:36:02	11	1108	838	6582	177746	1
40	CL0040	tRNA_synt_II	\N	Class II aminoacyl-tRNA and Biotin synthetases	Finn RD	anon	Aminoacyl-tRNA synthetases are key components of the protein translation  machinery that catalyse two basic reactions. First, the activation of  amino acids via the formation of aminoacyl adenylates and second, linking the activated amino acid to the cognate tRNAs. The aminoacyl-tRNA synthetases generate AMP as the second end product of this reaction, which differentiates them from the majority of ATP-dependent enzymes that produce ADP. In addition, there is a specific  aminoacyl-tRNA synthetases for each of the 20 amino acids and there are  two structurally distinct classes of aminoacyl-tRNA synthetases, each\	\	  encompassing 10 different specificities. The two classes have alternative modes of aminoacylation: class I aminoacylate the 2'OH of the cognate tRNA; class II aminoacylate 3'OH (with the exception of PheRS). Each class contain a conserved core domain  that is involved in ATP binding and hydrolysis and combines with  additional domains that determine the specificity of interactions with\	       the cognate amino acid and tRNA.  The class II core domain consist of a mixed-beta sheet, similar to that found in the biotin synthetases, hence why this family has also been included in  this clan.  The core domain contains three modestly conserved motifs  that are responsible for ATP binding.  The class II aminoacyl-tRNA  synthetases can contain additional nested domains, found inserted in the loops of the core domain [1] (and  reference therein).	2008-09-03 15:50:29	2004-11-08 11:24:57	16	514	340	5927	72316	1
41	CL0041	Death	\N	Death Domain Superfamily	Finn RD	anon	The death domain superfamily is composed of three families: the death domain (DD); the death effector domain (DED) and the caspase recruitment domain (CARD).  All of the members perform a pivotal role in signalling events that regulate apoptosis.   Protein-protein interactions are mediated by self-self associations, in which CARD-CARD, DD-DD and  DED-DED contacts are formed exclusively The three families possess remarkably similar structures, each comprising an antiparallel six helical bundle in the Greek Key topology.  Structurally, the DD and CARD families are the most dissimilar.  The former is comprised of two perpendicular three-helix bundles, whereas the latter CARD domain contains six helices that are almost parallel with each other.  Interestingly, the interactions in CARD or DD containing heterodimers are quite different [1]. 	2008-09-03 15:50:29	2004-11-11 10:28:31	12	135	742	249	6544	1
42	CL0042	Flavoprotein	\N	Flavoprotein	Finn RD	anon	Members of this clan are FMN or FAD-binding redox proteins.  Flavoproteins act in various electron-transport systems as  functional analogues of ferredoxin.  They are characterised by an open twisted alpha/beta structure consisting of five parallel  beta-sheets connected by alpha-helices which surround the sheet.	2008-09-03 15:50:29	2004-11-12 15:13:12	11	497	221	5019	35666	1
43	CL0043	Chelatase	\N	Chelatase Superfamily	Finn RD	anon	Metallated tetrapyrroles are used as prosthetic groups in  proteins involved in biologically important processes such as  photosynthesis, oxygen transport, drug metabolism and  nitric oxide synthesis. In living organisms, metallation is catalysed  by a group of enzymes called chelatases. This clan contains  ferrochelatase (heme) and cobalt chelatase [1]. 	2008-09-03 15:50:29	2004-11-12 16:49:49	11	77	45	4178	7625	1
44	CL0044	Ferritin		Ferritin-like Superfamily	Finn RD	anon	The members of this clan all share a distinctive four helical bundle. The four helices are arranged antiparallel with a left-handed twist. This helical bundle is distinguished from others by the long connection between the second and third helices.  Some of the members contain a Fe or Mn dimer at the centre of the helical bundle.  The ferritin fold was first described by Murzin AG and Chothia C, Cur Opin Struc Biol 1992, 2:895-903.	2008-09-03 15:50:29	2004-11-12 17:32:27	13	2058	121	6054	34310	1
45	CL0045	Rubredoxin	\N	Rubredoxin-like	Finn RD	anon	The Rubredoxin clan is comprised of three families:Rubredoxin, COX5B and desulforedoxin.Rubredoxin domains are small domains  (5-6 kDa) and bind one iron atom tetrahedrally bound by four cysteine  residues.Similar, desulforedoxin domains are small (4 kDa), but  usually form homodimers.  Each monomer binds one iron atom, but in  a distorted tetrahedral arrangement.  COX5B domains are membrane-anchored  rubredoxin-like domains. The domain in the Rubredoxin clan are usually comprised of 2 alpha helixes and 2-3 beta strands.	2008-09-03 15:50:29	2004-11-15 11:37:59	11	172	52	2672	4680	1
46	CL0046	Thiolase	\N	Thiolase-like Superfamily	Finn RD	anon	Thiolases are ubiquitous and form a large superfamily. Thiolases can function either degradatively, in the beta-oxidation  pathway of fatty acids, or biosynthetically. Biosynthetic thiolases  catalyse the formation of acetoacetyl-CoA from two molecules of  acetyl-CoA . This is one of the fundamental categories of carbon  skeletal assembly patterns in biological systems and is the first step  in a wide range of biosynthetic pathways [1].  Thiolase are usually dimeric or tetrameric enzymes.  Within each monomer there are two similar domains related by pseudo dyad.  The N-terminal of these two domains contains a large insertion of about 100 amino  acids.	2008-09-03 15:50:29	2004-11-15 12:47:24	15	575	1810	7516	102610	1
47	CL0047	CuAO_N2_N3	\N	Copper amine oxidase, domains 1 and 2	Finn RD	anon	Copper amine oxidase (CuAO) are comprised of three of four domains. In the case of the four domain CuAO, the N-terminal domain (termed N1, and is not present in the three domain CuAO) and the C-terminal catalytic domain sandwich two repeated domains (termed N2 and N3).  The function of these two homologous domains is uncertain.  N2 and N3 both have a cystatin-like fold [1].	2008-09-03 15:50:29	2004-11-15 13:04:24	11	186	31	504	1887	1
48	CL0048	LolA_LolB	\N	Lipoprotein localisation factors LolA/B	Finn RD	anon	Gram-negative bacteria lipoproteins are anchored to the periplasmic  surface of the inner or outer membrane depending on the sorting signal, which is the residue at position 2 of the polypeptide. Five Lol proteins  are involved in the sorting and membrane localisation of lipoprotein. An ATP-binding cassette (ABC) transporter, LolCDE, releases outer  membrane-specific lipoproteins from the inner membrane, causing the  formation of a complex between the released lipoproteins and the  periplasmic molecular chaperone LolA. When this complex interacts with  outer membrane receptor LolB, the lipoproteins are transferred from LolA  to LolB and then localised to the outer membrane. The structures of LolA  and LolB are remarkably similar to each other. Both have a hydrophobic  cavity consisting of an unclosed beta-barrel and an alpha-helical  lid [1,2].	2008-09-03 15:50:29	2004-11-15 13:13:26	11	10	5	2158	3976	1
49	CL0049	Tudor	\N	Tudor domain 'Royal family'	Finn RD, Bateman A	anon	This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains.  The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain.  The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins.\	More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain).  These are sequence neutral DNA binding proteins.\	The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary.  In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].	2008-09-03 15:50:29	2004-11-16 16:02:09	14	325	682	504	17304	1
50	CL0050	HotDog	\N	HotDog superfamily	Bateman A	anon	The HotDog fold was first observed in the structure of Escherichia coli beta-hydroxydecanoyl thiol ester dehydratase (FabA), where Leesong et al. noticed that each subunit of this dimeric enzyme contained a mixed alpha + beta 'hot dog' fold. They described the seven-stranded antiparallel beta-sheet as the 'bun', which wraps around a five-turn alpha-helical 'sausage', This superfamily contains a diverse range of enzymes. Membership includes numerous prokaryotic, archaeal and eukaryotic proteins involved in several related, but distinct, catalytic activities, from metabolic roles such as thioester hydrolysis in fatty acid metabolism, to degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. The superfamily also includes FapR, a non-catalytic bacterial homologue that is involved in transcriptional regulation of fatty acid biosynthesis [1].	2008-09-03 15:50:29	2004-11-19 13:30:09	11	673	1411	5349	52323	1
51	CL0051	NTF2		NTF2-like superfamily	Bateman A	anon	This superfamily contains a variety of enzymes such as Scytalone dehydratase, Delta-5-3-ketosteroid isomerase, Limonene-1,2-epoxide hydrolase among others. The family also includes presumed non-enzymatic homologues such as NTF2.	2008-09-03 15:50:29	2004-11-19 15:35:00	13	603	332	4350	23892	1
52	CL0052	NTN	\N	NTN hydrolase superfamily	Bateman A	anon	In the N-terminal nucleophile aminohydrolases (Ntn hydrolases) the N-terminal residue provides two catalytic groups, nucleophile and proton donor. These enzymes use the side chain of the amino-terminal residue, incorporated in a beta-sheet, as the nucleophile in the catalytic attack at the carbonyl carbon. The nucleophile is cysteine in GAT, serine in penicillin acylase, and threonine in the proteasome. All the enzymes share an unusual fold in which the nucleophile and other catalytic groups occupy equivalent sites. This fold provides both the capacity for nucleophilic attack and the possibility of autocatalytic processing [1].	2008-09-03 15:50:29	2004-11-19 17:25:18	17	2263	255	5468	47927	1
53	CL0053	4H_Cytokine		4-helical cytokine superfamily	Bateman A	anon	Cytokines are regulatory peptides that can be produced by various cells for communicating and orchestrating the large multicellular system. Cytokines are key mediators of hematopoiesis, immunity, allergy, inflammation, tissue remodeling, angiogenesis, and embryonic development [2]. This superfamily includes both the long and short chain helical cytokines.	2008-09-03 15:50:29	2004-11-21 12:08:45	14	272	33	865	5160	1
54	CL0054	Knottin_1	\N	Scorpion toxin-like knottin superfamily	Bateman A	anon	This clan includes a number of toxin families that share the knottin structure. These families come from scorpions, plants and arthropods.	2008-09-03 15:50:29	2004-11-22 17:39:28	12	164	12	369	2025	1
55	CL0055	Viral_ssRNA_CP	\N	Positive stranded ssRNA viruses coat protein	Finn RD	anon	The clan contains a set of viral coat protein families and peptidase A6. The only known peptidase  activity is an autolytic cleavage releasing a 44-residue  C-terminal fragment. The reaction is very slow and only occurs  within the assembled virion. There is debate whether this is actually a true peptidase. The virion with these coat or capsid\	proteins are icosahedral viruses containing sixty triangular  coat protein units, each unit consisting of three proteins. The coat  protein consists of two subdomains, an eight-stranded beta-barrel on  the surface and a three-helix bundle on the inner face.	2008-09-03 15:50:29	2004-11-24 13:16:32	12	790	144	9475	53300	1
56	CL0056	C_Lectin	\N	C-type lectin-like superfamily	Bateman A	anon	This clan contains domains that have a C-type lectin fold.  Many of these are known or expected to  mediate interactions with sugars.	2008-09-03 15:50:29	2004-11-24 13:34:58	11	581	825	748	15749	1
57	CL0057	Met_repress		MetJ/Arc repressor superfamily	Bateman A	anon	This superfamily contains the MetJ and Arc repressors that feature a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA [1].	2008-09-03 15:50:29	2004-11-24 15:10:49	13	185	88	3932	18127	1
58	CL0058	Glyco_hydro_tim		Tim barrel glycosyl hydrolase superfamily	Bateman A	anon	This large superfamily contains a range of glycosyl hydrolase enzymes that possess a TIM barrel fold. This CLAN merges clans GH-A, GH-D, GH-H and GH-K from CAZy.	2008-09-03 15:50:29	2004-11-25 11:37:58	15	2459	2481	7032	114169	1
59	CL0059	6_Hairpin		Six-hairpin glycosidase superfamily	Bateman A	anon	This Clan includes CAZy clans GH-L, GH-M and GH-G. The members of this clan share a common structure composed of 6 helical hairpins. Most members of this superfamily are glycosyl hydrolase enzymes.	2008-09-03 15:50:29	2004-11-26 15:47:32	14	530	867	4822	41246	1
60	CL0060	DNA_clamp	\N	DNA clamp superfamily	Bateman A	anon	Sliding DNA clamps are ring-shaped proteins that allow DNA polymerase to achieve high processivity during chromosome replication by tethering the polymerase catalytic subunit to DNA. All of the structures share a 12-fold symmetry around the ring consisting of a simple structural repeat, though there is structural divergence in some of the repeats. Bacterial beta-clamps contain six repeats per subunit with two subunits per ring while the eukaryotic and bacteriophage clamps contain four repeats per subunit with three subunits per ring. Pairs of these repeats form a domain, which has been termed the 'processivity fold'; thus the ring of the sliding clamp contains six domains and therefore is often described as having 6-fold symmetry. A structural representative of a fourth family of processivity fold proteins, namely the herpes simplex virus UL42 protein, is also available. UL42 does not form a ring-shaped clamp, however, but rather functions as a monomer and interacts with DNA quite differently than do sliding clamps; it has been suggested that UL42 resembles a primitive ancestor of sliding clamps [2].	2008-09-03 15:50:29	2004-11-26 17:13:41	11	241	64	5243	18116	1
61	CL0061	PLP_aminotran	\N	PLP dependent aminotransferase superfamily	Bateman A	anon	This superfamily contains a variety of PLP-dependent enzymes.	2008-09-03 15:50:29	2004-11-29 11:27:35	12	1560	574	7712	152775	1
62	CL0062	APC		APC superfamily	Bateman A	anon	This large superfamily contains a variety of transporters including amino acid permeases that according to TCDB belong to the APC (Amino acid-Polyamine-organoCation) superfamily.	2008-09-03 15:50:29	2004-11-29 18:13:15	12	36	417	5587	126928	1
63	CL0063	NADP_Rossmann		FAD/NAD(P)-binding Rossmann fold Superfamily	Finn RD	anon	A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme.  The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction.  Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1].  In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.	2008-09-03 15:50:29	2004-11-30 13:45:28	24	8681	8330	18998	984446	1
64	CL0064	CPA_AT	\N	CPA/AT transporter superfamily	Bateman A	anon	This Clan contains transporter proteins that belong to the CPA superfamily and AT superfamily according to TCDB [1].	2008-09-03 15:50:29	2004-12-02 10:12:55	11	10	163	5252	48799	1
65	CL0065	Cyclin	\N	Cyclin-like superfamily	Bateman A	anon	This Clan contains cyclins, Transcription factor IIB (TFIIB), and the Retinoblastoma tumour suppressor proteins. These were predicted to be related by sequence [1].	2008-09-03 15:50:29	2004-12-02 13:15:02	14	236	144	804	14080	1
66	CL0066	Trefoil	\N	Beta-trefoil superfamily	Bateman A	anon	This family corresponds to a large set of related beta-trefoil proteins [1].  The beta-trefoil is formed by six two-stranded hairpins [2]. Three of these form a barrel structure and the other three are in a triangular array that caps the barrel. The arrangement of the secondary structures gives the molecules a pseudo 3-fold axis.	2008-09-03 15:50:29	2004-12-06 15:34:20	13	659	720	1705	12929	1
67	CL0067	SIS	\N	SIS domain fold	Bateman A	anon	This catalytic domain catalyses isomerisation reactions of a variety of sugars [1].	2008-09-03 15:50:29	2004-12-06 16:11:44	12	275	84	6149	42474	1
68	CL0068	RIIa	\N	RIIa-like fold	Bateman A	anon	This clan includes both the RIIa dimerisation motif as well as the Dpy-30-like motif [1].	2008-09-03 15:50:29	2004-12-07 15:58:47	11	37	67	303	1405	1
69	CL0069	GFP	\N	GFP-like superfamily	Bateman A	anon	This superfamily has an unusual fold of an 11 stranded beta barrel enclosing an alpha-helix. This superfamily includes green fluorescent protein as well as a domain from nidogen.	2008-09-03 15:50:29	2004-12-08 17:25:21	11	623	171	194	602	1
70	CL0070	ACT	\N	ACT-like domain	Bateman A	anon	These domains are involved in binding to amino-acids and causing allosteric regulation of linked enzyme domains [1]. The relationship between these two families was first noticed in [2].	2008-09-03 15:50:29	2004-12-08 17:26:00	12	241	221	4906	47783	1
71	CL0071	His_phosphatase	PGM;	Histidine phosphatase superfamily	Finn RD, Rigden DJ	anon	The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle.  Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue.\	Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue.  The superfamily may be divided into two main branches [1].	2008-09-03 15:50:29	2004-12-09 14:54:21	11	292	168	4773	26470	1
72	CL0072	Ubiquitin	\N	Ubiquitin superfamily	Bateman A	anon	This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.	2008-09-03 15:50:29	2004-12-09 18:04:44	19	1053	1522	6169	107825	1
73	CL0073	P53-like	\N	Beta-sandwich DNA-binding domain	Bateman A	anon	This clan contains a variety of DNA-binding domains that contain an immunoglobulin-like fold. It includes the DNA-binding domains of NF-kappaB, NFAT, p53, STAT-1, the T-domain and the Runt domain [1].	2008-09-03 15:50:29	2004-12-10 09:44:45	12	340	136	553	5385	1
74	CL0074	Matrix	\N	Retroviral matrix superfamily	Bateman A	anon	This clan brings together matrix proteins from a variety of retroviruses.	2008-09-03 15:50:29	2004-12-10 10:07:15	12	41	88	280	38433	1
75	CL0075	Defensin	\N	Defensin/myotoxin-like superfamily	Bateman A	anon	This clan includes diverse defensins as well as myotoxins.	2008-09-03 15:50:29	2004-12-10 13:40:46	12	146	13	137	1375	1
76	CL0076	FAD_Lum_binding	\N	Riboflavin synthase/Ferredoxin reductase FAD binding domain	Finn RD	anon	Riboflavin nucleotide coenzymes and flavin adenine dinucleotide (FAD) are essential cofactors for a large number of flavoproteins involved in a diverse set of redox reactions.  There are thought to be four different FAD-binding folds [1].The FAD-binding fold of this clan is a cylindrical  beta-fold. More specifically, the domain forms a flattened six-stranded  antiparallel beta-barrel organised into two orthogonal sheets  (1-2-5 and 4-3-6) separated by one alpha-helix. The cylinder is open  between strands strand 4 and 5. This opening of the cylinder makes space  for the isoalloxazine and ribityl moieties of the FAD, to which hydrogen  bonds are formed from the open edges of the strands. The other end of  the cylinder is covered by the only helix of the domain,  which is essential for the binding of the pyrophosphate groups of the  FAD [1].The structural differences in the FAD-binding domain are  manifested mainly as loops of different length and extra extending  structural elements, which may be important for interactions with their  redox partners [1]. The structural core of all clan members is highly  conserved.	2008-09-03 15:50:29	2004-12-10 14:19:14	11	202	346	5130	31559	1
77	CL0077	FAD_PCMH	\N	PCMH-like FAD binding	Finn RD	anon	The FAD-binding domains contained in this family fall within the PCMH (p-cresol methyl-hydroxylase) family of FAD binding proteins as defined in [1].  In this family, the structure of the FAD binding domain is comprised of two subdomains.  Both of these subdomains have an alpha-beta fold.  The first subdomain is comprised of three parallel beta strands,  surrounded by alpha helices.  The second subdomain contains five antiparallel beta strands, also surrounded by alpha helices. The junction between these two subdomains forms the FAD bind pocket, where the ligand is bound by hydrogen and van der Waals bonds [1].	2008-09-03 15:50:29	2004-12-10 16:27:25	11	247	229	5425	25538	1
78	CL0078	DNA_ligase	\N	DNA/RNA ligase superfamily	Bateman A	anon	This superfamily contains both ATP-dependent and NAD dependent DNA ligase enzymes.  The family also includes mRNA capping enzymes.  The members of this clan were shown to be related by sequence in [1].	2008-09-03 15:50:29	2004-12-10 18:04:20	12	72	170	5269	10191	1
79	CL0079	Cystine-knot	\N	Cystine-knot cytokine superfamily	Bateman A	anon	The cytokine families in this clan have the cystine-knot fold.  In this 6 cysteines form three disulphide bridges that are interlinked.	2008-09-03 15:50:29	2004-12-14 17:03:09	12	253	73	2754	10562	1
