CL0001	EGF		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 cysteine residues.                                                           These cysteines 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 thought to largely perform a structural role. More often than not, these domains are arranged in tandem repeats in extracellular proteins.	2016-08-31 16:10:37	2004-03-17 16:02:08	27	912	10479	490	182627	1	1
CL0003	SAM	NULL	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 16:50:29	2004-03-17 16:21:50	21	193	1200	836	21219	1	1
CL0004	Concanavalin	NULL	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 16:50:29	2004-03-17 16:44:11	20	2760	6321	3665	92953	1	1
CL0005	Kazal	NULL	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 16:50:29	2004-03-17 17:00:11	27	110	449	423	10247	1	1
CL0006	C1	NULL	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 16:50:29	2004-03-17 17:47:56	20	53	1188	807	24312	1	1
CL0007	KH	NULL	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 16:50:29	2004-03-17 17:58:30	18	800	616	5411	57999	1	1
CL0009	ENTH_VHS	NULL	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 16:50:29	2004-03-18 10:53:33	20	88	216	802	9470	1	1
CL0010	SH3	NULL	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.\t       For example, SH3 domains in the Grb2 adaptor protein  are essential for protein-protein interactions and\t\t      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 16:50:29	2004-03-18 11:12:55	21	812	3364	3921	63665	1	1
CL0011	Ig	NULL	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 16:50:29	2004-03-18 16:23:40	26	6452	6145	420	170430	1	1
CL0012	Histone	NULL	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 16:50:29	2004-04-19 14:28:04	18	1879	444	1031	29426	1	1
CL0013	Beta-lactamase	NULL	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 16:50:29	2004-04-19 15:42:28	18	1608	516	5074	54442	1	1
CL0014	Glutaminase_I	NULL	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 16:50:29	2004-04-28 09:27:01	22	534	641	5325	69739	1	1
CL0015	MFS	NULL	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 16:50:29	2004-04-30 16:48:27	20	112	2353	5254	320665	1	1
CL0016	PKinase	NULL	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 16:50:29	2004-06-11 14:28:37	22	6557	11510	5146	382476	1	1
CL0018	bZIP	NULL	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 16:50:29	2004-06-16 18:30:26	15	368	213	778	17524	1	1
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 16:50:29	2004-06-21 18:12:39	25	2038	32280	5228	728669	1	1
CL0021	OB	NULL	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 16:50:29	2004-06-22 18:31:10	18	3580	2042	5470	231799	1	1
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 16:50:29	2004-06-23 16:13:12	32	577	8626	2380	250156	1	1
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 16:50:29	2004-06-23 17:05:20	34	9146	20381	5726	1615779	1	1
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 16:50:29	2004-06-29 14:19:46	14	870	9876	5400	264006	1	1
CL0026	CU_oxidase	NULL	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 16:50:29	2004-06-29 16:37:59	20	1386	479	3919	47174	1	1
CL0027	RdRP	NULL	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 16:50:29	2004-08-26 14:33:23	15	1416	1653	2653	37170	1	1
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 16:50:29	2004-08-29 17:32:06	22	3112	4583	5319	268228	1	1
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 16:50:29	2004-09-06 15:03:53	20	2157	2845	5245	200920	1	1
CL0030	Ion_channel	NULL	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 16:50:29	2004-09-08 16:21:26	16	1782	1507	4693	73895	1	1
CL0031	Phosphatase	NULL	Phosphatase superfamily	Bateman A	anon	This family includes tyrosine and dual specificity phosphatase enzymes.	2008-09-03 16:50:29	2004-10-26 13:53:48	13	1013	1488	5036	91705	1	1
CL0032	Dim_A_B_barrel	NULL	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 16:50:29	2004-10-26 16:31:17	15	778	360	4527	48434	1	1
CL0033	POZ	NULL	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 16:50:29	2004-10-27 13:52:11	14	414	1842	832	57250	1	1
CL0034	Amidohydrolase	NULL	Amidohydrolase superfamily	Bateman A	anon	This family includes a large family of metal dependent amidohydrolase enzymes [1].	2008-09-03 16:50:29	2004-10-27 17:19:50	15	1104	710	5407	91372	1	1
CL0035	Peptidase_MH	NULL	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 16:50:29	2004-10-28 13:48:22	16	1350	988	5267	79791	1	1
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 16:50:29	2004-10-28 15:12:01	24	5752	2260	5444	317392	1	1
CL0037	Lysozyme	NULL	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 16:50:29	2004-10-28 15:30:21	14	2246	761	5018	36770	1	1
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 16:50:29	2004-10-29 14:36:02	12	1640	1631	5443	207420	1	1
CL0040	tRNA_synt_II	NULL	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\t\t  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\t       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 16:50:29	2004-11-08 11:24:57	17	729	627	5420	76350	1	1
CL0041	Death	NULL	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 16:50:29	2004-11-11 10:28:31	13	326	1073	249	9248	1	1
CL0042	Flavoprotein	NULL	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 16:50:29	2004-11-12 15:13:12	12	709	330	4879	32596	1	1
CL0043	Chelatase	NULL	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 16:50:29	2004-11-12 16:49:49	12	505	143	4723	28557	1	1
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 16:50:29	2004-11-12 17:32:27	14	2939	266	5110	38310	1	1
CL0045	Rubredoxin	NULL	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 16:50:29	2004-11-15 11:37:59	12	223	85	3139	6077	1	1
CL0046	Thiolase	NULL	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 16:50:29	2004-11-15 12:47:24	16	1011	2563	4947	119589	1	1
CL0047	CuAO_N2_N3	NULL	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 16:50:29	2004-11-15 13:04:24	12	247	66	748	3789	1	1
CL0048	LolA_LolB		LolA/B superfamily	Finn RD, Bateman A	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].	2015-09-01 10:44:34	2004-11-15 13:13:26	12	46	52	2386	8581	1	1
CL0049	Tudor	NULL	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.\tMore 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.\tThe 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 16:50:29	2004-11-16 16:02:09	15	878	1291	4194	50861	1	1
CL0050	HotDog	NULL	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 16:50:29	2004-11-19 13:30:09	12	1049	1961	4844	61585	1	1
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 16:50:29	2004-11-19 15:35:00	14	935	568	4276	36855	1	1
CL0052	NTN	NULL	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 16:50:29	2004-11-19 17:25:18	18	8379	589	5173	65689	1	1
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 16:50:29	2004-11-21 12:08:45	15	417	73	112	3508	1	1
CL0054	Knottin_1	NULL	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 16:50:29	2004-11-22 17:39:28	13	140	20	132	1700	1	1
CL0055	Viral_ssRNA_CP	NULL	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\tproteins 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 16:50:29	2004-11-24 13:16:32	13	2220	56	88	176	1	1
CL0056	C_Lectin	NULL	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 16:50:29	2004-11-24 13:34:58	12	980	1452	2872	30641	1	1
CL0057	Met_repress		MetJ/Arc repressor, antitoxin of TA systems superfamily	Bateman A	anon	This superfamily contains many antitoxin families, all of which carry a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA [1].	2012-10-19 16:36:47	2004-11-24 15:10:49	14	244	140	3501	16918	1	1
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 16:50:29	2004-11-25 11:37:58	16	3710	4249	5087	146887	1	1
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 16:50:29	2004-11-26 15:47:32	15	745	1384	4242	61350	1	1