80	CL0080	Mss4-like	\N	Mss4-like superfamily	Bateman A	anon	This clan contains TCTP, Mss4 and SelR families [1].	2008-09-03 15:50:29	2004-12-14 17:24:43	11	51	31	4242	6196	1
81	CL0081	MBD-like	\N	MBD-like DNA-binding domain	Bateman A	anon	This clan contains proteins with a distinctive three stranded DNA-binding domain [1].	2008-09-03 15:50:29	2004-12-14 17:44:54	12	24	149	2355	10578	1
82	CL0082	MIF	\N	Tautomerase/MIF superfamily	Bateman A	anon	This clan groups 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI) and 4-oxalocrotonate tautomerase (4-OT) with macrophage inhibitory factor (MIF).  Interestingly they all share an amino-terminal proline. Members of this clan for homotrimers [1].	2008-09-03 15:50:29	2004-12-15 11:44:36	11	347	29	3218	5290	1
83	CL0083	Omega_toxin		Omega toxin-like	Finn RD	anon	This clan contains a set of related small protein toxins and what appears to be the functionally distinct Albumin I domain. All members of this clan have a knottin-like fold.  Additional information about this clan may be found from [1].  	2008-09-03 15:50:29	2004-12-16 13:53:46	14	83	23	290	1853	1
84	CL0084	ADP-ribosyl	\N	ADP-ribosylation Superfamily	Finn RD	anon	The members of this clan all represent ADP-ribosylating catalytic domains.  The structurally conserved regions are located at the NAD binding region [1]. According to SCOP, the ADP-ribosylation domain is  thought to have an "unusual fold".	2008-09-03 15:50:29	2004-12-16 14:31:35	12	208	320	842	3271	1
85	CL0085	FAD_DHS	\N	DHS-like NAD/FAD-binding domain	Finn RD	anon	The members of this family adopt a Rossmann fold, similar to CLAN:CL0063. However, the members of this family are distinguished in that the FAD/NAD cofactor is bound in the opposite direction.  In this arrangement, the adenosine moiety is found bound at the  second half of the fold.\	   In addition, the conserved GxGxxG motif found in classical NADP binding Rossmann folds is absent.  Finally, another distinguishing characteristic is the formation of an internal hydrogen bond in the FAD molecule [1].	2008-09-03 15:50:29	2004-12-16 15:32:59	13	399	174	5116	30822	1
86	CL0086	FAD_oxidored	\N	FAD-linked oxidoreductase	Finn RD	anon	The members of this clan adopt a TIM barrel fold, which is reminiscent of flavin mononucleotide binding proteins, rather than one similar to other flavin adenine dinucleotide binding domains. However, the way the FAD cofactor binds in quite different compared to  the binding of FMN in the TIM-barrel structures [1].	2008-09-03 15:50:29	2004-12-16 16:43:38	11	60	30	4179	7837	1
87	CL0087	Acyl-CoA_dh	\N	Acyl-CoA dehydrogenase, C-terminal domain-like	Finn RD	anon	The Acyl-CoA dehydrogenase FAD binding domain forms an mostly alpha helical domain, comprised of four helices\	arranged in up-and-down bundle. In Acyl-CoA oxidase II this domain appears to have been duplicated.	2008-09-03 15:50:29	2004-12-17 10:15:37	12	254	148	3538	31652	1
88	CL0088	Alk_phosphatase	\N	Alkaline phosphatase-like	Finn RD	anon	The members of this clan all share a common structure of their catalytic domains, which contain conserved metal binding residues [1].	2008-09-03 15:50:29	2004-12-17 11:25:45	15	217	321	5028	38421	1
89	CL0089	GlnB-like	\N	GlnB-like superfamily	Finn RD	anon	The members of this clan are characterised by the fact the domains, each comprised of four beta-strand and two alpha helices, tend to form tetrameric structures [1].	2008-09-03 15:50:29	2004-12-17 12:10:20	12	264	47	4170	11982	1
90	CL0090	Globin	\N	Globin-like	Finn RD	anon	The globin fold is an evolutionary conserved six helical fold that is  found in bacteria and eukaryotes.	2008-09-03 15:50:29	2004-12-17 12:17:06	11	2247	121	4808	13282	1
91	CL0091	NAD_Ferredoxin	\N	Ferredoxin / Ferric reductase-like NAD binding	Finn RD	anon	The Ferredoxin / Ferric reductase-like NAD binding domain is  adopts a Rossmann like fold.  However, these families have been excluded from the classical NAD(P) binding Rossmann clan (CLAN:CL0063), due to a divergence of the GxGxxG motif.  In this clan, the motif phosphate binding motif is G-T/S-G-A/I-P.  The changes in the motif are a reflection of the different way that the NAD(P)H is bound by this fold and the classical Rossmann fold [1,2].	2008-09-03 15:50:29	2004-12-17 14:54:00	11	192	335	4749	22088	1
92	CL0092	ADF	\N	Actin depolymerizing Factor	Finn RD	anon	For motile cells such as Amoeba to move, there must be the rapid recycling of their actin cytoskeleton to enable a dynamic change in their shape. Gelsolin (PFAM:PF00626) and Cofilin (PFAM:PF00241) are  two key domain families in this process.  Both of these domain are  structural and functional similar [1,2].  In particular, the beta sheet found at the core of the domain is structurally well conserved, with the helices that surround this sheet less conserved[2]. 	2008-09-03 15:50:29	2004-12-17 17:36:22	11	154	175	529	7818	1
93	CL0093	Peptidase_CD	\N	Peptidase clan CD	Finn RD	anon	The members of this clan are all endopeptidase that have the catalytic dyad histidine followed by cysteine.  The catalytic histidine is preceded  by a block of hydrophobic residues and a glycine, where as the cysteine is preceded by a block of hydrophobic residues and a glutamine and an alanine. The members with a know structure adopt an alpha/beta fold [1].	2008-09-03 15:50:29	2004-12-21 13:25:00	13	474	1163	1706	9782	1
94	CL0094	Peptidase_ME	\N	LuxS/MPP-like metallohydrolase	Finn RD	anon	All members of this clan are characterised by a HXXEH motif, which is  is involved in zinc binding.  Furthermore all members adopt an alpha and  beta fold. More specifically, there us a four to six stranded antiparallel beta sheet surrounded by five helices. However, LuxS (PFAM:PF02664) is not a peptidase, although its hydrolytic mechanism of catalysis appears to be conserved [1].	2008-09-03 15:50:29	2004-12-21 13:57:38	11	224	73	4739	30361	1
95	CL0095	Peptidase_ML	\N	Peptidase Clan ML	Finn RD	anon	This clan contains HybD-like domains.  HybD is a nickel binding  endopeptidase.  Structural and sequences analyses have highlighted the  presence of two highly conserved motifs that are shared with germination proteases and HybD [1].  Members of this clan adopt an alpha/beta fold,  comprised of a central beta sheet, surrounded by alpha helices.	2008-09-03 15:50:29	2004-12-21 15:54:20	12	12	11	1706	3673	1
96	CL0096	Pept_Inhib_IE	\N	Peptidase Inhibitor Clan IE	Finn RD	anon	The members of this clan are all cystine rich domains, which form a knottin scaffold.  This clan should also contain alpha-amylase but currently this family is a singleton and can not be put into Pfam. Also see [1].	2008-09-03 15:50:29	2004-12-22 12:16:32	11	34	2	22	52	1
97	CL0097	TypeIII_Chap	\N	Type III secretory system chaperone	Finn RD	anon	The translocation of pathogenic proteins into a host cell is mediated by the type III secretory system. A component of this system is a  chaperone, which binds to the protein which is going to be secreted in the bacterial cytosol and is involved in translocation of the secreted  protein, although the chaperone is not translocated itself. An individual  chaperone associates with one or two specific proteins [1].  There are a large number of type III secretory system chaperones, which are small acidic proteins and exhibit significant sequence divergence.   This clan groups type III secretory system chaperones. Members with a  known structure form small compact globular domains with an alpha-beta(3)- alpha-beta(2)-alpha like organisation [1].	2008-09-03 15:50:29	2004-12-22 12:58:31	11	45	14	1697	3343	1
98	CL0098	SPOUT	AB_Knot;	SPOUT Methyltransferase Superfamily	Finn RD	anon	A distinct class of methylases that includes the SpoU and TrmD  superfamilies and two superfamilies of predicted methylases defined  by the YbeA and MJ0421 proteins in bacteria and archaea,  respectively [1] (PFAM:PF00588 PFAM:PF01746). SPOUT is  structurally  distinct  compared to more classical methyltransferases [1]. More specifically, the members of this clan form alpha/beta knots. Knots are extremely rare in protein structures as they pose a\	folding problem. The mechanism that allow a domain to be folded as a knot are unclear, but are discussed in [2] and reference therein. All members with known structure form homodimers.	2008-09-03 15:50:29	2004-12-22 15:38:51	13	112	85	5028	32567	1
99	CL0099	ALDH-like	\N	ALDH-like superfamily	Finn RD	anon	The aldehyde dehydrogenases (ALDHs) are a superfamily of multimeric  enzymes which catalyse the oxidation of a broad range of aldehydes into  their corresponding carboxylic acids with the reduction of their cofactor, NAD(P) into NAD(P)H.  The way that the NAD is bound is distinct from other NAD(P)-dependent oxidoreductases.  The domain represented by this  clan consists of two similar subdomains.	2008-09-03 15:50:29	2004-12-22 15:45:47	12	614	141	5455	48240	1
100	CL0100	C1q_TNF	\N	C1q and TNF superfamily	Finn RD	anon	The members of the C1q and TNF superfamily are involved in a diverse set  of functions, which include: defense, inflammation, apoptosis, autoimmunity differentiation, organogenesis, hibernation and insulin-resistant\	obesity [1].  Both C1q and TNF domains form a compact jelly-roll beta- sandwich.  The core of these structures are conserved between the two families and corresponds to the detectable sequence similarity. Proteins containing both of these domains, form trimers before they are active.  However, the surfaces of the domains are quite different and  this difference is thought to give rise to the function difference between the clan members[1].  	2008-09-03 15:50:29	2004-12-22 15:46:56	12	294	48	443	3534	1
101	CL0101	PELOTA	RNA_ribose_bind;	Pelota - RNA ribose binding superfamily	Finn RD	anon	The members of this clan are all involved in binding to ribose sugar of RNA[1].  Indeed, the key RNA binding residues are conserved across the different families [1].  Members of this clan form mixed alpha-helical and beta-sheet structures [1][2].	2012-10-06 18:35:16	2005-01-04 15:00:27	11	212	56	5002	13986	1
103	CL0103	Gal_mutarotase	\N	Galactose Mutarotase-like superfamily	Bateman A	anon	This clan is composed of a beta-sandwich that was first observed in domain 5 of beta-galactosidase, then as the central domain of copper amine oxidase, the C-terminal domain of chondroitinase, the C-terminal domain of hyaluronate lyase, the N-terminal domain of maltose phosphorylase and in Galactose Mutarotase [1]. All these enzymes act on a sugar substrate.	2008-09-03 15:50:29	2005-01-28 16:18:34	11	539	313	4717	24927	1
104	CL0104	Glyoxalase	\N	VOC superfamily	Bateman A	anon	This clan contains the VOC metalloenzyme superfamily [1]. The known types of reactions that are catalysed include isomerizations (glyoxalase I), epimerizations (methylmalonyl-CoA epimerase), oxidative cleavage of C-C bonds (extradiol dioxygenase), and nucleophilic substitutions (fosfomycin resistance proteins) [1].	2008-09-03 15:50:29	2005-01-28 18:11:34	12	363	157	4720	43346	1
105	CL0105	Hybrid	\N	Barrel sandwich hybrid superfamily	Bateman A	anon	This superfamily contains proteins with a hybrid motif [1]. This motif is embedded in structurally diverse proteins.	2008-09-03 15:50:29	2005-01-31 16:15:18	12	394	669	6221	139176	1
106	CL0106	6PGD_C	\N	6-phosphogluconate dehydrogenase C-terminal-like superfamily	Bateman A	anon	This helical domain is found associated with Rossmann domains.	2008-09-03 15:50:29	2005-01-31 18:34:00	12	232	123	5955	39015	1
107	CL0107	KOW	\N	KOW domain	Bateman A	anon	This superfamily includes proteins involved in translation that have a KOW like SH3-fold.	2008-09-03 15:50:29	2005-03-18 14:03:54	11	584	79	6487	23716	1
108	CL0108	Actin_ATPase	\N	Actin-like ATPase Superfamily	Finn RD	anon	The actin-like ATPase domain forms an alpha/beta canonical fold. The domain can be subdivided into 1A, 1B, 2A and 2B subdomains. Subdomains 1A and 1B share the same RNAseH-like fold (a five-stranded beta-sheet decorated by a number of alpha-helices). Domains 1A and 2A are conserved in all members of this superfamily, whereas domain 1B and 2B have a variable structure and are even missing from some homologues [1].  Within the actin-like ATPase domain the ATP-binding site is highly conserved. The phosphate part of the ATP is bound in a cleft between subdomains 1A and 2A, whereas the adenosine moiety is bound to residues from domains 2A and 2B[1].	2008-09-03 15:50:29	2005-03-22 09:34:28	15	1022	508	11461	141414	1
109	CL0109	CDA		Cytidine deaminase-like (CDA) superfamily	Finn RD, Coin L, Iyer LM, Zhang D, Aravind L	anon	This clan contains both free nucleotide and nucleic acid deaminases that act on adenosine, cytosine, guanine and cytidine, and are  collectively known as the deaminase superfamily.  The conserved fold  consists of a three-layered alpha/beta/alpha structure with 3 helices  and 4 strands in the 2134 order [1,2].This superfamily is further  divided into two major divisions based on the presence of a  helix (helix-4) that renders the terminal strands (strands 4 and 5) either parallel to each other in its presence, or anti-parallel  in its absence [2]. Structurally, the deaminase-like fold is present in four other superfamilies including the JAB-like metalloproteins,  the C-terminal AICAR transformylase-catalyzing domains of PurH,  Tm1506 and the formate dehydrogenase accessory subunit FdhD. The active site of the deaminases is composed of three residues  that coordinate a zinc ion between conserved helices 2 and 3. The  residues are typically found as [HCD]xE and CxxC motifs at the  beginning of helices 2 and 3. The zinc ion activates a water  molecule, which forms a tetrahderal intermediate with the carbon  atom that is linked to the amine group. This is followed by  deamination of the base.  	2008-09-03 15:50:29	2005-03-22 09:57:40	11	208	1010	5319	27014	1
110	CL0110	GT-A		Glycosyl transferase clan GT-A	Bateman A	anon	This is the GT-A clan that contains diverse glycosyltransferases that possess a Rossmann like fold [1].	2008-09-03 15:50:29	2005-03-22 10:54:55	11	713	1496	7680	127750	1
111	CL0111	GT-C		Glycosyl transferase GT-C superfamily	Bateman A	anon	This is the GT-C clan that contains diverse glycosyltransferases that possess 8-13 predicted transmembrane segments [1].	2008-09-03 15:50:29	2005-03-22 13:52:31	10	19	303	4345	19864	1
112	CL0112	Yip1		Yip1/YIF1-like	Finn RD, Mistry J	anon	Yip1 and YIF1 are members of an integral membrane complex which bind to Ras-like GTPases and are required for membrane fusion of ER derived vesicles with the Golgi [1].	2008-09-03 15:50:29	2005-03-22 15:32:52	12	4	63	2706	5788	1
113	CL0113	GT-B	\N	Glycosyl transferase clan GT-B	Bateman A	anon	This is the GT-B clan that contains diverse glycosyltransferases that possess a Rossmann like fold [1].	2008-09-03 15:50:29	2005-03-22 17:19:24	12	539	1601	8102	141567	1
114	CL0114	HMG-box	\N	HMG-box like superfamily	Bateman A	anon	This clan includes the DNA-binding HMG-box proteins as well as the YABBY-like transcription factors.	2008-09-03 15:50:29	2005-03-23 13:44:43	11	62	241	1493	10953	1
115	CL0115	Steroid_dh	\N	Steroid oxidoreductase superfamily	Bateman A	anon	This clan includes several enzymes, including steroid dehydrogenases and isoprenylcysteine carboxyl methyltransferase enzymes. These protein contain a varying number of transmembrane regions.	2008-09-03 15:50:29	2005-03-23 14:15:40	11	1	60	2542	7438	1
116	CL0116	Calycin	\N	Calycin superfamily	Bateman A	anon	The calycin structural superfamily [1-3] includes the lipocalins, the fatty acid-binding proteins (FABPs).	2008-09-03 15:50:29	2005-03-23 14:57:38	12	662	102	3233	10920	1
117	CL0117	uPAR_Ly6_toxin	\N	uPAR/Ly6/CD59/snake toxin-receptor superfamily	Bateman A	anon	This superfamily contains snake toxins as well as extracellular cysteine rich domains.	2008-09-03 15:50:29	2005-03-30 14:52:26	10	228	28	268	2910	1
118	CL0118	Ribokinase	\N	Ribokinase-like superfamily	Bateman A	anon	All of these enzymes are phosphotransferases that have an alcohol group as an acceptor (EC:2.7.1.-). However, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase) catalyses two phosphorylation reactions: one to a hydroxymethyl group of hydroxymethyl pyrimidine (HMP) and the second to the phosphomethyl group of HMPP [1]. The common structural feature for the enzymes in this superfamily is a central eight-stranded sheet that is flanked by eight structurally conserved helices, five on one side and three on the other [1]. The active site is located in a shallow groove along one edge of the sheet, with the phosphate acceptor hydroxyl group and -phosphate of ATP close together in the middle of the groove, and substrate and ATP binding at the ends [1].	2008-09-03 15:50:29	2005-04-01 13:48:37	11	400	155	5041	42135	1
121	CL0121	Cystatin		Cystatin-like superfamily	Bateman A	anon	This superfamily includes cystatins and cathelicidins [1]. The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. Stefins - included in Pfam:PF00031 - remain encoded by a single or a small number of genes throughout the eukaryotes, whereas the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications [2].	2008-09-03 15:50:29	2005-04-05 16:56:37	11	86	26	392	2322	1
122	CL0122	UTRA	Chor_lyase;	Chorismate lyase/UTRA superfamily	Bateman A	anon	This clan includes chorismate lyase as well as the UTRA domain	2008-09-03 15:50:29	2005-04-05 17:05:44	10	71	33	3574	14169	1
123	CL0123	HTH		Helix-turn-helix clan	Bateman A	anon	This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.	2008-09-03 15:50:29	2005-04-05 17:52:07	17	2812	5699	10949	1020775	1
124	CL0124	Peptidase_PA		Peptidase clan PA	Bateman A	anon	This clan contains a diverse set of peptidases with the trypsin fold.	2008-09-03 15:50:29	2005-04-06 15:44:18	14	2540	1159	7202	60527	1
125	CL0125	Peptidase_CA		Peptidase clan CA	Bateman A	anon	This clan includes peptidases with the papain-like fold.	2008-09-03 15:50:29	2005-04-06 17:40:48	14	814	1796	6922	76571	1
126	CL0126	Peptidase_MA		Peptidase clan MA	Bateman A	anon	Clan MA is one of two zinc-dependent metallopeptidases that contain the HEXXH motif.  The two histidines are zinc ligands. The structures of this clan show the active site is between its two sub-domains.	2008-09-03 15:50:29	2005-04-07 08:52:20	17	981	1676	6188	88418	1
127	CL0127	ClpP_crotonase		ClpP/Crotonase superfamily	Bateman A	anon	This family includes several peptidases of peptidase clan SK as well as crotonase like proteins.	2008-09-03 15:50:29	2005-04-07 12:12:33	11	1093	331	8610	70137	1
128	CL0128	vWA-like		von Willebrand factor type A	Finn RD	anon	To add.	2008-09-03 15:50:29	2005-04-07 17:59:38	11	223	1340	4970	35661	1
129	CL0129	Peptidase_AA	\N	Peptidase clan AA	Bateman A	anon	This clan contains aspartic peptidases, including the pepsins and retropepsins. These enzymes contains a catalytic dyad composed of two aspartates. In the retropepsins one is provided by each copy of a homodimeric protein, whereas in the pepsin-like peptidases these aspartates come from a single protein composed of two duplicated domains.	2008-09-03 15:50:29	2005-04-08 09:36:39	13	1842	629	2629	138509	1
130	CL0130	Peptidase_AD	\N	Peptidase clan AD	Bateman A	anon	Members of this clan are peptidases that are integral membrane proteins. The catalytic aspartate is in the conserved GXGD motif.	2008-09-03 15:50:29	2005-04-08 11:13:31	10	5	33	3841	6449	1
131	CL0131	DoxD-like		DoxD-like	Mistry J	anon	The families in this clan are all membrane proteins.  The DoxD family is found on enzymes involved in elemental sulphur oxidation [1].  The other families in this clan are poorly characterised.	2008-09-03 15:50:29	2005-04-08 11:57:52	10	0	56	3235	10608	1
132	CL0132	AbrB	\N	AbrB/MraZ DNA-binding domain	Bateman A	anon	This superfamily includes the DNA-binding domain of AbrB as well as the presumed DNA-binding protein MraZ (per. comm. A Andreeva and A Murzin).	2008-09-03 15:50:29	2005-04-08 13:53:50	12	50	24	3586	11690	1
133	CL0133	AT14A-like	\N	AT14A-like	Mistry J	anon	This clan contains plant proteins.  DUF677 family members are AT14A-like proteins that have sequence similarity to fungal, insect and human integrins [1].  The other members of this clan are poorly characterised.	2008-09-03 15:50:29	2005-04-08 14:00:57	10	0	14	26	879	1