CL0060	DNA_clamp	NULL	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 16:50:29	2004-11-26 17:13:41	12	381	110	5249	18852	1	1
CL0061	PLP_aminotran	NULL	PLP dependent aminotransferase superfamily	Bateman A	anon	This superfamily contains a variety of PLP-dependent enzymes.	2008-09-03 16:50:29	2004-11-29 11:27:35	13	2338	1149	5409	169871	1	1
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 16:50:29	2004-11-29 18:13:15	13	170	1099	5126	147819	1	1
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 16:50:29	2004-11-30 13:45:28	25	13500	14751	5509	1183746	1	1
CL0064	CPA_AT	NULL	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 16:50:29	2004-12-02 10:12:55	12	37	311	5020	50520	1	1
CL0065	Cyclin	NULL	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 16:50:29	2004-12-02 13:15:02	15	368	359	1045	30836	1	1
CL0066	Trefoil	NULL	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 16:50:29	2004-12-06 15:34:20	14	1120	1198	1567	22936	1	1
CL0067	SIS	NULL	SIS domain fold	Bateman A	anon	This catalytic domain catalyses isomerisation reactions of a variety of sugars [1].	2008-09-03 16:50:29	2004-12-06 16:11:44	13	960	196	5379	41311	1	1
CL0068	RIIa	NULL	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 16:50:29	2004-12-07 15:58:47	12	82	113	687	2542	1	1
CL0069	GFP	NULL	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 16:50:29	2004-12-08 17:25:21	12	1050	301	224	546	1	1
CL0070	ACT	NULL	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 16:50:29	2004-12-08 17:26:00	13	292	313	4786	44079	1	1
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.\tStructure 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 16:50:29	2004-12-09 14:54:21	12	348	354	4917	36243	1	1
CL0072	Ubiquitin	NULL	Ubiquitin superfamily	Bateman A	anon	This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.	2008-09-03 16:50:29	2004-12-09 18:04:44	20	2349	3533	5363	124478	1	1
CL0073	P53-like	NULL	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 16:50:29	2004-12-10 09:44:45	13	519	245	637	8343	1	1
CL0074	Matrix	NULL	Retroviral matrix superfamily	Bateman A	anon	This clan brings together matrix proteins from a variety of retroviruses.	2008-09-03 16:50:29	2004-12-10 10:07:15	13	61	36	29	199	1	1
CL0075	Defensin	NULL	Defensin/myotoxin-like superfamily	Bateman A	anon	This clan includes diverse defensins as well as myotoxins.	2008-09-03 16:50:29	2004-12-10 13:40:46	13	211	15	95	1239	1	1
CL0076	FAD_Lum_binding	NULL	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 16:50:29	2004-12-10 14:19:14	12	174	566	4577	34748	1	1
CL0077	FAD_PCMH	NULL	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 16:50:29	2004-12-10 16:27:25	12	397	498	5040	36005	1	1
CL0078	DNA_ligase	NULL	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 16:50:29	2004-12-10 18:04:20	13	125	286	5203	13383	1	1
CL0079	Cystine-knot	NULL	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 16:50:29	2004-12-14 17:03:09	13	415	135	244	9075	1	1
CL0080	Beta-tent	Mss4-like;	Beta-tent fold	Bateman A	anon	This clan contains TCTP, Mss4 and SelR families [1]. The common fold of members of this superfamily has been termed the beta-tent fold [2]. This fold contains two four stranded antiparallel beta sheets. These are oriented at right angles and pinned together at their tip by a zinc ion [2].	2015-08-17 12:11:44	2004-12-14 17:24:43	12	184	223	4165	19411	1	1
CL0081	MBD-like	NULL	MBD-like DNA-binding domain	Bateman A	anon	This clan contains proteins with a distinctive three stranded DNA-binding domain [1].	2008-09-03 16:50:29	2004-12-14 17:44:54	13	40	335	2471	21064	1	1
CL0082	MIF	NULL	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 16:50:29	2004-12-15 11:44:36	12	696	56	2646	4997	1	1
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 16:50:29	2004-12-16 13:53:46	15	109	230	483	4799	1	1
CL0084	ADP-ribosyl	NULL	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 16:50:29	2004-12-16 14:31:35	13	827	695	2361	8595	1	1
CL0085	FAD_DHS	NULL	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.\t   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 16:50:29	2004-12-16 15:32:59	14	756	374	4930	35242	1	1
CL0086	FAD_oxidored	NULL	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 16:50:29	2004-12-16 16:43:38	12	87	58	4193	8905	1	1
CL0087	Acyl-CoA_dh	NULL	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\tarranged in up-and-down bundle. In Acyl-CoA oxidase II this domain appears to have been duplicated.	2008-09-03 16:50:29	2004-12-17 10:15:37	13	401	294	3817	45223	1	1
CL0088	Alk_phosphatase	NULL	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 16:50:29	2004-12-17 11:25:45	16	398	617	5090	46921	1	1
CL0089	GlnB-like	NULL	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 16:50:29	2004-12-17 12:10:20	13	394	85	4782	16629	1	1
CL0090	Globin	NULL	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 16:50:29	2004-12-17 12:17:06	12	2994	221	2951	10506	1	1
CL0091	NAD_Ferredoxin	NULL	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 16:50:29	2004-12-17 14:54:00	12	290	571	4430	29698	1	1
CL0092	ADF	NULL	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 16:50:29	2004-12-17 17:36:22	12	207	286	833	16048	1	1
CL0093	Peptidase_CD	NULL	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 16:50:29	2004-12-21 13:25:00	14	673	1576	2525	18753	1	1
CL0094	Peptidase_ME	NULL	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 16:50:29	2004-12-21 13:57:38	12	353	265	5373	52666	1	1
CL0095	Peptidase_ML	NULL	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 16:50:29	2004-12-21 15:54:20	13	13	17	1475	2735	1	1
CL0096	Pept_Inhib_IE	NULL	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 16:50:29	2004-12-22 12:16:32	12	40	2	5	22	1	1
CL0097	TypeIII_Chap	NULL	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 16:50:29	2004-12-22 12:58:31	12	74	39	2172	3835	1	1
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\tfolding 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 16:50:29	2004-12-22 15:38:51	14	238	174	5326	33002	1	1
CL0099	ALDH-like	NULL	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 16:50:29	2004-12-22 15:45:47	13	1184	393	4890	57562	1	1
CL0100	C1q_TNF	NULL	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\tobesity [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 16:50:29	2004-12-22 15:46:56	13	379	91	234	5123	1	1
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 19:35:16	2005-01-04 15:00:27	12	567	161	4813	18057	1	1
CL0103	Gal_mutarotase	NULL	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 16:50:29	2005-01-28 16:18:34	12	683	638	4527	28521	1	1
CL0104	Glyoxalase	NULL	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 16:50:29	2005-01-28 18:11:34	13	497	229	4505	44752	1	1
CL0105	Hybrid	NULL	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 16:50:29	2005-01-31 16:15:18	13	709	1172	5399	156842	1	1
CL0106	6PGD_C	NULL	6-phosphogluconate dehydrogenase C-terminal-like superfamily	Bateman A	anon	This helical domain is found associated with Rossmann domains.	2008-09-03 16:50:29	2005-01-31 18:34:00	13	576	466	5268	61364	1	1
CL0107	KOW	NULL	KOW domain	Bateman A	anon	This superfamily includes proteins involved in translation that have a KOW like SH3-fold.	2008-09-03 16:50:29	2005-03-18 14:03:54	12	2091	235	5413	29120	1	1
CL0108	Actin_ATPase	NULL	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 16:50:29	2005-03-22 09:34:28	16	1824	1056	5439	150464	1	1
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 16:50:29	2005-03-22 09:57:40	12	321	1926	5206	36216	1	1
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 16:50:29	2005-03-22 10:54:55	12	1122	2548	5413	168822	1	1
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 16:50:29	2005-03-22 13:52:31	11	32	587	4478	33138	1	1