135	CL0135	Arrestin_N-like	\N	Arrestin_N-like	Mistry J	anon	The families in this clan are involved in vacuolar protein trafficking, G protein signal termination and sporulation.  The Arrestin N terminal domain has an Ig-like beta sandwich fold which binds to receptors and impairs their capacity to active G proteins [1].  Arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways [2].	2008-09-03 15:50:29	2005-04-12 14:27:53	10	34	59	768	5476	1
136	CL0136	Plasmid_toxin	\N	Plasmid toxin-antitoxin system	Mistry J	anon	The families in this clan are plasmid encoded toxins involved in plasmid maintenance.  The plasmid encodes both a toxin and an antitoxin.  Upon loss of the plasmid the antitoxin is inactivated more rapidly than the toxin.  This allows the toxin to interact with its target thus killing the cell or impeding growth.	2008-09-03 15:50:29	2005-04-14 09:55:24	11	91	44	3558	18077	1
137	CL0137	HAD		HAD superfamily	Bateman A	anon	This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [1].	2008-09-03 15:50:29	2005-04-15 16:57:28	14	780	821	6664	120193	1
139	CL0139	GADPH_aa-bio_dh	\N	Amino acid biosynthesis and glycosomal dehydrogenase	Mistry J	anon	This clan contains the C terminal domains of dehydrogenase enzymes involved in the biosynthesis of arginine, aspartate and aspartate derived amino acids.  It also contains the C terminal domain of GAPDH, a dehydrogenase involved in glycolysis and gluconeogenesis.	2008-09-03 15:50:29	2005-04-18 13:42:09	10	525	39	9289	24271	1
140	CL0140	Viral_NABP	\N	Viral nucleic acid binding	Mistry J	anon	This clan contains viral nucleic acid binding protein families. Two of the families in this clan are known to contain zinc finger motifs [1][2].	2008-09-03 15:50:29	2005-04-18 14:24:28	10	0	5	71	578	1
141	CL0141	MtN3-like		MtN3-like, vesicle-trafficking cargo-receptors	Mistry J	anon	The clan forms a large and diverse family of proteins with seven transmembrane helices, common topology and, most likely, similar function. Their coding genes exist in all eukaryota and in several prokaryota. Some are responsible for metabolic diseases (cystinosis, congenital disorder of glycosylation), others are candidate genes for genetic disorders (cleft lip and palate, certain forms of cancer) or solute uptake and efflux (SWEETs) and many have not yet been assigned a function. Comparison with the properties of well-annotated clan members suggests that the proteins could be involved in protein trafficking and serve as cargo receptors in vesicle trafficking [3].	2008-09-03 15:50:29	2005-04-19 09:24:39	11	0	74	1425	7738	1
142	CL0142	Membrane_trans		Membrane and transport protein	Mistry J	anon	This clan contains membrane proteins involved in the transport of molecules including amino acids sugars and signalling molecules. It also includes integral membrane cell cycle proteins and some putative ammonia monooxygenases.	2008-09-03 15:50:29	2005-04-20 13:47:04	11	10	78	4928	72098	1
143	CL0143	B_Fructosidase		Beta fructosidase superfamily	Mistry J	anon	This beta fructosidase superfamily [4] is composed of glycosyl hydrolase families.  The members of this clan adopt a five-bladed beta-propeller fold [2-3]. The beta-fructosidase superfamily is also known as furanosidase superfamily [4].	2008-09-03 15:50:29	2005-04-25 11:24:48	15	191	281	2992	11034	1
144	CL0144	Periplas_BP	Periplas_BP-like;	Periplasmic binding protein like	Mistry J	anon	This clan includes proteins involved in chemotaxis, membrane transport of sugars and allocrites, and the LacI family transcriptional regulators.  It also includes some antigenic basic membrane lipoproteins.	2008-09-03 15:50:29	2005-04-25 15:04:24	12	462	379	4786	70533	1
145	CL0145	Golgi-transport	\N	Golgi-transport	Mistry J	anon	This clan contains families that are involved in intracellular transport and signalling.\	\	    Arfaptins are proteins which interact with small GTPases involved in vesicular budding at the Golgi complex.  They form an elongated dimer of three helix coiled coils and are structurally very similar to the BAR domain [1][2]. The Sec34 family is involved in tethering vesicles to the Golgi [3].	2008-09-03 15:50:29	2005-04-25 16:18:47	14	49	165	766	6140	1
146	CL0146	Herpes_glyco	\N	Herpes glycoprotein	Mistry J	anon	This clan contains herpes envelope glycoproteins [1][2].	2008-09-03 15:50:29	2005-04-25 16:48:44	11	0	3	78	288	1
147	CL0147	Traffic	\N	Trafficking protein	Mistry J	anon	The members of this clan are involved in protein trafficking. The Sec20 family are integral membrane proteins involved in ER to Golgi transport [1] and V-SNARES are involved in membrane fusion [2].	2008-09-03 15:50:29	2005-04-26 10:46:36	10	7	29	336	2129	1
148	CL0148	Viral_Gag	\N	Viral Gag protein	Mistry J	anon	This clan contains Gag proteins which are involved in viral assembly and replication [1][2].  	2008-09-03 15:50:29	2005-04-27 12:13:23	10	185	102	374	45347	1
149	CL0149	CoA-acyltrans	\N	CoA-dependent acyltransferase superfamily	Finn RD	anon	All characterised families in this clan are involved in CoA-dependent acyltransferase. All families have a characteristic HXXXD motif.	2008-09-03 15:50:29	2005-04-27 14:03:23	11	193	1986	4892	38354	1
151	CL0151	PK_TIM	\N	Pyruvate kinase-like TIM barrel superfamily	Bateman A	anon	This superfamily consists of a number of TIM barrel domains found in enzymes such as pyruvate kinase, malate synthase and citrate lyase.	2008-09-03 15:50:29	2005-05-03 14:40:00	11	507	138	6403	40855	1
153	CL0153	dUTPase	\N	dUTPase like superfamily	Bateman A	anon	This clan contains dUTPase and many viral proteins that appear to be related. dUTPases are important in virus replication.	2008-09-03 15:50:29	2005-05-04 09:16:52	10	268	42	4817	8241	1
154	CL0154	C2		C2 superfamily	Bateman A	anon	This superfamily includes C2 domains and C2-like domains.	2008-09-03 15:50:29	2005-05-04 15:46:49	10	222	791	571	27805	1
155	CL0155	CBM_14_19	\N	Carbohydrate binding domain 14/19 clan	Bateman A	anon	This clan includes two different carbohydrate binding modules.	2008-09-03 15:50:29	2005-05-04 15:50:34	10	1	158	335	6959	1
156	CL0156	Nucleocapsid	\N	Mononegaviral nucleocapsid superfamily	Bateman A	anon	This clan contains paramyxoviral and ebola type virus nucleocapsid proteins.	2008-09-03 15:50:29	2005-05-04 16:11:33	10	4	2	470	5978	1
157	CL0157	Kleisin	\N	Kleisin superfamily	Bateman A	anon	The kleisin superfamily includes ScpA, Scc1, Rec8, and Barren [1]. Scc1 interacts with SMC proteins through N- and C-terminal domains to form a ring-like structure [1].	2008-09-03 15:50:29	2005-05-04 16:26:02	10	4	11	3187	3510	1
158	CL0158	GH_CE	\N	Glycoside hydrolase/deacetylase superfamily	Bateman A	anon	This superfamily contains diverse enzymes that act on carbohydrates including both hydrolases and deacetylases.	2008-09-03 15:50:29	2005-05-04 16:44:41	11	125	249	4786	20178	1
159	CL0159	E-set		Ig-like fold superfamily (E-set)	Finn RD, Bateman A	anon	This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.	2008-12-15 16:59:57	2005-05-09 16:19:14	15	1072	9593	6497	213896	1
160	CL0160	Methionine_synt		Cobalamin-independent synthase	Finn RD	anon	The N-terminal and C-terminal cobalamin-independent synthase domains are structurally similar, adopting a TIM beta/alpha barrel. However, the two domain perform functionally different roles. The N-terminal domain and C-terminal domains both define a catalytic cleft in the enzyme.  The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain.  The N-terminal domain is also thought to stabilise a loop from the C-terminal domain. The C-terminal domain contains the active site residues[1].	2008-09-03 15:50:29	2005-05-09 16:58:23	10	56	28	4455	12453	1
161	CL0161	GAF	\N	GAF domain-like	Finn RD	anon	A clan of related transcriptional regulator domains.	2008-09-03 15:50:29	2005-05-09 18:32:14	11	220	3047	6850	47618	1
162	CL0162	FBA	\N	F-box associated	Finn RD	anon	Clan containing related F-box associated families.	2008-09-03 15:50:29	2005-05-09 18:41:19	10	0	47	50	1557	1
163	CL0163	Calcineurin		Calcineurin-like phosphoesterase superfamily	Bateman A	anon	This clan contains the calcineurin-like phosphoesterases. This clan also includes the apparently inactive homologues from the small DNA polymerase subunits [1].	2008-09-03 15:50:29	2005-05-10 16:59:39	10	274	576	5495	51255	1
164	CL0164	CUB	\N	CUB clan	Bateman A	anon	This clan contains the CUB domain [1,2].	2008-09-03 15:50:29	2005-05-10 17:23:26	12	31	892	190	13225	1
165	CL0165	Cache	\N	Cache-like domain	Finn RD	anon	The Cache domain an extracellular domain that is thought to have a role in small-molecule recognition in a wide range of proteins, including the animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors [1].	2008-09-03 15:50:29	2005-05-10 17:26:33	10	40	407	2883	12801	1
166	CL0166	PRD	\N	PRD domain superfamily	Bateman A	anon	The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator of the BglG family as well as in activators such as MtlR and LevR. The PRD domain is phosphorylated on a conserved histidine residue. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterised by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators (Pfam:PF03123, see also comments for this family)) or DNA (for activators), and a duplicated PRD module which is phosphorylated on conserved histidines by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations are thought to modify the stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain.	2008-09-03 15:50:29	2005-05-11 14:46:29	11	9	110	2060	16551	1
167	CL0167	Zn_Beta_Ribbon		Zinc beta-ribbon	Finn RD	anon	A clan of zinc-binding ribbon domains.	2008-09-03 15:50:29	2005-05-11 16:19:40	14	628	1382	6834	87461	1
168	CL0168	PAN	\N	PAN-like	Finn RD	anon	PAN domains have significant functional versatility fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions [1].  These domains contain a hair-pin loop like structure, similar to knottins, but the pattern of disulphide bonds differs.	2008-09-03 15:50:29	2005-05-11 16:56:50	14	59	399	404	5383	1
169	CL0169	Rep	\N	Rep-like domain	Bateman A	anon	This clan includes replication proteins for viruses and plasmids. This domain is known to bind DNA. The members of this clan have three motifs.  The central HXH is conserved in most families in the clan.	2008-09-03 15:50:29	2005-05-13 18:23:32	10	25	62	3938	11895	1
170	CL0170	Peptidase_MD	\N	Peptidase MD	Finn RD	anon	This clan is comprised of carboxypeptidases and the N-terminal domain from Sonic hedgehog proteins.  The structure of the latter is similar to the peptidases, but the N-terminal domain of hedgehog has been demonstrate not to be involved in peptidase activity, but is more likely involved in signal transduction [1].	2008-09-03 15:50:29	2005-05-19 09:30:19	10	53	142	3407	9216	1
171	CL0171	Phospoesterase	\N	inositol polyphosphate 1 phosphatase like superfamily	Bateman A	anon	Members of this clan show metal-dependent / lithium sensitive phosphomonoesterase activity. The clan includes inositol polyphosphate 1 phosphatase and fructose 1,6-bisphosphatase [1]. 	2008-09-03 15:50:29	2005-05-19 17:12:45	10	289	56	4585	15156	1
172	CL0172	Thioredoxin	Thioredoxin-like;	Thioredoxin-like	Mistry J	anon	This clan contains families related to the thioredoxin family. Thioredoxins are small enzymes that are involved in redox reactions via the reversible oxidation of an active centre disulfide bond. The thioredoxin fold consists of a 3 layer alpha/beta/alpha sandwich and a central beta sheet.	2008-09-03 15:50:29	2005-05-20 15:54:37	16	2327	1079	7198	142836	1
173	CL0173	STIR	\N	STIR superfamily	Fenech M	anon	Both members of this clan are thought to be involved in TOLL/IL1R-like pathways, by mediating protein-protein interactions between pathway components. The N-termini of SEFIR and TIR domains are similar, but the domains are more divergent towards the C-terminus [1].	2008-09-03 15:50:29	2005-08-11 10:18:06	10	27	1046	1412	7537	1
174	CL0174	TetR_C	\N	TetR protein, C-terminal domain-like	Fenech M	anon	This clan features families of transcriptional regulators for multidrug efflux pumps, which belong to the TetR superfamily. They are induced by the presence of a variety of factors, such as antibiotics or organic solvents. The C-terminal region featured in these families is thought to contain the inducer-binding site; the divergent sequences in this region allow for the binding of a variety of different inducers [1-4].	2008-09-03 15:50:29	2005-08-11 10:47:22	9	244	37	2464	10523	1
175	CL0175	TRASH		TRASH superfamily	Fenech M	anon	TRASH-like domains contain well-conserved cysteine residues that are thought to be involved in metal coordination. These domains are thus expected to be involved in metal trafficking and heavy-metal resistance. It has been suggested that the members adopt a 'treble-clef' fold, with 3/4 beta strands preceding a C-terminal alpha helix [1].	2008-09-03 15:50:29	2005-08-15 13:59:13	10	149	389	2803	12513	1
176	CL0176	Chemosens_recp	\N	Chemosensory 7tm receptor superfamily	Finn R, Fenech M	anon	The members of this clan are families of various gustatory and odorant receptors. They are described as being seven-transmembrane receptors, and in fact all show characteristic regions of hydrophobicity on the alignment.	2008-09-03 15:50:29	2005-08-15 14:20:45	9	0	50	129	5871	1
177	CL0177	PBP	\N	Periplasmic binding protein clan	Bateman A	anon	Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors [2].	2008-09-03 15:50:29	2005-08-22 13:15:50	15	1664	837	5964	242652	1
178	CL0178	PUA	\N	PUA/ASCH superfamily	Bateman A	anon	This clan consists of the RNA binding PUA domain and ASCH domain. It also contains uncharacterised protein families.	2008-09-03 15:50:29	2005-08-22 16:11:13	15	169	216	5007	19669	1
179	CL0179	ATP-grasp	\N	ATP-grasp superfamily	Bateman A	anon	The ATP-grasp domain is found in a wide variety of carboxylate-amine/thiol ligases [1]. It is composed of two subdomains, with ATP being bound in the cleft between the two.	2008-09-03 15:50:29	2005-08-23 14:07:58	13	397	518	7468	61819	1
181	CL0181	ABC-2	\N	ABC-2-transporter-like clan	Fenech M	anon	These families are similar to the ABC-2 transporter subfamily, as described in [1] (Pfam:PF01061). Members of this family are involved in drug transport and resistance. CcmB protein family (Pfam:PF03379) members are also transporters; they are required for haem export into the periplasm [2].	2008-09-03 15:50:29	2005-08-23 16:06:40	9	3	239	5481	49701	1
182	CL0182	IT	\N	IT (Ion Transporter) superfamily	Bateman A	anon	This superfamily of secondary carriers specific for cationic and anionic compounds, has been termed the ion transporter (IT) superfamily [1].	2008-09-03 15:50:29	2005-08-23 18:40:04	12	0	126	4842	49966	1
183	CL0183	PAS_Fold	PAS;	PAS domain clan	Bateman A	anon	This clan contains PAS domains that are found in a wide variety of bacterial signaling proteins.	2008-09-03 15:50:29	2005-08-24 15:20:49	13	311	6949	5998	88093	1
184	CL0184	DMT		Drug/Metabolite transporter superfamily	Bateman A	anon	This clan contains a variety of transporters which have 4, 5, 9 or 10 membrane spanning helices. Many of the 10 membrane spanning transporters appear to be a duplication of the 5 spanning unit [1].  Many of these families contain a characteristic glycine rich motif close to the C-terminus.	2008-09-03 15:50:29	2005-08-25 11:36:38	10	12	341	5620	114318	1
186	CL0186	Beta_propeller		Beta propeller clan	Bateman A	anon	This large clan contains proteins that contain beta propellers. These are composed of between 6 and 8 repeats. The individual repeats are composed of a four stranded sheet. The clan includes families such as WD40 Pfam:PF00400 where the individual repeats are modeled.  The clan also includes families where the entire propeller is modeled such as Pfam:PF02239 usually because the individual repeats are not discernible. These proteins carry out a very wide diversity of functions including catalysis.	2008-09-03 15:50:29	2005-08-26 09:32:54	13	1163	8240	11212	356413	1
187	CL0187	LysM	\N	LysM-like domain	Fenech M	anon	The LysM domain (Pfam:PF01476) is thought to be a general peptidoglycan-binding module. Although originally described in bacterial proteins, it has been also found in some eukaryotic sequences. It takes up a beta-alpha-alpha-beta conformation, with the beta strands forming an antiparallel beta sheet and the two alpha helices packing on one side of this sheet [1].	2008-09-03 15:50:29	2005-08-26 09:44:43	10	8	614	4599	29820	1
188	CL0188	CH	\N	Calponin homology domain	Fenech M	anon	The calponin homology (CH) domain is found in a variety of contexts, ranging from proteins involved in signalling pathways to cytoskeletal proteins. They seem to have diverse cellular functions, which are thought to include actin binding, involvement in the MAP kinase signalling pathway, and regulation of GEF activity in Rho family GTPase pathways. Structurally, they are organised into three layers, with two parallel alpha helices in the core being sandwiched between another two helices, one on each side [1].	2008-09-03 15:50:29	2005-08-30 18:32:49	9	107	636	512	11687	1
189	CL0189	Endonuclease	\N	Endonuclease V-like superfamily	Wuster A	anon	This clan contains DNA repair proteins.  In E. coli endonuclease V initiates DNA repair of deaminated DNA bases and has similarity to motifs required for the catalytic activity of the UvrC endonuclease [1].	2008-09-03 15:50:29	2005-08-31 14:14:38	9	20	27	4568	5628	1
190	CL0190	HSP20		HSP20-like chaperone superfamily	Fenech M	anon	The small heat shock proteins (sHSPs) prevent protein aggregation during heat shock and oppose regulated cell death. A conserved arginine residue in the HSP20/alpha-crystallin domain (Pfam:PF00011) has in fact been implicated in the development of cataracts and myopathies [1]. The CS family (Pfam:PF04969) includes proteins that are known to bind HSP90 [2], as well as p23 (Swiss:Q15185), which is an HSP90 co-chaperone [3].	2008-09-03 15:50:29	2005-09-01 14:25:02	11	201	170	4085	13158	1
191	CL0191	POTRA	\N	POTRA domain superfamily	Fenech M	anon	The polypeptide-transport-associated (POTRA) domain is predicted to be organised into three beta-strands and two alpha helices, the latter being found between strands 2 and 3. It is usually found associated with a beta-barrel outer membrane domain. It is thought to have a chaperone-like function; the proteins it is found in are involved in processes as diverse as bacterial septation and protein transport across membranes [1].	2008-09-03 15:50:29	2005-09-01 14:31:22	10	20	53	4354	20069	1
192	CL0192	GPCR_A		Family A G protein-coupled receptor-like superfamily	Fenech M	anon	This clan contains various seven-transmembrane receptors and related proteins. A major member is Pfam:PF00001, members of which have been considered to be typical members of the rhodopsin superfamily. Many members of this clan are Caenorhabditis proteins, suggesting great expansion of the relevant families in these nematode worms.	2008-09-03 15:50:29	2005-09-02 12:58:56	12	304	924	9484	92105	1
193	CL0193	MBB		Outer membrane beta-barrel protein superfamily	Bateman A	anon	This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.	2008-09-03 15:50:29	2005-09-05 10:13:31	13	356	515	4665	118601	1
194	CL0194	DNA_pol_B-like	\N	DNA polymerase B like	Mistry J	anon	DNA polymerases replicate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of a growing chain of DNA.  They use a complementary DNA chain as a template.`	2008-09-03 15:50:29	2005-09-05 13:42:41	9	181	97	2623	7651	1
195	CL0195	DBL	\N	Duff-binding like superfamily	Bateman A	anon	This clan includes DBL (Duffy-binding like) domains from a variety of plasmodium surface proteins.	2008-09-03 15:50:29	2005-09-05 15:25:46	9	4	55	9	832	1
196	CL0196	DSRM	\N	DSRM-like clan	Bateman A	anon	This clan contains RNA-binding domains.	2008-09-03 15:50:29	2005-09-08 18:03:50	11	267	170	5456	15069	1
197	CL0197	GME	\N	GME superfamily	Bateman A, Shirai H	anon	This superfamily contains a number of related enzymes such as AstB, peptidyl-arginine deiminase, arginine deiminase and amidinotransferase [1,2].	2008-09-03 15:50:29	2005-09-15 15:15:35	9	117	27	3437	6472	1
198	CL0198	HHH		Helix-hairpin-helix superfamily	Bateman A	anon	This superfamily includes Helix-hairpin-helix DNA-binding domains.	2008-09-03 15:50:29	2005-09-16 17:04:15	15	655	587	6368	81507	1
199	CL0199	DPBB	\N	Double Psi beta barrel glucanase	Bateman A	anon	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 [1,2]. This clan represents the barwin like barrels.	2008-09-03 15:50:29	2005-09-16 17:23:52	11	29	104	3343	9071	1
200	CL0200	Prefoldin	\N	Prefoldin	GriffithsJones S, Finn RD, Mistry J	anon	The Prefoldin domain forms a coiled-coil structure that is involved in substrate-binding in the the chaperone co-factor prefoldin (PFD).  Each PFD is assembled from two alpha and four beta subunits. Each alpha subunit contains two, and each beta subunit one, central beta-hairpin that is flanked N- and C-terminally by coiled-coil helices. The N-terminal regions, the prefoldin domain, are found facing into the central cavity of the chaperone. Here exposed hydrophobic patches form an interaction with the substrate (an unfolded protein) [1].	2008-09-03 15:50:29	2005-09-19 13:51:59	9	9	52	526	2970	1
201	CL0201	Peptidase_SH	\N	Peptidase clan SH	Bateman A	anon	This clan includes the serine peptidase assemblin from herpes virus as well as other viral peptidase families predicted to be related [1].	2008-09-03 15:50:29	2005-09-20 12:38:50	9	47	16	1555	2100	1
202	CL0202	GBD		Galactose-binding domain-like superfamily	Bateman A	anon	This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].	2008-09-03 15:50:29	2005-09-20 16:50:13	10	807	2917	4159	38880	1
203	CL0203	CBD	\N	Carbohydrate binding domain superfamily	Bateman A	anon	This superfamily includes several carbohydrate binding domains. These domains have a beta sandwich structure.	2008-09-03 15:50:29	2005-09-21 11:02:43	11	97	423	950	3904	1
204	CL0204	Adhesin	\N	Bacterial adhesin superfamily	Bateman A	anon	This superfamily includes a variety of bacterial adhesins that have a jelly-roll beta-barrel fold [1]. These domains are involved in sugar recognition.	2008-09-03 15:50:29	2005-09-21 11:17:50	10	156	136	1489	19890	1
205	CL0205	Di-copper	\N	Di-copper centre-containing domain	Bateman A	anon	This superfamily includes tyrosinases and hemocyanins that share a di-copper centre [1].	2008-09-03 15:50:29	2005-09-23 12:59:27	10	106	90	1801	4482	1
206	CL0206	TRB	\N	Transcriptional repressor beta-barrel domain	Bateman A	anon	This beta-barrel domain is found at the C-terminus of a variety of transcriptional repressor proteins.	2008-09-03 15:50:29	2005-09-23 14:02:56	10	132	32	4239	8501	1
207	CL0207	Rhomboid-like	\N	Integral membrane protein / protease	Mistry J	anon	This clan contains proteins from both bacteria and eukaryotes. The Rhomboid protein is an intramembrane serine protease which is involved in epidermal growth factor (EGF)-dependent signalling pathways [1]. The DER1 family is involved in degradation of misfolded ER proteins [2].	2008-09-03 15:50:29	2005-12-01 11:27:30	9	16	91	4052	9025	1
208	CL0208	UBC	\N	Ubiquitin conjugating enzyme like superfamily	Bateman A	anon	This superfamily includes a diverse set of proteins that bind to ubiquitin [1].	2008-09-03 15:50:29	2005-12-02 15:22:57	10	294	238	870	12063	1
209	CL0209	Bet_V_1_like	\N	Bet V 1 like	Mistry J	anon	The Bet_V_I family is composed of sequences related to the major Birch (Betula verrucose) pollen antigen Betv1.  This allergen is known to cause hayfever, dermatitis, asthma and occasionally anaphylactic shock.  The other families in this clan share the same structure as Betv1 which is composed of antiparallel beta sheets and alpha helices.  There is a cavity between the beta sheet and a long C terminal helix.  The cavity appears to play roles in the binding of lipid molecules [1][2][3] which seems a common feature of the families in this clan.	2008-11-07 17:26:25	2005-12-02 17:50:32	10	443	245	4418	23609	1
210	CL0210	HNOX-like	\N	Heme NO and oxygen binding like	Mistry J	anon	This clan contains families that bind small molecules and are predominantly involved in signalling.  Members include the heme NO binding domain.  This domain is related to soluble guanylate cyclases and is mainly alpha helical in structure.\	      Other members of this clan include V4R, which is predicted to be a small molecule binding domain, and a domain often found adjacent to this that is found on activators of aromatic catabolism, and on signalling molecules.	2008-09-03 15:50:29	2005-12-06 09:55:10	10	54	47	793	1692	1
212	CL0212	SNARE	\N	SNARE-like superfamily	Bateman A	anon	This clan includes part of the SNARE like superfamily.	2008-09-03 15:50:29	2005-12-08 17:07:43	8	44	96	372	5553	1
213	CL0213	ShK-like	\N	Sea anemone toxin k like	Mistry J	anon	Members of this clan include the Crisp domain which is involved in ryanodine receptor Ca2+ signalling, and the ShK domain which is named after the ShK channel inhibitor toxin.  Both domains are cysteine rich and contain multiple disulphide bonds [1][2][3].	2008-09-03 15:50:29	2006-01-03 16:32:02	8	27	121	194	2516	1
214	CL0214	UBA	\N	UBA superfamily	Bateman A	anon	This superfamily includes domains related to the UBA domain. These domains are often involved in ubiquitin binding.	2008-09-03 15:50:29	2006-01-05 15:54:42	12	148	350	5009	18121	1
217	CL0217	Rotavirus_VP7	\N	Rotavirus VP7 protein	Bateman A	anon	This clan consists of several Rotavirus major outer capsid protein VP7 sequences. The rotavirus capsid is composed of three concentric protein layers. Proteins VP4 and VP7 comprise the outer layer. VP4 forms spikes and is the viral attachment protein. VP7 is a glycoprotein and the major constituent of the outer protein layer [1].	2008-09-03 15:50:29	2006-01-24 14:08:46	8	28	2	702	4849	1
218	CL0218	ox_reductase_C	\N	Oxidoreductase C terminal like	Mistry J	anon	This clan contains the C terminal region of oxidoreductase proteins and putative oxidoreductase proteins.  Families in this clan form an alpha/beta structure and are usually found adjacent to an N terminal Rossman fold.	2008-09-03 15:50:29	2006-01-26 11:16:09	11	193	37	3633	12363	1
219	CL0219	RNase_H	\N	Ribonuclease H-like superfamily	Bateman A	anon	This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H.	2008-09-03 15:50:29	2006-01-31 17:56:29	13	1007	2352	7614	190937	1
220	CL0220	EF_hand	\N	EF-hand like superfamily	Bateman A	anon	The EF hand is a calcium binding domain found in a wide variety of proteins [1].	2008-09-03 15:50:29	2006-02-01 09:23:33	11	1170	2215	3113	56360	1
221	CL0221	RRM	\N	RRM-like clan	Bateman A	anon	This clan contains families that are related to the RNA recognition motif domains.  However, not all these families are RNA binding.	2008-09-03 15:50:29	2006-03-05 12:30:44	10	736	1162	5818	73704	1
222	CL0222	MviN_MATE	\N	MviN, MATE-like superfamily	Bateman A	anon	This superfamily consists of a variety of integral membrane protein families. The MATE family are known to be transporters. Other proteins have been implicated in virulence and polysaccharide biosynthesis.	2008-09-03 15:50:29	2006-03-05 13:21:19	7	4	109	5014	53746	1
223	CL0223	MACRO	\N	MACRO domain superfamily	Bateman A	anon	This superfamily includes the Macro domain as well as the amino terminal domain from peptidase M17 proteins.	2008-09-03 15:50:29	2006-03-06 10:58:15	7	147	130	4353	8980	1
224	CL0224	DHQS	\N	Dehydroquinate synthase-like superfamily	Bateman A	anon	This superfamily includes Dehydroquinate synthase and Iron containing alcohol dehydrogenase which have a similar active site organisation [1].	2008-09-03 15:50:29	2006-03-06 13:57:58	7	116	47	4875	18804	1
225	CL0225	FtsL	\N	FtsL-like superfamily	Bateman A	anon	This clan includes two proteins that are known to interact, FtsL and DivIC which are part of a trimeric complex with DivIB [2]. DivIC and FtsL are bacterial proteins essential for cell division.	2008-09-03 15:50:29	2006-03-06 15:46:31	7	0	9	3920	6384	1
226	CL0226	M6PR	\N	Mannose 6-phosphate receptor	Bateman A	anon	This clan includes cation dependent and independent mannose 6-phosphate receptors.	2008-09-03 15:50:29	2006-03-06 16:32:14	8	48	95	319	2892	1
227	CL0227	Enolase_N	\N	Enolase N-terminal domain-like superfamily	Bateman A	anon	This domain is found at the N-terminus of the catalytic Tim barrel-like domain in enolase and other enzymes.	2008-09-03 15:50:29	2006-03-06 16:37:34	8	887	42	5636	14408	1
228	CL0228	Acyltransferase		Acyltransferase clan	Bateman A	anon	This clan includes several families of related acyltransferases.	2008-09-03 15:50:29	2006-03-06 16:43:34	7	2	169	4885	24321	1
229	CL0229	RING	\N	Ring-finger/U-box superfamily	Bateman A	anon	This clan includes the Ring zinc finger domains as well as the U-box domain that appears to have lost the zinc coordinating cysteine residues [1].	2008-09-03 15:50:29	2006-03-06 16:54:46	10	159	1983	4407	49901	1
230	CL0230	HO	\N	Heme oxygenase-like superfamily	Bateman A	anon	This clan includes the Heme oxygenase family as well as the TENA/THI-4/PQQC family that are less well characterised [2].	2008-09-03 15:50:29	2006-03-06 16:57:26	7	195	41	2847	5166	1
231	CL0231	MazG	\N	all-alpha NTP pyrophosphohydrolase superfamily	Bateman A	anon	This superfamily includes MazG, HisE and dimeric dUTPases (Not yet in Pfam) [1].	2008-09-03 15:50:29	2006-03-06 17:03:44	8	112	46	4768	13122	1
232	CL0232	NifU	\N	NifU C-terminal domain-like superfamily	Bateman A	anon	This clan includes the C-terminal domain of NifU as well as a large family of uncharacterised domains.	2008-09-03 15:50:29	2006-03-06 17:10:22	7	28	49	4450	9837	1
233	CL0233	SufE_NifU	\N	SufE/NifU superfamily	Bateman A	anon	This clan includes iron sulfur cluster assembly proteins.	2008-09-03 15:50:29	2006-03-06 17:18:24	7	30	26	4741	7304	1
234	CL0234	CTPT	\N	CTP transferase-like superfamily	Bateman A	anon	This clan includes the integral membrane CTP transferase family as well as a large family of uncharacterised proteins that may also function as nucleotidyltransferases.	2008-09-03 15:50:29	2006-03-06 17:30:58	7	0	20	4821	6518	1
235	CL0235	PspA	\N	PspA/ESCRT-III	Bateman A	anon	This clan includes PspA like proteins that are transcriptional activators as well as Snf7, a protein involved in cellular trafficking.	2008-09-03 15:50:29	2006-03-07 09:10:43	8	24	36	2194	5578	1
236	CL0236	PDDEXK		PD-(D/E)XK nuclease superfamily	Bateman A	anon	This clan includes a large number of nuclease families related  to holliday junction resolvases [1,2].	2012-10-03 14:09:06	2006-03-07 10:09:50	16	584	895	6041	71985	1
237	CL0237	HD_PDEase	\N	HD/PDEase superfamily	Bateman A	anon	This clan includes a range of phosphohydrolase enzymes with a common helical fold.	2008-09-03 15:50:29	2006-03-07 17:08:35	7	446	682	5155	45938	1
238	CL0238	PP2C	\N	PP2C-like superfamily	Bateman A	anon	This clan includes the PP2C family of phosphatases as well as the SpoIIE family.  This suggests SpoIIE proteins may also be phosphatases.	2008-09-03 15:50:29	2006-03-08 17:11:21	7	81	723	3947	17476	1
239	CL0239	Insulin	\N	Insulin-like superfamily	Bateman A	anon	This superfamily includes the insulin like hormones.	2008-09-03 15:50:29	2006-03-09 13:10:30	7	895	8	341	1563	1
240	CL0240	PFK	\N	PFK-like superfamily	Bateman A	anon	This clan includes two SCOP superfamilies. Strong similarities between NAD kinases, DAG kinase, sphingosine kinase and PFK have previously been shown[1].	2008-09-03 15:50:29	2006-03-09 16:35:37	7	146	173	5088	20115	1
241	CL0241	ABC_membrane	\N	ABC transporter membrane domain clan	Bateman A	anon	This clan includes families that are the membrane components of ABC transporter complexes. In general these regions are composed of six transmembrane helices [1].	2008-09-03 15:50:29	2006-03-09 17:38:52	7	22	211	5258	54224	1
242	CL0242	DNA_primase_lrg	\N	DNA primase large subunit like	Mistry J	anon	This clan contains the large subunit of archaeal and eukaryotic DNA primase, an enzyme which synthesises the oligoribonucleotide primers essential to DNA replication.  The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays a roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [1].  The clan also contains the Lef-2 family, which is required for the expression of late genes.  There is some evidence to suggest that LEF2 binds to both DNA and the DNA primase small subunit LEF-1 [3].	2008-09-03 15:50:29	2006-04-21 14:57:17	8	11	11	506	609	1
243	CL0243	AEP		Archaeo-eukaryotic primase	Mistry J	anon	This clan includes the small subunit of 2 and eukaryotic DNA primase, and primase-helicase proteins from bacteriophages and plasmids.  All known cellular life forms use primases to synthesis a short RNA primer which is extended during DNA replication by a polymerase.  Bacterial DNA primase adopts a different fold to archaeal and eukaryotic primases and belongs to a different superfamily.	2008-09-03 15:50:29	2006-04-24 16:40:55	9	21	52	1612	2766	1
244	CL0244	PGBD	\N	PGBD superfamily	Bateman A	anon	This clan consists of small putative peptidoglycan binding domains composed of three alpha helices.	2008-09-03 15:50:29	2006-05-16 17:51:06	8	23	345	3348	11009	1
245	CL0245	EDD	\N	EDD superfamily	Bateman A	anon	The EDD superfamily was identified as an evolutionarily conserved domain (EDD) common to three different folds: mannose transporter EIIA domain (EIIA-man), dihydroxyacetone kinase (Dak), and DegV [1]. Both Dak and EIIA-man perform similar phosphotransfer reactions, suggesting a phosphotransferase activity for the DegV-like family of proteins, whose function other than lipid binding revealed in the crystal structure remains unknown [1].	2008-09-03 15:50:29	2006-05-17 09:35:18	8	92	62	3559	18450	1
246	CL0246	ISOCOT_Fold	NagB-like;	Isomerase,CoA transferase & Translation initiation factor Superfamily	Bateman A, Anantharaman V	anon	This superfamily contains a variety of enzymes and non-enzymatic  ligand binding domains.	2008-09-03 15:50:29	2006-05-17 13:20:27	7	279	161	5233	53370	1
247	CL0247	2H	\N	2H phosphoesterase superfamily	Bateman A	anon	This clan includes a number of phosphoesterases that contain an internal duplication.	2008-09-03 15:50:29	2006-05-17 15:53:15	8	24	78	2901	4878	1
248	CL0248	ParBc	\N	ParB-like superfamily	Bateman A	anon	This superfamily includes nucleases related to ParB as well as uncharacterised proteins.	2008-09-03 15:50:29	2006-06-02 16:12:35	7	28	97	4788	13574	1
249	CL0249	Phage_tail_L	\N	Phage minor tail protein L clan	Bateman A	anon	This clan includes the phage minor tail protein L as well as a group of uncharacterised proteins that are also presumably phage components.	2008-09-03 15:50:29	2006-06-02 18:35:28	7	0	7	706	1564	1
250	CL0250	GAD	\N	GAD domain superfamily	Bateman A	anon	This domain is found as an insert within aspartyl-tRNA synthetase as well as GatB proteins.	2008-09-03 15:50:29	2006-07-27 15:00:10	6	16	17	4522	4847	1
251	CL0251	MORN	\N	MORN repeat	Mistry J	anon	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 as dynamic component of cell division apparatus [1].\	It has been hypothesised to function as a linker protein between certain membrane regions and the parasite's cytoskeleton [1].	2008-09-03 15:50:29	2006-07-31 12:59:47	7	27	334	1412	30871	1
252	CL0252	NfeD-like	\N	NfeD like	Mistry J	anon	This clan includes the NfeD family which contains several proteins described as nodulation efficiency protein D (NfeD). The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of the Sinorhizobium meliloti strain GR4 on alfalfa roots [1]. The specific function the NfeD family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts.	2008-09-03 15:50:29	2006-07-31 13:35:37	6	3	8	2902	4042	1
254	CL0254	THDP-binding		Thiamin diphosphate-binding superfamily	Mistry J, Bateman A	anon	This clan includes pyruvate dehydrogenases, branched chain alpha-keto acid decarboxylases, phosphoketolases and the pyrimidine binding region of transketolases.	2008-09-03 15:50:29	2006-07-31 17:23:48	8	598	271	5650	93998	1
255	CL0255	ATP_synthase		ATP synthase F0 subunit	Mistry J	anon	This clan contains subunits of the F0 complex of ATP-synthase. The F0 complex is the non-catalytic unit of ATPase and is involved in proton translocation across membranes.	2008-09-03 15:50:29	2006-08-01 13:45:46	8	29	78	10710	23627	1
256	CL0256	Enolase_TIM	\N	Enolase like TIM barrel	Mistry J	anon	This clan contains enzymes which adopt a TIM barrel fold.	2008-09-03 15:50:29	2006-08-01 15:00:35	6	1004	67	6025	21543	1
257	CL0257	Acetyltrans	Acetyltrans-like;	N-acetyltransferase like	Mistry J	anon	This clan contains families related to N-acetyltransferases. N-acetyltransferases catalyse the transfer of acetyl groups from acetyl-CoA to arylamines.	2008-09-03 15:50:29	2006-08-02 14:16:08	8	664	967	6524	128815	1
258	CL0258	DALR	\N	DALR superfamily	Bateman A	anon	Members of this family are anticodon binding domains from various tRNA synthetases.	2008-09-03 15:50:29	2006-08-17 18:00:51	6	13	28	4898	11747	1
259	CL0259	OstA	\N	OstA superfamily	Bateman A	anon	This superfamily includes the OstA family as well as a large family of uncharacterised proteins.	2008-09-03 15:50:29	2006-08-22 10:05:45	6	11	32	2407	6093	1
260	CL0260	NTP_transf	\N	Nucleotidyltransferase superfamily	Bateman A	anon	This clan contains a diverse set of nucleotidyltransferase enzymes.	2008-09-03 15:50:29	2006-08-22 16:46:46	7	338	577	5508	42917	1
261	CL0261	NUDIX		NUDIX superfamily	Bateman A	anon	This superfamily contains the NUDIX family and one related family.	2008-09-03 15:50:29	2006-08-24 18:58:30	6	360	321	5236	48986	1
262	CL0262	Trigger_C	\N	Trigger factor/SurA domain	Bateman A	anon	This helical domain is found in two families of chaperones.  It is found at the N terminus of the SurA proteins and at the C-terminus of the trigger factors where presumably it shares a common but as yet unknown function.	2008-09-03 15:50:29	2006-08-30 10:54:44	6	20	54	4464	9322	1
263	CL0263	His-Me_finger		His-Me finger endonuclease superfamily	Bateman A	anon	This superfamily defined originally by SCOP contains a diverse range of endonucleases. Later Grishin identified the MH1 domain as belonging to the superfamily [1].	2008-09-03 15:50:29	2006-09-06 17:41:01	7	141	462	5328	22334	1
264	CL0264	SGNH_hydrolase	\N	SGNH hydrolase superfamily	Bateman A	anon	This superfamily contains a diversity of hydrolytic enzyme activities.	2008-09-03 15:50:29	2006-09-07 09:23:58	6	122	427	4610	21200	1
265	CL0265	HIT	\N	HIT superfamily	Bateman A	anon	The HIT superfamily are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides [1].	2008-09-03 15:50:29	2006-11-09 16:05:44	6	147	99	4930	15333	1
266	CL0266	PH	\N	PH domain-like superfamily	Bateman A	anon	Members of this clan share a PH-like fold. Many families in this clan bind to short peptide motifs in proteins and are involved in signalling.	2008-09-03 15:50:29	2006-11-10 10:42:30	8	419	1526	2586	41992	1
267	CL0267	S11_L18p	\N	Ribosomal protein S11/L18p superfamily	Bateman A	anon	This superfamily includes two ribosomal proteins S11 and L18p as well as a domain from eukaryotic peptide chain release factor. This superfamily is likely to share an RNA-binding function.	2008-09-03 15:50:29	2006-11-10 14:46:27	7	451	37	5925	12981	1
268	CL0268	Pec_lyase-like	Pec_lyase; Pectate_lyase;	Pectate lyase-like beta helix	Bateman A	anon	This superfamily all contain a right handed beta helix similar to that first found in pectate lyase [1].	2008-09-03 15:50:29	2006-11-10 15:10:57	6	217	1681	4399	45644	1
269	CL0269	Maf	\N	Maf/Ham1 superfamily	Bateman A	anon	This superfamily includes the Maf-like proteins and ITPases related to YjjX [1].	2008-09-03 15:50:29	2006-11-10 17:10:08	7	21	29	3802	6399	1
270	CL0270	Iso_DH	\N	Isocitrate/Isopropylmalate dehydrogenase-like superfamily	Bateman A	anon	This superfamily of enzymes form dimers and have an active site between the two halves.	2008-09-03 15:50:29	2006-11-10 17:50:17	6	323	67	6496	27220	1
271	CL0271	F-box	\N	F-box-like domain	Bateman A	anon	This clan includes classical F-boxes and the PRANC domain found in pox ankyrin proteins.	2008-09-03 15:50:29	2006-11-22 13:28:07	6	29	805	512	18595	1
272	CL0272	RGS	\N	RGS-like superfamily	Bateman A	anon	This clan includes RGS domains that possess an alpha helical fold.	2008-09-03 15:50:29	2006-11-27 17:23:03	6	92	152	303	4401	1
273	CL0273	CYTH	\N	CYTH-like phosphatase superfamily	Bateman A	anon	CyaB like adenylyl cyclase and the mammalian thiamine triphosphatases define a novel superfamily of catalytic domains called the CYTH domain that is present in all three superkingdoms of life. The catalytic core of these enzymes contain a novel alpha beta scaffold with 6 conserved acidic residues and 4 basic residues [1].	2008-09-03 15:50:29	2006-12-05 13:50:23	6	48	23	3410	3949	1
274	CL0274	WRKY-GCM1	\N	WRKY-GCM1 superfamily	Bateman A	anon	WRKY and GCM1 are metal chelating DNA-binding domains (DBD) which share a four stranded fold [1]. We present evidence that they share a stabilising core, which suggests a possible origin from a BED finger-like intermediate that was in turn ultimately derived from a C2H2 Zn-finger domain [1].	2008-09-03 15:50:29	2006-12-05 13:57:43	7	5	215	443	6439	1
275	CL0275	HAS-barrel	\N	HAS-barrel superfamily	Bateman A	anon	The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family [1].	2008-09-03 15:50:29	2006-12-06 11:13:24	8	401	41	11124	22310	1
276	CL0276	Nucleot_cyclase	\N	Nucleotide cyclase superfamily	Bateman A	anon	This superfamily includes adenylyl cyclase and the GGDEF domain [1].	2008-09-03 15:50:29	2006-12-06 14:41:38	7	119	2538	3679	52683	1
277	CL0277	FAD-oxidase_C	\N	FAD-linked oxidase C-terminal domain superfamily	Bateman A	anon	This clan consists of a duplicated subdomain in a variety of FAD-liked oxidase/dehydrogenase enzymes.	2008-09-03 15:50:29	2006-12-07 10:48:02	6	129	128	3530	14475	1
278	CL0278	AIG2	\N	AIG2/ChaC-like superfamily	Bateman A	anon	The structure consists of a five-stranded beta-barrel surrounded by two alpha-helices and a small beta-sheet.\	Conservation of residues in a hydrophilic cavity able to bind small ligands in some members suggests that this may also serve as an active site.	2008-09-03 15:50:29	2006-12-12 14:39:36	7	20	48	2219	4183	1
279	CL0279	GatB_YqeY	\N	YqeY-like superfamily	Bateman A	anon	This superfamily includes a domain from GatB as well as one from YqeY. Although being structurally distinct they share a common sequence relationship.	2008-09-03 15:50:29	2007-01-24 12:42:11	6	38	17	4060	6337	1
280	CL0280	PIN	\N	PIN domain superfamily	Bateman A	anon	This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.	2008-09-03 15:50:29	2007-01-25 17:50:12	6	117	241	5231	29721	1
281	CL0281	CCT	\N	CCT like-motif	Bateman A	anon	This clan includes the CCT motif as well as a related motif that is similar to the first half of the CCT motif.	2008-09-03 15:50:29	2007-01-29 13:51:28	6	21	28	152	1759	1
282	CL0282	Serum_albumin	\N	Serum albumin superfamily	Bateman A	anon	This superfamily includes serum albumin and related families.	2008-09-03 15:50:29	2007-01-30 15:32:33	6	113	8	71	738	1
283	CL0283	LigB	\N	LigB-like superfamily	Bateman A	anon	This clan includes the LigB subunit of the aromatic ring opening dioxygenase LigAB [1]. The clan also includes the Memo-like proteins.	2008-09-03 15:50:29	2007-02-12 17:08:37	6	13	17	2285	4015	1
284	CL0284	Allatostatin	\N	Allatostatin superfamily	Mistry J	anon	Allatostatins are pleiotropic neuropeptides.  In some insects they are known to inhibit the synthesis of juvenile hormone, an important regulator of development and reproduction.  The full role of allatostatins in hormone production is still unclear [1].	2008-09-03 15:50:29	2007-05-04 14:22:41	5	0	16	41	455	1
285	CL0285	YycI_YycH	\N	YycI/YycH superfamily	Bateman A	anon	Both, YycH and YycI are always found in a pair on the chromosome, downstream of the essential histidine kinase YycG. Additionally, both proteins share a function in regulating the YycG kinase with which they appear to form a ternary complex. Structural studies show that these two protein families share two related domains.	2008-09-03 15:50:29	2007-05-14 11:16:06	6	13	4	723	1328	1
286	CL0286	GCS	\N	gamma-glutamylcysteine synthetase/glutamine synthetase clan	Bateman A, Pei J	anon	This clan represents a superfamily of carboxylate-amine/ammonia ligases [1] that includes Gamma-Glutamylcysteine synthetase (gamma-GCS) and glutamine synthetase (GS). Gamma-Glutamylcysteine synthetase (gamma-GCS) catalyses the first step in the de novo biosynthesis of glutathione.	2008-09-03 15:50:29	2007-08-10 14:04:49	5	394	88	9114	22193	1
287	CL0287	Transthyretin	\N	Transthyretin superfamily	Bateman A	anon	This clan unifies several SCOP superfamilies that all share a 7 stranded beta sandwich fold.	2008-09-03 15:50:29	2007-08-14 16:23:44	6	929	1227	4080	40864	1
288	CL0288	DAP_epimerase	\N	DAP epimerase superfamily	Bateman A	anon	This superfamily includes DAP epimerase and proline racemase as well as the PrpF protein. It has been suggested that this fold may have evolved from the HotDog fold [1].	2008-09-03 15:50:29	2007-08-17 11:58:37	5	61	43	3955	13393	1
289	CL0289	FBD	\N	Folate binding domain	Bateman A	anon	This folate binding domain is found in the GCV T protein as well as the sarcosine oxidase gamma subunit [1].	2008-09-03 15:50:29	2007-08-17 13:17:41	5	63	59	4863	12811	1
290	CL0290	EPT_RTPC	\N	EPT/RTPC-like superfamily	Bateman A	anon	This superfamily includes Enolpyruvate transferase (EPT) and RNA 3'-terminal phosphate cyclase (RTPC).	2008-09-03 15:50:29	2007-08-17 13:33:07	5	195	54	4992	12126	1
291	CL0291	KNTase_C		Nucleotidyltransferase substrate binding domain	Bateman A	anon	This alpha helical domain is found associated with a variety of nucleotidyltransferase domains.	2008-09-03 15:50:29	2007-08-20 15:49:55	6	35	91	3566	11834	1
292	CL0292	LysE		LysE transporter superfamily	Bateman A	anon	This clan includes a diverse range of transporter families [1].	2008-09-03 15:50:29	2007-10-04 12:03:53	5	0	68	4993	52424	1
293	CL0293	CDC	\N	Cholesterol-dependent cytolysin superfamily	Bateman A	anon	This superfamily includes the MACPF domain as well as the Cholesterol-dependent cytolysins [1].	2008-09-03 15:50:29	2007-10-19 12:42:17	5	21	68	720	2339	1
294	CL0294	Sec10	\N	Sec10-like superfamily	Bateman A	anon	This superfamily includes large proteins that are parts of the conserved oligomeric Golgi complex and exocyst complex.	2008-09-03 15:50:29	2007-11-20 17:02:32	5	0	34	298	1198	1
295	CL0295	Vps51		Vps51 domain superfamily	Bateman A	anon	This clan includes an N-terminal domain from several vesicle transport proteins that are related to Vps51.	2008-09-03 15:50:29	2007-11-20 17:11:52	6	11	168	380	6736	1
296	CL0296	GroES	\N	GroES-like superfamily	Bateman A	anon	This superfamily includes the GroES protein as well as the N-terminal GroES-like domain from Alcohol dehydrogenase.	2008-09-03 15:50:29	2008-02-08 16:40:31	4	569	527	6115	49027	1
297	CL0297	PhoU	\N	PhoU-like superfamily	Bateman A	anon	This superfamily includes PhoU and its relatives that contain a three helical bundle domain structure.	2008-09-03 15:50:29	2008-02-08 17:40:34	4	21	32	4083	13356	1
298	CL0298	tRNA_bind_arm	\N	tRNA-binding arm superfamily	Bateman A	anon	This domain is found in Phe and Ser tRNA synthetases at the N-terminus, and at the C-terminus of Val tRNA synthetase. The domain is composed of two helices.	2008-09-03 15:50:29	2008-02-12 16:57:18	4	43	35	4877	13679	1
299	CL0299	Peptidase_SF	\N	Peptidase clan SF	Mistry J, Rawlings N	anon	This clan includes the peptidase S24 and S26 families.  These families adopt a mainly beta fold.  Members of the family S24 have an additional C-terminal domain containing a bundle of three helices presumably important for binding DNA.	2008-09-03 15:50:29	2008-02-25 12:55:51	4	47	75	5096	20383	1
300	CL0300	TAT	\N	Twin-Arginine Translocation Motif	Bateman A	anon	This motif is found in a wide range of secreted proteins. It is named after the conserved pair of arginines that is followed by a hydrophobic stretch.	2008-09-03 15:50:29	2008-02-29 15:32:23	4	26	172	1437	2441	1
301	CL0301	PA14	\N	PA14 superfamily	Bateman A	anon	This clan includes the PA14 domain and related families.	2008-09-03 15:50:29	2008-03-03 17:31:48	5	32	336	731	2126	1
302	CL0302	Arginase	\N	Arginase/deacetylase superfamily	Bateman A	anon	This superfamily includes arginase enzymes as well as histone deacetylases and related enzymes [1].	2008-09-03 15:50:29	2008-04-30 14:26:28	5	410	86	3456	11530	1
303	CL0303	H2TH	\N	Helix-two-turns-helix superfamily	Bateman A	anon	This domain is thought to play a role in binding nucleic acids. It is DNA binding in nucleases and RNA-binding in ribosomal S13.	2008-09-03 15:50:29	2008-05-28 16:24:30	4	289	53	5430	13968	1
304	CL0304	CheY	\N	CheY-like superfamily	Bateman A	anon	This clan includes the CheY-like response regulators from bacteria [1-2].	2008-09-03 15:50:29	2008-06-04 14:50:30	4	475	3478	5545	154594	1
305	CL0305	PTH2	\N	Peptidyl-tRNA hydrolase II superfamily	Bateman A	anon	This clan includes Peptidyl-tRNA hydrolase II as well as a large family of uncharacterised proteins called DUF2000. A structure for DUF2000 shows a similar structure to PTH2. It is not clear if the DUF2000 family are also Peptidyl-tRNA hydrolases. Both families contain a conserved positively charged residue close to the amino terminus that may be part of the active site.	2008-09-03 15:50:29	2008-06-05 14:00:28	4	24	15	963	1328	1
306	CL0306	HeH	\N	LEM/SAP HeH motif	Bateman A	anon	This superfamily includes protein domains with the helix-extended loop-helix (HeH) structure.	2008-09-03 15:50:29	2008-09-03 10:49:37	3	74	240	4102	7665	1
307	CL0307	FUSC		Fusaric acid resistance protein-like superfamily	Bateman A	anon	Members of this clan are likely to be integral membrane bound transporters.	2008-09-05 13:12:16	2008-09-05 14:12:16	3	0	73	3485	13824	1
308	CL0308	DMSO_reductase	\N	Dimethyl sulfoxide reductase type II family	Coggill P	anon	This clan includes members that are type II dimethyl sulfoxide reductase families, all of which are also membrane anchor proteins belonging to the iron-sulfur molybdoenzyme (CISM) family [1].	2008-09-23 15:56:29	2008-09-23 16:56:29	3	8	25	1456	4376	1
310	CL0310	DinB		DinB-like superfamily	Bateman A	anon	This superfamily are thought to be metalloenzymes.  They possess a four helical bundle core structure with a beta hairpin. Members of the superfamily have a predicted active site composed of three histidines that chelate Nickel or Zinc.  In some cases these histidines are replaced with Aspartate or Glutamate.  Mostly they form a dimeric structure. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of the clan. The protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function).  Most (but not all) clan members seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif.  The proteins that share the fold exhibit four different quaternary structures: monomeric and three different dimeric forms [1].	2008-10-08 12:01:30	2008-10-08 13:01:30	3	36	73	2472	9715	1
311	CL0311	SCP2	\N	SCP-2 sterol transfer superfamily	Bateman A	anon	This superfamily includes the SCP2 family as well as a domain from the mycothiol dependent maleylpyruvate isomerase.	2008-10-13 14:19:21	2008-10-13 15:19:21	3	29	62	2115	4976	1
312	CL0312	HemS_ChuX	\N	Heme iron utilization protein-like superfamily	Bateman A	anon	This superfamily includes HemS and ChuX like protein families.	2008-10-22 16:49:13	2008-10-22 17:49:13	3	13	11	760	1473	1
314	CL0314	PP-binding	\N	ACP-like superfamily	Bateman A	anon	\N	2008-11-19 12:30:53	2008-11-19 12:30:53	3	127	3226	5406	42314	1
315	CL0315	Gx_transp		Gx transporter superfamily	Bateman A	anon	This superfamily includes a wide range of transporters that contain many conserved glycine residues in the presumed transmembrane regions.	2008-11-21 16:40:49	2008-11-21 16:40:49	3	4	132	4338	23854	1
316	CL0316	Acyl_transf_3	\N	Membrane acyl transferase superfamily	Bateman A	anon	This superfamily includes a wide variety of integral membrane acyltransferase enzymes that often acylate sugars.	2008-11-24 13:14:42	2008-11-24 13:14:42	3	0	72	4090	17608	1
317	CL0317	Multiheme_cytos		Multiheme cytochrome superfamily	Coggill P	anon	This family includes cytochromes that contain multiple CxxCH motifs.	2008-12-10 17:38:20	2008-12-10 17:38:20	3	247	280	1655	11292	1
318	CL0318	Cytochrome-c		Cytochrome c superfamily	Coggill P	anon	This family includes proteins where a covalently-bound haem completes the core. The core is three helices in an open folded leaf formation. The members are monodomain cytochromes.	2008-12-12 14:30:33	2008-12-12 14:30:33	3	552	457	3452	28903	1
319	CL0319	SHS2	Rob_SOUL;	SHS2 domain	Bateman A, Anantharaman V	anon	SHS2 is a novel domain with a simple fold containing a core of 3  strands, forming a curved sheet, and a single helix in a  strand-helix-strand-strand (SHS2) configuration [1]. SHS2 is found in the bacterial cell division ATPase FtsA, the archaeo-eukaryotic RNA  polymerase subunit Rpb7p, the GyrI superfamily, and the  uncharacterized MTH1598/Tm1083-like proteins [1]. The fold exists as single copy versions in FtsA (where it is inserted into the RNAseH fold), Rbp7p and Dodecin [1]. It is found as a diad in the GyrI  superfamily. In MTH1598/Tm1083-like proteins two copies of SHS2 are found with one inserted into another [1]. The single-copy versions in FtsA and Rbp7 mediate protein–protein interactions, while the one in  Dodecin is a small molecule binding domain. The GyrI also binds small molecule, while the MTH1598 is predicted to be enzymatic [1].	2008-12-12 19:39:43	2008-12-12 19:39:43	3	250	83	4602	13173	1
320	CL0320	PepSY	\N	PepSY domain-like superfamily	Bateman A	anon	This family includes the PepSY domain as well as a family of uncharacterised proteins.	2008-12-15 13:39:08	2008-12-15 13:39:08	3	53	124	3218	10624	1
321	CL0321	PLAT	\N	PLAT domain like superfamily	Bateman A	anon	This domain has an 8-stranded sandwich structure.	2008-12-15 14:40:00	2008-12-15 14:40:00	3	91	192	284	3462	1
322	CL0322	RND_permease	\N	RND permease superfamily	Bateman A	anon	Different members of the RND superfamily have been shown to transport hydrophobic drugs, fatty acids, bile salts, organic solvents, heavy metals, autoinducers and lipooligosaccharides in bacteria [1].	2008-12-18 12:52:06	2008-12-18 12:52:06	3	91	154	4816	43065	1
323	CL0323	Patatin	\N	Patatin/FabD/lysophospholipase-like superfamily	Bateman A	anon	This superfamily of enzymes contains a Ser/Asp catalytic dyad. Members of this superfamily are all serine acylhydrolase enzymes.	2008-12-18 16:43:32	2008-12-18 16:43:32	3	75	1413	5254	25679	1
324	CL0324	Homing_endonuc	\N	Homing endonuclease-like superfamily	Bateman A	anon	This superfamily includes a variety of LAGLIDADG-like homing endonuclease like families.	2009-01-08 17:06:53	2009-01-08 17:06:53	3	109	309	2676	6450	1
325	CL0325	Form_Glyc_dh	\N	Formate/glycerate dehydrogenase catalytic domain-like superfamily	Bateman A	anon	This superfamily includes the catalytic domain of a variety of dehydrogenase enzymes. The domain has a flavodoxin-like fold and contains an inserted Rossman fold NAD-binding domain.	2009-01-09 10:02:56	2009-01-09 10:02:56	3	370	93	4952	24576	1
326	CL0326	Reo_sigma	\N	Virus attachment protein superfamily	Bateman A	anon	This superfamily includes virus attachment proteins that share a common beta sandwich domain.	2009-01-09 10:44:19	2009-01-09 10:44:19	3	291	20	282	678	1
327	CL0327	Pilus	\N	Pilus subunit	Mistry J	anon	This is a clan contains bacterial pilus subunits and proteins involved in secretion.  Pili proteins enable the transfer of plasmid between bacteria. The families in this clan adopt an alpha helical structure which is packed against a beta sheet [2-3].	2009-01-12 11:15:14	2009-01-12 11:15:14	3	115	552	3218	21160	1
328	CL0328	2heme_cytochrom		Transmembrane di-heme cytochrome superfamily	Bateman A	anon	This superfamily includes a variety of different heme binding cytochromes.	2009-05-08 19:48:23	\N	3	111	270	42880	138619	1
329	CL0329	S5	\N	Ribosomal protein S5 domain 2-like superfamily	Bateman A	anon	This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.	2009-05-08 19:52:37	\N	3	764	344	6126	79017	1
330	CL0330	AVL9		Late secretory pathway transport machinery	Bateman A	anon	Members of this clan are involved in vesicle formation/trafficking.	2009-05-08 19:52:58	\N	3	2	129	304	2924	1
331	CL0331	EpsM		General secretion pathway protein M	Coggill P	anon	These families are involved in the general secretory pathways of bacteria and are normally membrane-bound.	2009-05-08 19:53:19	\N	3	6	33	1882	7823	1
332	CL0332	AcetylDC-like		Acetyl-decarboxylase like superfamily	Coggill P	anon	These families are double psi-beta barrel structures.	2009-05-08 19:53:39	\N	3	175	114	3736	19949	1
333	CL0333	gCrystallin	gCrystallin-like;	Gamma-Crystallin-like superfamily	Coggill P	anon	This superfamily includes a number of mammalian crystallins as well as ancestral beta gamma-crystallin precursor structures.	2009-05-08 19:54:54	\N	3	107	65	320	3580	1
334	CL0334	THBO-biosyn		Tetrahydrobiopterin biosynthesis-like enzyme superfamily	Coggill P	anon	The families in this clan bind purine or ptein in topologically similar sites between subunits.	2009-05-08 19:57:58	\N	3	423	52	4568	17543	1
335	CL0335	FumRed-TM		Fumarate reductase respiratory complex transmembrane subunits	Coggill P	anon	This superfamily constitutes two distinct families: in one family the common fold is contained in a single-chain subunit, in the other it is formed by two chains.	2009-05-08 19:58:20	\N	3	154	20	3092	7355	1
336	CL0336	FMN-binding		FMN-binding split barrel superfamily	Coggill P	anon	This includes those related to the ferredoxin reductase-like FAD-binding domain and those that are Pyridoxine 5'-phosphate oxidase (PNP)-like.	2009-05-08 19:58:45	\N	3	224	139	4634	22171	1
337	CL0337	RF	\N	Release factor superfamily	Coggill P	anon	These families are peptide chain release factors.	2009-05-08 19:59:09	\N	3	19	24	4802	12227	1
339	CL0339	PFL-like		PFL-like glycyl radical enzyme superfamily	Coggill P	anon	The N- and C-terminal halves of the structure have similar topologies but in some cases only one is represented by the members here, viz; the C-terminal domain of the R1 subunit of ribonucleotide reductase, and the N-terminal of PFL. The full-length structure is modelled by NRDD.	2009-05-08 19:59:52	\N	3	156	130	5379	23959	1
340	CL0340	PTase-anion_tr		Phosphotransferase/anion transport protein superfamily	Coggill P	anon	The families here are the cytoplasmic regions of anion transporter proteins.	2009-05-08 20:00:18	\N	3	25	126	3482	19584	1
341	CL0341	LDH_C	\N	LDH C-terminal domain-like superfamily	Bateman A	anon	This superfamily includes the C-terminal domain of lactate/malate dehydrogenase as well as the C-terminal domain of the glycosyl hydrolase 4 family.	2009-05-08 20:00:39	\N	3	454	19	7644	15125	1
342	CL0342	TolB_N		TolB, N-terminal domain	Bateman A	anon	Members of this superfamily appear to behave like the N-terminal fold of the TolB transport-portal complex protein, which is beta-stranded.	2009-05-08 20:00:59	\N	3	23	67	2109	6978	1
343	CL0343	MHC		MHC antigen-recognition domain	Coggill P	anon	This superfamily includes all the Class I-related antigen-recognition domain families.	2009-05-08 20:01:29	\N	3	1002	27	843	46029	1
344	CL0344	4Fe-4S		4Fe-4S ferredoxins	Bateman A	anon	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.	2009-05-08 20:01:52	\N	3	366	2266	6690	129668	1
345	CL0345	Aerolisin_ETX		Aerolysin/ETX pore-forming domain superfamily	Coggill P	anon	This superfamily includes pore-forming venoms and toxins from bacteria, plants, insects and fish.	2009-05-08 20:02:15	\N	3	26	17	136	416	1
346	CL0346	Ribo_L29	\N	Ribosomal protein L29, L29p, superfamily	Coggill P	anon	Superfamily includes Ribosomal protein L29 family and its corresponding mitochondrial ribosomal family, L47.	2009-05-08 20:02:37	\N	3	242	12	4897	5412	1
347	CL0347	Tetraspannin		Tetraspannin-like	Mistry J, Finn RD	anon	This clan includes the tetraspanin family which contains four transmembrane regions.  The CD20 family also has four transmembrane regions, but its members are not considered true tetraspanins as they lack nearly all of the key functional tetraspanin residues [1].	2009-05-08 20:04:53	\N	3	8	50	746	6471	1
348	CL0348	Phage_tail		Phage virion morphogenesis superfamily	Finn RD, Coggill P	anon	Families involved in joining the tail to the head of the  phage as well as those completing the head are included herein.   	2009-05-08 20:05:12	\N	3	0	8	1841	2993	1
349	CL0349	DprA		MoCo carrier protein-like superfamily 	Bateman A	anon	Known family members of this superfamily are required for natural chromosomal and plasmid transformation. DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation [1]. Superfamily includes lysine_decarboxylases.	2009-05-08 20:05:29	\N	3	59	53	4587	10964	1
350	CL0350	PRC-barrel	\N	PRC-barrel like superfamily	Finn RD, Coggill P	anon	The PRC-barrel is an all beta barrel domain found in the photosynthetic reaction centre subunit H of the purple bacteria [1]. 	2009-05-08 20:05:48	\N	3	122	34	4098	7238	1
351	CL0351	CHCH		Coiled-coil helix coiled-coil helix superfamily	Bateman A	anon	The conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain) superfamily members include NADH-ubiquinone oxidoreductases, some cytochrome oxidases and yeast mitochondrial ribosomal proteins. Within each helix of the CHCH domain there are two cysteines present in a C-X9-C motif.	2009-05-08 20:06:07	\N	3	58	39	353	2801	1
352	CL0352	EsxAB		WXG100-A/WXG100-B dimer	Finn RD	anon	The WXG100 protein secretion system (Wss) is responsible for the secretion of WXG100 proteins (PF06013), such as ESAT-10 (6 kDa early secreted antigenic target) and CFP-10 (10 kDa culture filtrate protein) in Mycobacterium tuberculosis or EsxA (ESAT-6-like extracellularly secreted protein A) and EsxB in Staphylococcus aureus. These two proteins, generally encoded in the same gene cluster, form a 1:1 heterodimeric complex. These proteins are virulence factors involved in host-pathogen interaction [1], as demonstrated in Mycobacterium tuberculosis, Staphylococcus aureus or Bacillus anthracis. The Wss is encoded in many other Gram-positive (monoderm) bacteria. This superfamily contains a number of DUFs which are closely related and may or may not represent the same family of proteins.	2009-05-08 20:06:25	\N	3	34	135	901	12295	1
353	CL0353	TIMP-like	\N	TIMP-like superfamily	Bateman A	anon	This superfamily consists of the C-terminal domains of netrins, complement proteins C3, C4, C5, secreted frizzled-related proteins, and type I procollagen C-proteinase enhancer proteins, as well as the homologous N-terminal domains of tissue inhibitors of metalloproteinases (TIMPs).	2009-05-08 20:06:43	\N	3	69	60	208	1675	1
354	CL0354	bBprotInhib	\N	beta-Barrel protease inhibitors	Coggill P	anon	Superfamily consists of both metalloprotease- inhibitors and staphostatins.	2009-05-08 20:07:02	\N	2	12	6	424	573	1
355	CL0355	CheC-like		CheC-like superfamily	Bateman A, Tuff TJ	anon	The chemotactic response regulator superfamily are CheY-P phosphatases. Their structure is two intertwined alpha-beta-(X)-beta(2) motifs. This superfamily comprises two classes of proteins each shown to interact with the chemotaxis response regulator CheY: the FliM switch proteins and the CheC-type phosphatases [1]. FliM is a component of the flagellar switch found across the bacteria and is responsible for binding CheY-P and changing the rotational direction of the flagella. The N-terminal domain is CheC-like and the C-terminal shares the SpoA domain with FliN and FliY. The CheC family is broadly broken down into three phosphatase subfamilies: CheC, CheX, and FliY. All three have an active site consensus sequence of D/S-X(3)-E-X(2)-N-X(22)-P.	2009-05-08 20:07:19	\N	3	20	27	2027	5059	1
356	CL0356	AMP_N-like		Creatinase/prolidase N-terminal domain superfamily	Coggill P	anon	Bacterial amino-peptidases and creatinases, where the fold is a ribonuclease H-like motif, are grouped in this superfamily.	2009-05-08 20:07:37	\N	3	91	34	4808	10134	1
357	CL0357	SMAD-FHA		SMAD/FHA domain superfamily	Bateman A	anon	Superfamily members carry a few short helices inserted in loops within the 11 strands in 2 sheets (greek-key) of the parent fold.	2009-05-08 20:07:54	\N	3	135	399	2102	12462	1
359	CL0359	Intron-mat_II	\N	Type II intron maturase-like superfamily	Bateman A	anon	Superfamily includes a variety of transcription factors that bind intron RNA during reverse transcription and splicing.	2009-05-08 20:08:30	\N	3	14	51	26168	39344	1
360	CL0360	MTH1187-YkoF		MTH1187/YkoF-like superfamily	Coggill P	anon	Putative cell-wall biogenesis proteins and HMP-binding proteins, all with the same Ferredoxin fold, are included in this superfamily.	2009-05-08 20:08:47	\N	3	35	7	1666	2146	1
361	CL0361	C2H2-zf		Classical C2H2 and C2HC zinc fingers	Coggill P	anon	Superfamily of classical and closely related C2H2 or beta-beta-alpha zinc finger DNA-binding domains.	2009-05-08 20:09:05	\N	3	241	8637	2337	328673	1
362	CL0362	RAMPS-Cas5-like		CRISPR-associated (Cas) Repair Associated Mysterious Proteins	Bateman A, Coggill P	anon	This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats [1]. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation [2]. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers [3].	2009-05-08 20:09:23	\N	3	24	24	1529	4925	1
363	CL0363	H-int		Hedgehog/intein (Hint) superfamily	Bateman A	anon	This superfamily includes Hedgehog C-terminal (Hog) autoprocessing domain and Intein (protein splicing domain) families.	2009-05-08 20:09:41	\N	3	29	477	1142	3298	1
364	CL0364	Leu-IlvD	\N	LeuD/IlvD-like	Bateman A	anon	Superfamily includes LeuD-like, IlvD/EDD C-terminal domain-like, and AF0055-like families.	2009-05-08 20:09:58	\N	3	36	36	4411	10971	1
365	CL0365	MurF-HprK_N		MurF and HprK N-domain-like superfamily	Bateman A	anon	This includes both the MurE/MurF-ligases N-terminal domain and HPr kinase/phosphatase HprK N-terminal domain superfamilies.	2009-05-08 20:10:16	\N	3	14	40	3206	4809	1
366	CL0366	JAB	Mov34-like;	JAB-like superfamily	Bateman A, Iyer LM, Zhang D, Aravind L	anon	This superfamily includes a number of proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits, regulators of transcription factors and ubiquitination-assisting protein families. In eukaryotes and in prokaryotic cognates of the ubiquitin-based  modification pathway, they function as ubiquitin isopeptidases/ deubiquitinases. JAB domains are also found in diverse metabolic pathways in prokaryotes such as siderophore and cysteine   biosynthesis. Other distinct versions of the JAB domain,  such as RadC are predicted to function as nucleases. Structurally, the  JAB domain is  related to the nucleotide deaminase and binds a Zinc ion in a similar structural location.	2009-05-08 20:10:33	\N	3	35	121	4285	10806	1
367	CL0367	CI-2		CI-2 family of serine protease inhibitors	Bateman A	anon	This superfamily includes a range of universally found subtilases, that are serine proteases.	2009-05-08 20:10:50	\N	3	54	6	411	761	1
368	CL0368	PhosC-NucP1	\N	Phospholipase C/P1 nuclease superfamily	Coggill P	anon	This superfamily includes the Phospholipase C and P1-nuclease families.	2009-05-08 20:11:07	\N	3	26	29	2543	5327	1
369	CL0369	GHD		Glycosyl hydrolase domain superfamily	Bateman A	anon	This domain is C-terminal to the catalytic beta/alpha barrel domain. The superfamily includes the C-terminal domain of a number of sugar-lytic families.	2009-05-08 20:11:24	\N	3	345	276	4003	18678	1
370	CL0370	Uteroglobin		Uteroglobin-like superfamily	Coggill P	anon	Members of this superfamily are disulfide-linked dimers of two identical chains, with 4 helices in each. They constitute important new cat, rat and rabbit allergens that are contributing to asthma world-wide.	2009-05-08 20:11:41	\N	3	12	2	47	309	1
371	CL0371	Inovirus-Coat	\N	Inovirus (filamentous phage) major coat protein	Coggill P	anon	Superfamily contains a number of filamentous phage coat-protein families.	2009-05-08 20:11:58	\N	3	29	3	67	82	1
372	CL0372	Hy-ly_N	\N	Hyaluronate lyase-like catalytic, N-terminal domain	Bateman A	anon	This contains virus envelope protein, Chondroitin AC lyase and hyaluronate lyase families.	2009-05-08 20:12:16	\N	3	44	53	774	1055	1
373	CL0373	Phage-coat		Phage coat superfamily	Coggill P	anon	A number of different phage coat-proteins are collected together in this superfamily.	2009-05-08 20:12:33	\N	3	76	25	2757	4895	1
374	CL0374	PEP-carboxyk	\N	PEP carboxykinase-like superfamily	Bateman A	anon	This includes the PEP carboxykinase C-terminal domain and HPr kinase HprK C-terminal domain families.	2009-05-08 20:12:50	\N	3	100	16	5373	7630	1
375	CL0375	Transporter		Transporter superfamily	Bateman A	anon	The members of this superfamily are probably all transporter protein domains.	2009-05-08 20:13:08	\N	3	0	42	409	5210	1
376	CL0376	Oxa1		Cytochrome oxidase biogenesis family	Bateman A	anon	The cytochrome oxidase biogenesis families are membrane transporters akin to the E coli protein YidC. For those proteins whose N-termini must reside in the intermembrane space, export is mediated by the Oxa1p export machinery, machinery that depends upon the membrane potential. Qxa1p homologues are found in all living organisms. TCDB:2.A.9.	2009-05-08 20:13:27	\N	3	0	30	4817	6863	1
377	CL0377	FAH	\N	Fumarylacetoacetate hydrolase, C-terminal domain, superfamily	Bateman A	anon	Superfamily contains fumarylacetoacetate hydrolase and related enzymes,	2009-05-08 20:13:45	\N	3	104	39	3513	10941	1
378	CL0378	ANL	Ac-CoA-synth;	ANL superfamily	Bateman A	anon	This superfamily consists of enzymes including luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely-related synthetases as well as a plant auxin-responsive promoter family.  The name ANL derives from from three of the subfamilies - Acyl-CoA synthetases, the NRPS adenylation domains, and the Luciferase enzymes [1].  Members of this superfamily catalyse the initial adenylation of a carboxylate to form an acyl-AMP intermediate, followed by a second partial reaction, most commonly the formation of a thioester [1].	2009-05-08 20:14:02	\N	3	149	2269	6257	68785	1
379	CL0379	PgaPase	\N	Pyroglutamate aminopeptidase superfamily	Bateman A	anon	This is a collection of pyrrolidone carboxyl peptidase or pyroglutamate aminopeptidase families from bacteria and archaea.	2009-05-08 20:14:20	\N	3	60	16	1654	2070	1
380	CL0380	IDO-like		Indolic compounds 2,3-dioxygenase-like superfamily	Bateman A	anon	Superfamily contains bacterial tryptophan 2,3-dioxygenase and indoleamine 2,3-dioxygenase-like families.	2009-05-08 20:14:37	\N	3	60	18	837	1644	1
381	CL0381	Metallo-HOrase	\N	Metallo-hydrolase/oxidoreductase superfamily	Bateman A	anon	This superfamily of enzymes including beta-lactamases, thiolesterases, members of the glyoxalase II family that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid all bind two ions of zinc. An additional family of competence proteins essential for natural transformation do not appear to bind zinc, and might be a transporter involved in DNA uptake.	2009-05-08 20:14:54	\N	3	403	305	5380	50665	1
382	CL0382	DNA-mend	\N	DNA breaking-rejoining enzyme superfamily	Bateman A	anon	This is a superfamily of DNA recombinases, topoisomerases and integrases.	2009-05-08 20:15:13	\N	3	116	209	6017	46990	1
383	CL0383	PheT-TilS		Phenylalanine- and lysidine-tRNA synthetase domain superfamily	Coggill P	anon	Families here are thought to contain a putative tRNA-binding structural motif. The families are the C-terminal domains of tRNA-Ile-lysidine and the phenylalanine-tRNA synthetases.	2009-05-08 20:15:30	\N	3	31	54	4735	8465	1
384	CL0384	PLC		PLC-like phosphodiesterases	Coggill P	anon	Superfamily consists of Glycerophosphoryl diester phosphodiesterase and phosphatidylinositol-specific phospholipase C families.	2009-05-08 20:15:48	\N	3	108	279	4173	15000	1
385	CL0385	Hydrophilin	\N	Hydrophilin-like superfamily	Coggill P	anon	This superfamily includes plant and bacterial hydrophilin families.	2009-05-08 20:16:05	\N	3	0	17	752	2456	1
386	CL0386	Ant-toxin_C	\N	Superantigen toxins, C-terminal domain superfamily	Coggill P	anon	Superfamily contains bacterial super-antigen toxins and the MAP family.	2009-05-08 20:16:23	\N	3	216	9	194	4767	1
387	CL0387	DHFred	\N	Dihydrofolate reductase-like	Coggill P	anon	Superfamily contains the dihydrofolate reductases and the RibD C-terminal domain-like including HTP reductase families.	2009-05-08 20:16:40	\N	3	474	41	4883	12238	1
388	CL0388	FadR-C	\N	Fatty acid responsive transcription factor FadR, C-terminal domain	Coggill P	anon	Superfamily includes C-terminal domain ligand-binding GntR families and families of fatty acid responsive transcription factors. This C-terminal domain, an antiparallel array of six alpha helices, forms a barrel-like structure, while a seventh alpha helix forms a 'lid' at the end closest to the N-terminal domain - a separate, DNA-binding winged-helix, domain.	2009-05-08 20:16:57	\N	3	24	47	3168	21611	1
389	CL0389	TRAF	\N	TRAF domain-like superfamily	Coggill P	anon	Superfamily has a circularly permuted immunoglobulin-fold topology with extra an extra beta-strand. Families include the Math and the SIAH, or Seven in absentia, members.	2009-05-08 20:17:16	\N	3	106	201	1094	6315	1
390	CL0390	zf-FYVE-PHD		FYVE/PHD zinc finger superfamily	Coggill P	anon	Superfamily contains a number of zinc-fingers, of the FYVE/PHD type, which are found in several groups of proteins including myelin-associated oligodendrocytic basic proteins (MOBP) Rabphilins, melanophilins, exophilins and myosin-VIIA and Rab-interacting protein families.	2009-05-08 20:17:33	\N	3	184	1096	1231	20485	1
391	CL0391	CAP_C-like		Adenylate cyclase associated (CAP) C terminal like 	Mistry J	anon	Families in this clan adopt a beta super helix structure [1-2].  The clan includes the C terminal domain of adenylate cyclase which binds binds actin [1].	2009-05-08 20:17:50	\N	3	14	29	324	1064	1
392	CL0392	Chaperone-J	\N	Chaperone J-domain superfamily	Coggill P	anon	The J-domain is found in a number of stress-response proteins.  It is found at the N-terminal of Hsc20, DnaJ-chaperone in E. coli,  and viral large T-antigen proteins; it is also in Hsc40, mammalian  auxilin and in both animal and plant DnaJ proteins. It is also  found in degenerate form in Pam16 proteins.	2009-05-08 20:18:07	\N	3	72	636	5592	28318	1
393	CL0393	FucI-AraA_C	\N	FucI/AraA C-terminal domain-like [50443] 	Coggill P	anon	The enzymes in this superfamily function as a hexamer, which is the largest structurally known ketol isomerase, that has no  sequence or structural similarity to other ketol isomerases.	2009-05-08 20:18:26	\N	3	24	7	1558	2470	1
394	CL0394	DsrEFH-like	\N	DsrEFH-like superfamily	Bateman A	anon	This is a superfamily of small proteins from phototrophic sulfur bacteria that are involved in oxidisation of  intracellular sulfur.	2009-05-08 20:18:45	\N	3	54	21	2423	6201	1
395	CL0395	Tubby_C		Tubby C-terminal domain-like 	Bateman A	anon	This superfamily contains the scramblase protein family, the Tub family and the DUF567, a family of plant and bacterial proteins of hitherto unknown function. All members are membrane-tethered transcription factors.	2009-05-08 20:19:04	\N	3	9	44	886	2617	1
396	CL0396	Marvel-like		MARVEL domain containing superfamily	Bateman A	anon	The MAL and related proteins for vesicle trafficking and membrane link (MARVEL) domain is a module with a four transmembrane-helix architecture that has been identified in proteins of the myelin and lymphocyte (MAL), physins, gyrins and occludin families.	2009-05-08 20:19:22	\N	3	0	28	346	3075	1
397	CL0397	TusA-like	SirA-like;	TusA-like superfamily	Bateman A	anon	Member families include sulfurtransferase TusA.	2009-05-08 20:19:39	\N	3	8	61	3075	6124	1
398	CL0398	RMMBL_DRMBL	\N	RNA/DNA-metabolising metallo-beta-lactamase motif	Mistry J	anon	This clan contains the fifth motif found in RNA and DNA metabolising metallo-beta-lactamases.  The fifth motif appears to be specific to function [1].	2009-05-08 20:19:56	\N	3	52	66	3672	6801	1
399	CL0399	Asp-glut_race		Aspartate/glutamate racemase superfamily	Bateman A	anon	Superfamily contains aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase families from fungi, plants, bacteria and archaeal species.	2009-05-08 20:20:14	\N	3	108	17	4346	8931	1
400	CL0400	GG-leader	\N	Double-Glycine leader-peptide cleavage motif	Coggill P	anon	This is a collection of short bacterial families that  carry a distinctive GG-cleavage motif. Conservation C-terminal to the GG-motif is not apparent. However, the families are  all interconnected with critical virulence attributes of one  kind or another.	2009-05-08 20:20:32	\N	3	5	10	475	1960	1
401	CL0401	AsmA-like		AsmA-like OmpF regulator protein superfamily 	Bateman A	anon	Families in this collection are AsmA-like. Mutations in the AsmA gene restore the assembly of OmpF, a trimeric outer membrane porin from E coli and related bacteria necessary for the cytotoxic action of group-A colicins.	2009-05-08 20:20:49	\N	3	0	60	2432	11866	1
402	CL0402	Cdc48_2-like		Cdc48 domain 2-like	Coggill P	anon	Superfamily contains C-terminal domains of N-ethylmaleimide sensitive fusion proteins, VCP-like ATPases, membrane fusion ATPase p97 domain 2, peroxisome biogenesis factor 1 (PEX-1), domain 2, and ubiquitin fusion degradation protein UFD1 families.	2009-05-08 20:21:06	\N	3	52	46	547	1899	1
403	CL0403	ADC-like	\N	Acetoacetate decarboxylase-like	Finn RD	anon	Superfamily contains the acetoacetate decarboxylase enzyme family EC:4.1.1.4, and a family of uncharacterized proteins from bacteria.	2009-05-08 20:21:23	\N	3	20	14	682	968	1
404	CL0404	BPD_transp_1	BPD_transp_1-like;	BPD transporter like	Mistry J, Finn RD	anon	This clan contains families that are involved in transport of molecules across membranes.  It includes the bacterial binding protein-dependent transport system inner membrane component, Pfam:PF00528, which is ATP dependent system involved in transport of a range of substrates [1-2].	2009-05-08 20:21:41	\N	3	36	162	5100	199771	1
405	CL0405	DNA_b-psBarrel	DNA-bdg_psBarrel;	DNA-binding pseudo-barrel domain	Finn RD	anon	Superfamily consists of type II restriction endonuclease effector (N-term) domain and plant B3 DNA binding domain families.	2009-05-08 20:21:58	\N	3	5	51	174	2348	1
406	CL0406	YjbJ-CsbD-like		YjbJ-CsbD-like superfamily	Finn RD	anon	CsbD is a bacterial general stress response protein. It's expression is mediated by sigma-B, an alternative sigma factor [1]. The role of CsbD in stress response is unclear. YjbJ is a hypothetical protein with a similar structure.	2009-05-08 20:22:16	\N	3	2	5	2526	5640	1
407	CL0407	TBP-like		TATA-binding protein like	Mistry J, Finn RD	anon	TBP is a transcription factor whose DNA binding fold is composed of a curved antiparallel beta-sheet [1].  This fold is also found in the N terminal region of DNA repair glycosylases.  The N terminal domain of DNA glycosylase has only a single copy of the fold, whereas TBP contains a duplication of this fold [2-3].	2009-05-08 20:22:35	\N	3	138	32	2007	3848	1
408	CL0408	PUP	\N	Purine and uridine phosphorylase superfamily	Bateman A	anon	superfamily contains a number of purine nucleoside phosphorylase, uridine nucleoside phosphorylase, and various nucleosidase families of proteins.	2009-05-08 20:22:53	\N	3	825	229	4830	16130	1
409	CL0409	GAP	\N	GTPase activation domain superfamily	Finn RD	anon	Superfamily contains BCR-homology GTPase activation domain (BH-domain) and p120GAP domain-like, including the GAP related domain of neurofibromin, families.	2009-05-08 20:23:11	\N	3	42	410	365	9451	1
410	CL0410	LEF-8-like		LEF-8 like region of RNA polymerase Rpb2	Mistry J, Finn RD	anon	Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to domain 6 of the second largest subunit of prokaryotic DNA-directed  RNA polymerase[1].	2009-05-08 20:23:28	\N	3	138	141	12554	17032	1
411	CL0411	Vir		Antigenic variants from Plasmodium cell-surface	Finn RD	anon	Several families of paralogous proteins are included in this superfamily, largely from Plasmodium species. The genome expresses great numbers of them, and they vary subtly from each other.	2009-05-08 20:23:45	\N	3	0	7	9	1914	1
412	CL0412	Frag1-like	\N	Frag1 like	Mistry J, Finn RD	anon	This clan contains the Frag1/DRA</Sfk1 Pfam family (Pfam:PF10277) and related families.	2009-05-08 20:24:02	\N	3	0	22	963	1905	1
413	CL0413	Toprim-like		Toprim domain	Finn RD	anon	This is families that have a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins [1].	2009-05-08 20:24:21	\N	3	91	322	8438	38368	1
414	CL0414	TerB	AB-resistance;	Tellurits and antibiotic resistance superfamily	Finn RD	anon	A number of families which show resistance to antibiotics or tellurite are included here.	2012-09-28 17:52:30	\N	3	5	36	1833	3980	1
416	CL0416	Anoctamin-like	\N	Transmembrane protein families of the Anoctamin type	Finn RD, Coggill P	anon	The families are transmembrane families, where some of the members have sodium tolerance activity.	2009-05-08 20:25:15	\N	3	0	98	322	3409	1
417	CL0417	BIR-like	\N	BIR-like domains	Mistry J, Finn RD	anon	Clan of domains all involved in binding nucleic acid and sharing the sequence motif C3HC.	2009-05-08 20:25:32	\N	3	187	45	401	2356	1
418	CL0418	GIY-YIG	\N	GIY-YIG endonuclease superfamily	Finn RD, Coggill P	anon	Based on the analysis of genomic distribution, patterns of domain fusions and phylogenetic considerations for individual families, an evolutionary scenario is proposed that explains the emergence and development of the major branches of the GIY-YIG superfamily that links the Slx-type with the UvrC-like endonucleases. Most families appear to target DNA. The GIY-YIG domain has been quite successful in forming monomeric nucleases that utilise additional domains to recognise its DNA targets; this collection of domains can range from extremely simple DNA-binding elements (as in the case of I-TevI) to modules with independent enzymatic activities (as in the case of UvrC or the Penelope elements) [1].	2009-05-08 20:25:49	\N	3	20	115	5010	11825	1
419	CL0419	T3SS-Chaperone	\N	Type III secretion system types a and b chaperone	Finn RD, Coggill P	anon	Type III secretion systems of the two forms, a - translocation-associated, and b - bacterial flagellum, share homology between comparable parts. This superfamily includes the chaperone proteins FliJ and HrpB7.	2009-05-08 20:26:06	\N	3	1	5	1738	1982	1
420	CL0420	GlpM-like	\N	Bacterial membrane GlpM-like group	Finn RD, Coggill P	anon	This is a group of membrane proteins of the GlpM type.	2009-05-08 20:26:23	\N	3	0	3	964	1206	1
421	CL0421	LppaM	\N	Lipo-protein attachment motif superfamily	Bateman A	anon	Superfamily consists of those protein families wherein the lipo-protein attachmnet motif, usually at the N-terminus, is found. regions of sequence downstream of this motif may not be conserved between families in the clan.	2009-05-08 21:19:03	\N	3	0	25	1166	2588	1
422	CL0422	Fibrinogen_C		Fibrinogen C-terminal domain-like	Finn RD	anon	This is a collection of families with C-terminal domains that are of similar structure.	2009-05-08 21:19:20	\N	3	239	308	1080	6291	1
423	CL0423	AhpD-like	\N	AhpD-like superfamily	Bateman A	anon	Superfamily contains CMD-like, and Antioxidant defense protein AhpD families.	2009-05-08 21:19:37	\N	3	112	49	3494	9816	1
424	CL0424	T3SS-hook		Type III secretion system-derived superfamily, hook-related	Coggill P	anon	There is homology between the proteins forming the flagellar system and those involved in translocation of effector proteins at host-infection.  Both systems, in Gram-negative bacteria, are Sec-independent but ATPase-dependent.  There are up to 9 proteins that are homologous between the two systems.  It is not clear, however, why HpaP proteins, which are essentially suppressants of HrpB2, an essential pathogenicity factor, should also be homologous to any of these families.	2009-05-08 21:19:55	\N	3	1	12	3179	4912	1
425	CL0425	ComplexI-N	\N	NADH dehydrogenase I, subunit N	Bateman A	anon	This superfamily contains proteins from the families Oxidored_q1 and NADHdeh_related. The Oxidored_q1 family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. Many members of the NADHdeh_related family are archaeal and bacterial, indicating the evolutionary origins of ComplexI.	2009-05-08 21:20:12	\N	3	6	58	35038	91907	1
426	CL0426	HRDC-like	\N	HRDC-like superfamily	Coggill P	anon	Superfamily includes HRDC domain from helicases, RNA polymerase II subunit RBP4, RNase D C-terminal domains, and EXOSC10 HRDC domain-like families.	2009-05-08 21:20:30	\N	3	84	86	3700	6906	1
428	CL0428	TolA-TonB-Cterm		TolA/TonB C-terminal	Mistry J, Finn RD	anon	This clan contains the TolA and TonB C terminal domains.  These domains adopt a structure containing anti-parallel beta sheets with some alpha helical regions. The TolA family contains an extra N-terminal helix over the common fold, and the TonB is an isolated domain that can form different segment-swapped dimers depending on the fragment length [1].	2009-05-08 21:28:43	\N	3	17	93	2250	7994	1
429	CL0429	UcrQ-like	\N	UcrQ-like	Finn RD	anon	The families here include those that are the H and S chains of cytochrome c subunit B1.	2009-05-08 21:29:01	\N	3	51	6	247	299	1
430	CL0430	CopD_like		Copper resistance protein D	Mistry J	anon	This clan contains families that are related to the CopD family of proteins.\	    CopD, together with CopC, performs copper uptake into the cytoplasm.	2009-05-08 21:29:20	\N	3	0	20	2640	4510	1
431	CL0431	PF		Profilin-like superfamily	Bateman A	anon	The families here all show the Profilin-like fold, and represent both the Profilin (actin-binding protein) (55770) and the Roadblock/LC7 domain-type (103196) superfamilies.	2009-05-08 21:29:38	\N	3	97	27	918	3101	1
433	CL0433	SPFH	\N	SPFH superfamily	Bateman A	anon	This superfamily includes the SPFH family as well as the shoulder domain from the Major Vault Protein [1].	2009-07-06 09:16:10	\N	3	46	70	4547	14789	1
434	CL0434	Sialidase		Sialidase superfamily	Bateman A	agb	This superfamily includes sialidases enzymes.  Several viruses use sialic acid as a cell surface receptor for host invasion. These viruses then have cell surface neuraminidase enzymes to cleave sialic acid from cell surface proteins allowing them to leave the host cell after replication.  This superfamily are composed of six beta-sheets that form a six-fold beta-propeller structure. Many members of this superfamily contain BNR sequence motifs Pfam:PF02012.	2009-08-03 11:40:27	2009-08-03 12:40:27	3	387	191	30583	37487	1
435	CL0435	NPR		Nitrogen permease regulator family	Coggill P	pcc	The several protein families of nitrogen permease regulators, that complex together and regulator TORC1 in response to amino acid starvation are likely to have arisen by a gene duplication event.	2009-08-24 12:51:07	2009-08-24 13:51:07	3	0	11	254	791	1
436	CL0436	FliG		Flagellar motor switch family	Coggill P	pcc	This superfamily is characterised by a fragmented superhelix consisting of 3-4 helical motifs and connecting helices. Memebers include the direct flagellar motor as well as the MG2+ families.	2009-08-24 13:45:28	2009-08-24 14:45:28	3	22	37	3585	10762	1
437	CL0437	EF-G_C		Transcription elongation factor G C-terminal	Coggill P	pcc	This superfamily is characterised by being an alpha-beta 2-Layer Sandwich. It is found in EF2 proteins from both prokaryotes and eukaryotes, as well as in some tetracycline resistance proteins, peptide chain release factors ], and in the C-terminal region of the bacterial hypothetical protein, YigZ.	2009-08-24 15:16:01	2009-08-24 16:16:01	3	77	100	5888	33570	1
438	CL0438	TTHA10132-281		Transcriptional regulators of TTHA1013 andTTHA0281 type	Coggill P	pcc	These families are characterised by sharing a 2-layer, beta(3)-alpha-beta topology. Domains dimerise via the long C-terminal strand with the formation of a single beta-sheet.	2009-08-24 16:09:48	2009-08-24 17:09:48	3	12	22	1503	2871	1
439	CL0439	NusG-like		NusG-like	Mistry J	jm14	Members of this clan are related to the NusG transcription termination factor.  The eukaryotic orthologue of NusG is Spt5 [1].	2009-08-25 13:27:05	2009-08-25 14:27:05	3	24	30	4806	6515	1
441	CL0441	AlbA		RNA-DNA binding Alba-like superfamily	Coggill P	pcc	This is a family of DNA and RNA binding proteins found from archaea to humans.	2009-08-27 10:57:56	2009-08-27 11:57:56	3	32	9	406	878	1
442	CL0442	Tubulin-like	Tubulin_C;	Tubulin, FtsZ and Misato and their C-termini, GTPase	Coggill P	pcc	This superfamily is characterised by being of alpha-beta two-layer sandwich structures.  A segmental duplication early on in the primate lineage has led to the creation of up to three tubulin-like domains in the higher primates. The most N-terminal one is the Misato domain, which probably represents the original domain [3].	2009-08-28 12:07:36	2009-08-28 13:07:36	3	172	73	11198	35977	1
444	CL0444	YNI		YcfA-nrd-intein domain	Coggill P	pcc	This superfamily is characterised by a short approx. 55 residue fold that is found in domains associated with flagellum formation and a short region withiin the homing endonucleases.	2009-09-10 10:49:46	2009-09-10 11:49:46	3	3	8	2112	3558	1
445	CL0445	SNARE-fusion		SNARE-fusion membrane complex superfamily	Coggill P	pcc	The SNARE-fusion complex families are characterised by being tetrameric coiled-coil structures.	2009-09-10 14:55:14	2009-09-10 15:55:14	3	106	90	533	8433	1
446	CL0446	Bacteriocin_TLN		Translocation domain of colicin-like bacteriocins	Coggill P	pcc	A number of different bacterial species produce bacteriocins to kill competitor species, and the colicin class is a group of complex three-domain structures. The receptor-binding domain recognises and binds to specific cell surface receptors on the target cells; the N-terminal translocation domain interacts with cell membrane proteins to gain access to the cell interior; the C-terminal domain specifies a killing activity, such as pore formation or nuclease activity. This superfamily is a collection of the translocating domains.	2009-11-02 18:54:23	2009-11-02 18:54:23	2	20	31	181	342	1
447	CL0447	Hypoth_1		DUF1304/DUF3784 clan	Bateman A	agb	This superfamily includes two related families of short uncharacterised proteins from bacteria.	2009-11-06 14:19:03	2009-11-06 14:19:03	2	0	9	1408	1614	1
448	CL0448	Cargo_bd_muHD		Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	Coggill P	pcc	Internalisation of diverse transmembrane cargos from the plasma membrane requires a similarly diverse array of specialized adaptors, this domain is the binding domain of these endocytioc adaptors. The muHD binds directly to the cytosolic tail of the Mid2 (for the transmembrane stress sensor protein Mid2) cargo protein and mediates Mid2 internalization [1]. These are all-beta proteins.	2009-11-10 17:50:06	2009-11-10 17:50:06	2	32	35	501	2637	1
449	CL0449	G-PATCH		DExH-box splicing factor binding site	Coggill P	pcc	This superfamily is characterised by domains which are related to the G-patch domain in proteins with RNA-binding/splicing activity. This domain affects RNA-splicing by binding to a DExH-box splicing factor.	2009-11-12 13:38:49	2009-11-12 13:38:49	2	0	141	389	3724	1
450	CL0450	FimbA		Fimbriae A and Mfa superfamily	Xu Q, Finn RD, Coggill P	pcc	To add the reference from ActaF when it is published, A conserved fold for fimbriae components revealed by the crystal structure of a putative fimbriae assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Angstrom resolution.  This family includes the fimbrillin-A set of fimbrial proteins and the shorter Mfa1 fimbrial set and their asoociated anchor-proteins Mfa2.	2009-11-25 16:52:50	2009-11-25 16:52:50	2	11	10	96	707	1
451	CL0451	FnI-like		von Willebrand Factor like superfamily	Coggill P	pcc	This superfamily is characterised by being disulfide-rich, all-beta with an extra C-terminal domain in the fibronectin-like, Fn1, members.	2009-12-18 14:27:48	2009-12-18 14:27:48	2	8	460	161	4895	1
452	CL0452	Tropomyosin-lke		Tropomyosin-like superfamily	Coggill P	pcc		2009-12-18 15:27:21	2009-12-18 15:27:21	2	54	27	554	1620	1
453	CL0453	Apoptosis-Inhib		Inhibitors of suppressors of apoptosis Bax/Bak 	Coggill P	pcc	This family includes members which are Bax inhibitors.	2009-12-23 16:41:04	2009-12-23 16:41:04	2	0	14	4078	6492	1
454	CL0454	Protease_inhib		Protease inhibitor toxin superfamily	Coggill P	pcc	This superfamily includes several families of toxins which seem to act as protease inuibitors.	2010-01-05 09:18:17	2010-01-05 09:18:17	2	215	445	329	6504	1
455	CL0455	MIM-OM_import		Mitochondrial membrane transporting or complex assembly	Coggill P	pcc	This superfamily is characterised by being mitochondrial membrane proteins with importing activities.	2010-01-07 14:15:14	2010-01-07 14:15:14	2	1	8	326	612	1
456	CL0456	Golgi_traff		Shuttling between cyosol and Golgi, peripheral membrane family	Coggill P	pcc	This superfamily is characterised by comprising multiple-pass membrane proteins that are associated with various aspects of trafficking of molecules into and out of the Golgi apparatus.	2010-01-08 15:41:51	2010-01-08 15:41:51	2	0	13	303	639	1
457	CL0457	4HB_MCP		Aspartate chemoreceptor, signal-transduction ligand-binding	Ulrich L, Coggill P	pcc	This superfamily is characterised by a four-helix bundle structure that forms a ubiquitous sensory module in prokaryotic signal-transduction. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors.	2010-01-11 14:55:11	2010-01-11 14:55:11	2	16	242	1922	9476	1
458	CL0458	IIaaRS-ABD		Class II aaRS Anticodon-binding domain-like	Coggill P	pcc	This superfamily is characterised by including the anticodon-binding domain of Class II aaRS and the Brix domain.	2010-02-01 17:01:44	2010-02-01 17:01:44	2	142	103	4984	18087	1
459	CL0459	BRCT-like		BRCT like 	Coggill P	pcc	The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage.	2010-02-01 17:02:12	2010-02-01 17:02:12	2	112	343	4755	10126	1
461	CL0461	Metallothionein		Metal-bound fold, usually iron, metallothionein superfamily	Coggill P	pcc	This superfamily contains related families of metallothioneins, prokaryotes and eukaryotes.	2010-02-03 17:36:45	2010-02-03 17:36:45	2	24	9	332	753	1
462	CL0462	TPA-repeat		Transcription elongation factor C-terminal nonapeptide repeat	Coggill P	pcc	This superfamily includes several families of this nonapeptide repeat, that carries a characteristic TPA motif. 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.	2010-02-04 11:33:22	2010-02-04 11:33:22	2	10	36	254	580	1
464	CL0464	5_3_exonuc_C		5'-3'-exonuclease C-terminal sub-region	Coggill P	pcc	This superfamily includes C-terminal domains from a number of DNA-processing enzymes including T4 RNase H, 5' to 3' exonuclease domain of DNA polymerase Taq, T5 5'-exonuclease, Flap endonuclease-1 (Fen-1 nuclease), and other eukaryotic endonucleases.	2010-02-04 17:13:51	2010-02-04 17:13:51	2	38	66	5048	8326	1
465	CL0465	Ank		Ankyrin repeat superfamily	Bateman A	agb	The ankyrin repeat is a short sequence region that is about 30-34 amino-acids in length. Multiple copies of the repeat composed of two beta strands and two alpha helices combine to form long arrays. In general these repeats are involved in protein-protein interactions. This superfamily also includes some families that are arrays of several repeats.	2010-02-18 14:19:32	2010-02-18 14:19:32	2	168	6571	3000	134027	1
466	CL0466	PDZ-like		PDZ domain-like peptide-binding superfamily	Coggill P	pcc	This superfamily comprises families of PDZ domains, which are peptide binding sites.	2010-02-23 10:29:00	2010-02-23 10:29:00	2	615	901	4966	46701	1
468	CL0468	Malectin-like		Malectin-like superfamily	Coggill P	pcc	This superfamily includes several families of Malectin-type domains.	2010-02-24 16:54:44	2010-02-24 16:54:44	2	3	227	339	1899	1
469	CL0469	l-integrase_N		lambda integrase N-terminal domain	Coggill P	pcc	This superfamily is characterised by families having 4-5 helices in a bundle of two orthogonally packed alpha-hairpins that are involved in interactions with DNA and proteins.	2010-02-24 17:58:15	2010-02-24 17:58:15	2	29	85	4649	20176	1
470	CL0470	UMP_1		Uncharacterised membrane protein superfamily (UMP1)	Bateman A	agb	This superfamily includes two related families of membrane proteins. One of these is known as DUF1212. As yet there is no known function for any of these proteins.	2010-02-25 14:21:20	2010-02-25 14:21:20	2	0	13	2781	7529	1
471	CL0471	DUF362		DUF362-like superfamily	Bateman A	agb	This superfamily incldues two uncharacterised families: DUF362 and DUF2088. These families contain a number of potential conserved metal binding residues and may be metalloenzymes.	2010-03-01 12:56:12	2010-03-01 12:56:12	2	2	26	685	1641	1
472	CL0472	Peptidase_U		Peptidase clan U	Bateman A	agb	This superfamily includes proteins classed as clan U by the MEROPS database. The proteins are membrane bound peptidases.  The clan also includes Pfam:PF10086 which is a related family of uncharacterised proteins.	2010-03-11 15:27:58	2010-03-11 15:27:58	2	0	61	3770	14791	1
474	CL0474	SICA_like		SICA alpha/beta like extracellular domains	Finn RD	rdf	The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of three domains (alpha, beta and C-terminal).  The two extracelullar domains, termed SICA alpha and beta, occur with varying copy number.  The alpha domain, although it appears to be related to the beta domain, contains few cysteine residues and is found between 1 and 2 times, compared with the beta domain that occurs between 1 and 10 times (when present) [1].	2010-03-17 15:36:20	2010-03-17 15:36:20	2	0	38	2	575	1
475	CL0475	Cyclophil-like		Cyclophilin-like superfamily	Coggill P	pcc	This superfamily is characterised by being the core, closed, beta barrel of cyclophilin with complex topology, with some family members lacking the N-terminal strand of cyclophilin but retaining a closed barrel.	2010-03-22 18:14:27	2010-03-22 18:14:27	2	310	183	4947	18056	1
476	CL0476	tRNA-IECD_N		tRNA-intron endonuclease catalytic domain-like N-term	Coggill P	pcc	This superfamily contains families of the N-termini of tRNA-splicing endonucleases.	2010-04-13 08:59:45	2010-04-13 09:59:45	2	33	16	391	617	1
477	CL0477	TRD		DNA methylase specificity domain	Bateman A	agb	This superfamily includes domains that are found associated with restriction modification methylase enzymes. These domains are involved in defining the DNA substrate specificity.	2010-05-04 15:55:02	2010-05-04 16:55:02	2	29	59	3119	12266	1
478	CL0478	ATPase_I_AtpR	F_N_ATPase_a;	F-type and N-type ATPase, I/AtpR subunit 	Galperin M, Finn RD	rdf	These two subunits from the F-type and N-type ATPases have been demonstrated to from functionally distinct components of these two different ATPases[1].	2010-05-19 12:41:39	2010-05-19 13:41:39	2	0	2	1835	2145	1
479	CL0479	PLD		Phospholipase D superfamily	Bateman A	pcc	This superfamily includes proteins that are related to Phospholiase D.	2010-06-17 09:09:37	2010-06-17 10:09:37	2	68	157	5070	25964	1
480	CL0480	Ribosome_L1		Ribosomal L1 protein superfamily	Coggill P	pcc	This is a superfamily of Ribosomal L1 protein families.	2010-06-29 09:40:59	2010-06-29 10:40:59	2	95	18	4960	6004	1
481	CL0481	HUH		His-hydrophobic-His tranposase Y1,Y2 superfamily	Coggill P	pcc	This superfamily consists of families of transposases that use tyrosine as nucleophiles and contain a conserved HUH motif where U is a non-conserved hydrophobic residue. Particular examples are the Y1 and Y2 transposases. Y1 transposases come from the IS608 group and the Y2 from the IS91 group. These transposases are nucleases involved in initiating rolling-circle plasmid replication, in initiating replication of certain single-strand (ss) DNA viruses (Rep proteins), and in initiation of conjugative plasmid transfer (relaxases). The IS91 transposase contains two of the three conserved protein sequence motifs identified in RCR proteins, a His-hydrophobic-His (HUH) motif required for metal ion binding, and a YxxxY motif containing two conserved catalytic tyrosine residues. The HUH motif participates in coordinating divalent metal ions essential for catalysis.  This clan is also known as the Transposase IS200-like whose members contain extra N-terminal hairpin and C-terminal helix, both or which are involved in dimerisation; there can be helix-swapping in the dimer.	2010-07-13 12:33:47	2010-07-13 13:33:47	2	40	49	2384	6860	1
482	CL0482	Prolamin		Di-sulfide bond pairrings	Coggill P	pcc	This superfamily is characterised by families with only slightly differing disulfide-bonding patterning.	2010-07-21 12:41:48	2010-07-21 13:41:48	2	54	35	364	5909	1
483	CL0483	PreATP-grasp		Probable substrate-binding preceding ATP-grasp domain	Coggill P	pcc	This superfamily is characterised by bein g the copies of the domain that precedes the ATP-grasp domain common to all superfamily members, and it can contain a substrate-binding function.	2010-07-21 12:47:06	2010-07-21 13:47:06	2	32	18	1652	2776	1
484	CL0484	Peroxisome		Peroxisome-like domain	Coggill P	pcc	This superfamily combines peroxisome families and a family found at the C-terminus of metazoan phosphoribosyltransferases.	2010-07-21 12:49:56	2010-07-21 13:49:56	2	0	76	283	1175	1
486	CL0486	Fer2		2Fe-2S iron-sulfur cluster binding domain	Bateman A	agb	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domani is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.	2010-07-24 11:00:26	2010-07-24 12:00:26	2	362	461	5503	37176	1
487	CL0487	FKBP		FKBP-like superfamily	Bateman A	agb	This superfamily includes the FKBP domain which catalyses the peptidyl-prolyl cis-trans isomerisation reaction. The superfamily also includes the C-terminal domain of GreA and the c-terminal dmoain of 3-mercaptopyruvate sulfurtransferase.	2010-07-25 11:45:24	2010-07-25 12:45:24	2	104	100	4781	19148	1
488	CL0488	FixH-like		FixH-like	Coggill P	pcc	This is a superfamily of FixH-like proteins of unknown function.	2010-07-28 13:48:41	2010-07-28 14:48:41	2	0	16	1183	1566	1
489	CL0489	AFP_III-like		Type III antifreeze and spore coat polysaccharide	Coggill P	pcc	This is a superfamily of antifreeze proteins, flagellar FlgA, pilus and spore coat polysaccharide families.	2010-07-29 13:32:26	2010-07-29 14:32:26	2	26	28	2940	6862	1
490	CL0490	PepSY_TM-like		PepSY_TM-like	Coggill P	pcc	This is a superfamily of PepSY-transmembrane-like domain families.	2010-08-04 15:51:29	2010-08-04 16:51:29	2	0	70	1771	6672	1
491	CL0491	LYR-like		Complex1_LYR-like superfamily	Coggill P	pcc	This is a superfamily of sequences with the characteristic LYR, or similar, motif. In some yeasts this family plays a role in Fe-S cluster biogenesis in mitochondria.	2010-08-19 16:20:34	2010-08-19 17:20:34	2	0	33	323	2362	1
492	CL0492	S4		S4 domain superfamily	Bateman A	agb	This superfamily includes diverse proteins related to the ribosomal S4 protein.	2010-08-27 15:46:09	2010-08-27 16:46:09	2	226	44	10099	38684	1
493	CL0493	PTS_EIIC		Phosphotransferase system, EIIC superfamily	Bateman A	agb		2010-09-02 14:47:12	2010-09-02 15:47:12	2	4	39	2905	27857	1
494	CL0494	DnaA_N		DNA-A N-terminal domain-like superfamily	Bateman A	agb	This superfamily includes the N-terminal domain from DnaA and the N-terminal domain from DNA polymerase III alpha subunit.	2010-09-17 12:39:03	2010-09-17 13:39:03	2	2	33	3617	4495	1
496	CL0496	Tad-like		Flp pilus-biogenesis Tad-like superfamily	Coggill P	pcc	This is a superfamily of Tad-like protein families all involved in Flp pilus biogenesis.	2010-09-28 15:11:00	2010-09-28 16:11:00	2	0	22	1048	3415	1
497	CL0497	GST_C		Glutathione S-transferase, C-terminal domain	Bateman A	agb	This clan represents the C-terminal domain of Glutathione S-transferase.	2010-10-04 10:28:59	2010-10-04 11:28:59	2	839	219	3208	23337	1
498	CL0498	Nribosyltransf		N-(deoxy)ribosyltransferase-like superfamily	Bateman A	agb	This superfamily includes the N-deoxyribosyltransferase and ADP-ribosyl cyclase-like families as well as the family that includes the hypothetical protein PA1492 for which the structure is known. PA1942 has a very similar putative active site and is predicted by SCOP to have a deoxyribosyltransferase activity [1].	2010-10-07 15:46:04	2010-10-07 16:46:04	2	193	14	1181	1635	1
499	CL0499	O-antige_ligase		O-antigen-ligase like superfamily	Coggill P	pcc	This superfamily is characterised by a group of bacterial proteins that are membrane proteins, and include O-antigen ligases and putative hydrogen carbonate transporters [1].	2010-10-07 17:04:39	2010-10-07 18:04:39	2	0	73	3419	7279	1
500	CL0500	Glycine-zipper		Glycine-zipper TM superfamily	Coggill P	pcc	This superfamily is characterised by having long glycine-zipper motifs, characteristically GxxxGxxxG [1], often with several contiguous copies. The x following the G is frequently found to be an alanine. This sequence region can be found in both symmetric and non-symmetrical membrane structures, and is relatively common. The fact that such a large fraction of the relatively few known membrane channel structures use the glycine zipper suggests that the sequence motif plays a special role in forming these homo-oligomeric bundles [1].	2010-10-14 10:24:07	2010-10-14 11:24:07	2	0	44	2301	7226	1
501	CL0501	Gram-pos_anchor		Cell wall anchoring	Coggill P	pcc	This superfamily is characterised by families involved in the various mechanisms by which listerial proteins are attached at the bacterial surface and their many functions, including peptidoglycan metabolism, protein processing, adhesion to host cells, and invasion of host tissues.	2010-10-26 16:08:05	2010-10-26 17:08:05	2	20	882	1222	13906	1
502	CL0502	STAS		STAS domain superfamily	Bateman A	agb	This superfamily includes proteins that have a STAS domain.	2010-10-28 16:36:18	2010-10-28 17:36:18	2	44	161	3695	13648	1
503	CL0503	SOR		Superoxide reductase-like superfamily	Bateman A	agb	According to SCOP this superfamily includes the superoxide reductase domain as well as the C-terminal domain of desulfoferrodoxin.	2010-11-08 17:40:12	2010-11-08 17:40:12	2	55	13	767	1038	1
504	CL0504	Phage_barrel		Phage tail beta-barrel superfamily	Bateman A	agb	This superfamily consists of a variety of bacteriophage protein families. Structurally members of this family contain a beta barrel.	2010-11-22 16:23:10	2010-11-22 16:23:10	2	18	106	2048	9306	1
505	CL0505	Pentapeptide		Pentapeptide repeat	Bateman A	agb	This clan includes proteins that form a four sided parallel beta helix. They are generally compoased of pentapeptide repeat motifs.	2010-11-26 10:06:54	2010-11-26 10:06:54	2	43	484	2438	18381	1
506	CL0506	Succ_CoA_synth		Succinyl-CoA synthetase flavodoxin domain superfamily	Bateman A	agb	This superfamily includes the flavodoxin like domain of succinyl-CoA synthetase and other related enzymes.	2010-12-02 12:48:20	2010-12-02 12:48:20	2	70	59	3740	11176	1
507	CL0507	Fungal_trans		Fungal specific transcription factor domain	Bateman A	agb	This putative domain is found in fungal transcription factors.	2010-12-06 17:47:20	2010-12-06 17:47:20	2	0	306	239	14641	1
508	CL0508	YkuD		L,D-transpeptidase catalytic domain	Bateman A	agb	This superfamily incldues the L,D-transpeptidase catalytic domain.	2010-12-08 12:28:21	2010-12-08 12:28:21	2	8	84	3166	11690	1
509	CL0509	RBP11-like		RBP11-like subunits of RNA polymerase	Coggill P	pcc	This superfamily is characterised by all members carrying RNA Polymerase alpha subunit, chain A, domain 2. The member families form homo- and hetero-dimers.	2010-12-09 14:07:20	2010-12-09 14:07:20	2	280	32	6187	8189	1
511	CL0511	Retroviral_zf		Retrovirus zinc finger-like domains	Coggill P	pcc	This superfamily has zinc-finger domains from GAG proteins, HIV nucleocapsids, nucleocapsid proteins from mason-pfizer monkey virus, and from other nucleic-acid binding proteins. Sometimes the domains appears in duplicate.	2011-01-17 16:09:42	2011-01-17 16:09:42	2	46	796	752	52586	1
512	CL0512	CRAL_TRIO		CRAL-TRIO domain superfamily	Bateman A	agb	This superfamily includes the CRAL-TRIO domain.	2011-01-21 18:16:17	2011-01-21 18:16:17	2	28	141	377	5546	1
513	CL0513	LCCL-domain		LCCL-domain like	Coggill P	pcc	This superfamily is characterised by an unusual fold exemplified in PDB:1jbi. Vertebrate members are the cysteine-rich secretory protein LCCL domain-containing proteins including Colchin. The fungal members are found to be necessary for histone de-acetylation.	2011-01-28 14:34:24	2011-01-28 14:34:24	2	1	51	235	1023	1
515	CL0515	LTXXQ-like		LTXXQ-like superfamily	Coggill P	pcc	This is a superfamily of members all carrying the repeated LTxxQ paired sequence-motif region.	2011-02-10 14:04:19	2011-02-10 14:04:19	2	36	8	1376	2943	1
516	CL0516	ISP-domain		Rieske-like iron-sulphur domain	Coggill P	pcc	This superfamily is characterised by Rieske Iron-sulfur families of the [2Fe-2S] type including NADH-nitrite reductase small subunit NirD proteins. This domain has an all-beta rubredoxin-like fold.	2011-02-14 16:52:53	2011-02-14 16:52:53	2	328	118	3882	14974	1
517	CL0517	MBOAT-like		Membrane-bound O-acyltransferase,MBOAT,superfamily	Coggill P	pcc	This is a large superfamily of different enzymes. All biochemically characterised members of the superfamily encode enzymes that transfer organic acids, typically fatty acids, onto hydroxyl groups of membrane-embedded targets.	2011-02-16 11:16:11	2011-02-16 11:16:11	2	0	40	2323	5182	1
520	CL0520	Keratin_assoc		Keratin_associated superfamily	Coggill P	pcc	Families in this clan are cysteine-rich and are from proteins associated with Keratin.	2011-03-09 11:23:29	2011-03-09 11:23:29	2	0	33	65	2969	1
521	CL0521	GOLD-like		Sec14-like superfamily of golgi trafficking	Coggill P	pcc	This superfamily is characterised by proteins with a sandwich structure of 8 strands in 2 sheets as a jelly-roll.  The structure has similarity to the Nucleoplasmin-like/VP fold. The members are all involved in golgi trafficking.	2011-03-21 16:36:53	2011-03-21 16:36:53	2	5	40	359	2519	1
522	CL0522	YbjQ-like		YbjQ-like superfamily	Coggill P	pcc	This superfamily is characterised by chains that form pentamers. Family structures are beta/alpha-propellers with additional short beta-strands that promote oligomeric assembly. Family members appear to be heavy-metal binding proteins.	2011-05-13 14:50:08	2011-05-13 15:50:08	2	25	7	1982	2593	1
523	CL0523	GAG-polyprotein		LTR-copia-type polyprtien segments	Coggill P	pcc	This superfamily is characterised by family members that ar derived from retrotransposons of the copia-type.	2011-05-13 16:31:38	2011-05-13 17:31:38	2	0	851	262	10309	1
524	CL0524	MPT63-MPB63		Antigen MPT63/MPB63 (immunoprotective extracellular	Coggill P	pcc	This superfamily is characterised by extracellular proteins with immuno-protectivce receptor domains on their surfaces resembling Ig domains. These are putative lipoproteins.	2011-05-23 13:54:12	2011-05-23 14:54:12	2	5	23	844	1193	1
525	CL0525	pap2		Acid phosphatase/Vanadium-dependent haloperoxidase	Coggill P	pcc	The PAP2 superfamily is characterised by being mult-helical, with the core consisting of a 5-helical bundle. Normally the family will bind cofactor at the beginning of the third helix. The superfamily includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. The family also includes a variety of haloperoxidases [1,2] that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.	2011-06-02 14:59:14	2011-06-02 15:59:14	2	44	106	4454	15593	1
526	CL0526	SUKH		SUKH superfamily	Zhang D, Iyer LM, Aravind L	la_psag	SUKH superfamily unites a diverse group of proteins including  Smi1/Knr4, PGs2, Fbxo3, Skip16, Syd, herpesviral US22, IRS1 and TRS1, and their bacterial homologs [1].	2011-07-18 20:15:40	2011-07-18 21:15:40	2	8	49	1725	4317	1
527	CL0527	Sm-like		Sm (Small RNA binding protein domain)	Anantharaman V	la_psag	Conserved domain of core RNA-binding proteins of mRNA splicing and rRNA processing complexes, with a SH3-like Beta-barrel	2011-09-10 05:20:17	2011-09-10 06:20:17	2	515	85	2737	9033	1
528	CL0528	DUF1214		DUF1214-like	Finn RD	rdf	Members of this clan usually appear in pairs on the same sequence. In cases where there is only a single example of the domain, there is often a second protein containing a single domain that is located sequentially along the chromosome. The crystal structure of pdb:2P3Y reveals that Pfam:PF06863 and Pfam:PF06742 come together to from a deep, positively charged pocket or cleft.  Structural comparisons reveal that this may this pocket that may bind some form of carbohydrate. Conserved residues are predominantly found on the surface of the positively charged cleft [Jayaraman et al. personal communication].	2011-09-23 21:21:03	2011-09-23 22:21:03	2	9	15	656	2556	1
529	CL0529	FMN-dep-NRtase		FMN-dependent nitroreductase-like	Coggill P	pcc	This superfamily is involved in the reduction of nitrogen containing compounds. Members of this family utilise FMN as a cofactor and are often found to be homodimers. Possible characteristics include Oxygen-insensitive NAD(P)H nitroreductase (FMN-dependent nitroreductase) (Dihydropteridine reductase) and NADH dehydrogenase. A number of the proteins are described as oxidoreductases. They are primarily found in bacterial lineages though a number of eukaryotic homologues have been identified: Caenorhabditis elegans, Drosophila melanogaster, mouse and human. These protein are not found in photosynthetic eukaryotes; sequences containing this entry in photosynthetic organisms are possible false positives.	2011-11-17 15:49:14	2011-11-17 15:49:14	1	206	111	4539	16601	1
530	CL0530	DNase_I-like		DNase I-like	Coggill P	pcc	This superfamily is characterised by members with an alpha-beta four-layer sandwich structure. It includes DNase I-like families of DNA-repair enzyme exonuclease III, DNA repair endonucleases, deoxyribonuclease I, endonuclease domain of retro-transposons. It also includes families of inositol polyphosphatases and shingomyelins-phosphodiesterases.	2011-11-29 11:19:36	2011-11-29 11:19:36	1	148	496	4823	22404	1
531	CL0531	AMP-binding_C		AMP-binding enzyme C-terminal domain superfamily	Eberhardt R	re3	This superfamily contains domains found at the C-terminus of AMP-binding enzyme.	2011-12-02 13:00:41	2011-12-02 13:00:41	1	111	1767	5099	46854	1
532	CL0532	LIG		Lipid-binding Ig-like superfamily	Bateman A	agb	This superfamily includes a number of lipid binding families that have a similar topology to the immunoglobulin fold. The family includes The ML domain Pfam:PF02221. It includes the uncharacterised family Pfam:PF06477.	2011-12-21 10:45:29	2011-12-21 10:45:29	1	68	32	336	2678	1
533	CL0533	PRTase-like		PRPP synthetase-associated protein 1 	Coggill P	pcc	This superfamily of phosphoribosyl-transferases (PRTases) and phosphoribosyl-pyrophosphate synthetase-like protein families is characterised by a core fold of three layers, a/b/a with a mixed beta-sheet of six strands. In one of the families consists of two domains of this fold.	2012-01-09 11:27:00	2012-01-09 11:27:00	1	392	122	5229	42734	1
534	CL0534	YjgF-like		YjgF-like superfamily	Coggill P	pcc	This superfamily is characterised by proteins that form trimers with three closely packed beta-sheets. Some member proteins are chorismate mutases, others are endoribonucleases active on single-stranded mRNA. It is the highly conserved YjgF/YER057c/UK114 protein superfamily. Homologues of this protein occur in eubacteria, archaea, and eukaryotes. Proteins are functionally diverse and are involved in a variety of enzymatic and non-enzymatic functions. The high sequence and structural similarity between members of this protein superfamily offer an example of minimalistic changes leading to functional diversification. This feature is best exemplified by the three close homologues of YjgF proteins in mammals (human, rat, and goat) with sequence identity better than 85%. These homologues perform different functions, including tumour antigen activity in the goat homologue, translation inhibition in the human and rat homologues (hp14.5 and rp14.5), endoribonuclease activity in rp14.5, calpain activation in the bovine homologue, molecular chaperone activity in DUK114, and involvement in the regulation of purine and removal of toxic metabolites in YjgF7, and involvement in isoleucine biosynthetic pathways (YjgF, YER057c, Ibm1). In addition, members of this protein family have also been shown to regulate mitochondrial maintenance (Ibm1) in yeast. Proteins from the YjgF family in plants are involved in photosynthesis and chromoplastogenesis (CHRD).	2012-01-18 11:20:47	2012-01-18 11:20:47	1	251	69	4391	13028	1
535	CL0535	CBM		Carbohydrate-binding superfamily	Coggill P	pcc	This clan includes families of two different carbohydrate binding modules, chitin- and cellulase-binders.	2012-01-23 14:31:27	2012-01-23 14:31:27	1	41	221	1097	3033	1
536	CL0536	HEXAPEP		Hexapeptide repeat superfamily	Coggill P	pcc	This superfamily is characterised by superhelical turns made up of three short strands duplicated many times; the sequence hexapeptide repeats correspond to individual strands. These hexapeptide repeat regions occur in a range of transferase enzymes.	2012-01-23 14:56:06	2012-01-23 14:56:06	1	380	348	5071	79539	1
537	CL0537	CCCH_zf		CCCH-zinc finger	Coggill P	pcc	This superfamily is characterised by families of proteins with several Cys3His zinc-binding domains in tandem.	2012-01-26 16:19:39	2012-01-26 16:19:39	1	17	263	457	8803	1
538	CL0538	DRMIP-like		MAPK-interacting Drmip-like superfamily	Coggill P	pcc	This superfamily contains members that are similar to the MAPK-interacting DRMIP-like family.	2012-02-01 16:26:27	2012-02-01 16:26:27	1	0	20	175	786	1
539	CL0539	RNase_III		RNase III domain-like superfamily	Coggill P	pcc	This superfamily is characterised structurally by having a core of 5 helices where one of the helices is surrounded by the others.  Many members have the endonuclease catalytic domain.	2012-02-06 18:13:43	2012-02-06 18:13:43	1	62	100	4733	7980	1
540	CL0540	GCP		Gamma-tubulin complex superfamily	Coggill P	pcc	This superfamily carries families of proteins all derived via gene-duplication events that act together in the gamma-tubulin complex. This complex is required for microtubule nucleation at the centrosome.	2012-02-09 14:22:48	2012-02-09 14:22:48	1	1	23	316	1604	1
541	CL0541	SH2-like		SH2, phosphotyrosine-recognition domain superfamily	Coggill P	pcc	This superfamily is characterised by proteins with the SH2-like fold. The proesence of this domain guides signal-transduction towards the phosphorylated tyrosine residues on its interacting protein-partner.	2012-02-21 16:19:05	2012-02-21 16:19:05	1	387	421	453	9393	1
542	CL0542	RAS_GEF_N		Ras guanyl-nucleotide exchange factor activity N-term	Coggill P	pcc	This is the more N-terminal domain of the RAS-GEF superfamily.	2012-02-29 11:57:43	2012-02-29 11:57:43	1	14	157	277	2682	1
543	CL0543	Viral_gly_cn_dm		Viral glycoprotein central and dimerisation domains	Eberhardt R	re3	Flavivirus and alpha virus glycoprotein E/E1 consists of three domains. A dimerisation domain, a central domain and an immunoglobulin-like domain. The dimerisation and central domains are intertwined [1-3].	2012-03-23 15:37:00	2012-03-23 15:37:00	1	93	37	200	12815	1
544	CL0544	AcylCoA_ox_dh_N		Acyl-coenzyme A oxidase/dehydrogenase N-terminal	Eberhardt R	re3	Acyl-CoA dehydrogenases and acyl-coenzyme A oxidases consist of three domains. An N-terminal all alpha domain, a beta-barrel middle domain and a C-terminal catalytic domain [1-2].	2012-03-27 08:17:33	2012-03-27 09:17:33	1	223	112	3478	26792	1
545	CL0545	APCOP-app_sub		Clathrin (AP) and COPI appendage platform  subdomain	Coggill P	pcc	This superfamily is characterised by subdomains from the clathrin and coatomer appendages. The superfamily possesses a single protein/protein interaction site that in yeast binds to the ARFGAP Glo3p, and in mammalian gamma-COP binds to a Glo3p orthologue, ARFGAP2 [1].	2012-04-18 13:17:34	2012-04-18 14:17:34	1	0	11	303	446	1
546	CL0546	Hexosaminidase		beta-N-acetylhexosaminidase-like domain	Coggill P	pcc	This superfamily is characterised by a mixed beta sheet with connection over the free side of the sheet. The fold is like a zincin fold lacking the catalytic centre.	2012-04-30 14:53:24	2012-04-30 15:53:24	1	124	150	1212	3278	1
547	CL0547	GF_recep_C-rich		Growth factor receptor Cys-rich	Eberhardt R	re3	The cysteine-rich regions of growth factor receptor tyrosine kinases consist of eight disulphide-linked modules [1].	2012-05-01 09:19:56	2012-05-01 10:19:56	1	49	88	140	2125	1
548	CL0548	IHF-likeDNA-bdg		IHF-like DNA-binding protein supewrfamily	Coggill P	pcc	This superfamily is characterised by being a dimer of identical subunits of a core of four helices in a bundle, partly opened, capped with a beta-sheet. All members appear to be prokaryotic DNA-binding domains.	2012-05-01 16:00:04	2012-05-01 17:00:04	1	60	13	4459	12213	1
549	CL0549	NicO_HupE_DsbD		NicO/HupE/DsdD superfamily	Eberhardt R	re3	This clan contains the nickel transpot family NicO [1-2] and the HupE/UreJ proteins, which may be involved in nickel binding. NicO and HupE contain a conserved GxxHxxxDH motif, which may bind to nickel.	2012-05-31 10:50:16	2012-05-31 11:50:16	1	0	55	3953	10451	1
550	CL0550	SRCR		SRCR-like	Eberhardt R	re3		2012-07-11 13:20:22	2012-07-11 14:20:22	1	19	402	139	9451	1
551	CL0551	BCLiA		Bcl-2 inhibitors of programmed cell death	Coggill P	pcc	This superfamily is characterised by families of proteins that inhibit apoptosis, They are regulated by all BH3-only proteins to promote apoptosis.	2012-08-31 14:55:14	2012-08-31 15:55:14	1	151	28	348	1402	1
552	CL0552	Hect		Hect, E3 ligase catalytic domain	Coggill P	pcc	This superfamily is characterised by fmailies with E3-ligase catalytic acitvity.  The fold consists of two alpha+beta domains; where the N-terminal domain is an array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit.	2012-09-07 15:42:50	2012-09-07 16:42:50	1	23	249	342	4684	1
553	CL0553	HBMR		Helical backbone metal receptor superfamily	Coggill P	pcc	This superfamily is characterised by a long alpha helical insertion in the interdomain linker in the Chelatase-like fold. Representative families include the periplasmic ferric siderophore binding proteins, the TroA-like nitrogenase iron-molybdenum proteins and the putative iron(III) transporter family, TM0189-like, or periplasmic-binding family.	2012-09-12 10:08:39	2012-09-12 11:08:39	1	190	51	4828	19772	1