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 16:50:29	2005-03-22 15:32:52	13	4	94	2550	6095	1	1
CL0113	GT-B	NULL	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 16:50:29	2005-03-22 17:19:24	13	894	2786	5365	185874	1	1
CL0114	HMG-box	NULL	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 16:50:29	2005-03-23 13:44:43	12	78	411	826	17330	1	1
CL0115	Steroid_dh	NULL	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 16:50:29	2005-03-23 14:15:40	12	3	163	3204	13839	1	1
CL0116	Calycin	NULL	Calycin superfamily	Bateman A	anon	The calycin structural superfamily [1-3] includes the lipocalins, the fatty acid-binding proteins (FABPs).	2008-09-03 16:50:29	2005-03-23 14:57:38	13	1098	241	4075	16673	1	1
CL0117	uPAR_Ly6_toxin	NULL	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 16:50:29	2005-03-30 14:52:26	11	269	72	226	3521	1	1
CL0118	Ribokinase	NULL	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 16:50:29	2005-04-01 13:48:37	12	590	282	5220	38980	1	1
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 16:50:29	2005-04-05 16:56:37	12	138	177	1376	5610	1	1
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 16:50:29	2005-04-05 17:05:44	11	114	36	2805	9877	1	1
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 16:50:29	2005-04-05 17:52:07	18	5172	9260	5518	1091672	1	1
CL0124	Peptidase_PA		Peptidase clan PA	Bateman A	anon	This clan contains a diverse set of peptidases with the trypsin fold.	2008-09-03 16:50:29	2005-04-06 15:44:18	15	3537	1459	5053	45124	1	1
CL0125	Peptidase_CA		Peptidase clan CA	Bateman A	anon	This clan includes peptidases with the papain-like fold.	2008-09-03 16:50:29	2005-04-06 17:40:48	15	1354	2937	5235	100616	1	1
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 16:50:29	2005-04-07 08:52:20	18	1525	2800	5439	125279	1	1
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 16:50:29	2005-04-07 12:12:33	12	1694	607	5291	76860	1	1
CL0128	vWA-like		von Willebrand factor type A	Finn RD	anon	To add.	2008-09-03 16:50:29	2005-04-07 17:59:38	12	431	2282	4596	52099	1	1
CL0129	Peptidase_AA	NULL	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 16:50:29	2005-04-08 09:36:39	14	3022	893	2580	33204	1	1
CL0130	Peptidase_AD	NULL	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 16:50:29	2005-04-08 11:13:31	11	31	64	4098	8008	1	1
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 16:50:29	2005-04-08 11:57:52	11	0	82	3541	12426	1	1
CL0132	AbrB	NULL	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 16:50:29	2005-04-08 13:53:50	13	55	20	3851	11270	1	1
CL0133	AT14A-like	NULL	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 16:50:29	2005-04-08 14:00:57	11	0	29	58	2558	1	1
CL0135	Arrestin_N-like	NULL	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 16:50:29	2005-04-12 14:27:53	11	69	136	1214	10695	1	1
CL0136	Plasmid-antitox	Plasmid_toxin;	Plasmid toxin-antitoxin system	Mistry J	anon	The families in this clan are plasmid encoded anti-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.	2012-10-18 10:56:11	2005-04-14 09:55:24	12	172	56	3248	18743	1	1
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 16:50:29	2005-04-15 16:57:28	15	1231	1741	5425	145151	1	1
CL0139	GADPH_aa-bio_dh	NULL	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 16:50:29	2005-04-18 13:42:09	11	617	78	5238	17166	1	1
CL0140	Viral_NABP	NULL	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 16:50:29	2005-04-18 14:24:28	11	0	2	4	4	1	1
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 16:50:29	2005-04-19 09:24:39	12	21	201	1853	18051	1	1
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 16:50:29	2005-04-20 13:47:04	12	20	128	4927	68907	1	1
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 16:50:29	2005-04-25 11:24:48	16	403	495	2552	16165	1	1
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 16:50:29	2005-04-25 15:04:24	13	899	627	4226	71009	1	1
CL0145	Golgi-transport	NULL	Golgi-transport	Mistry J	anon	This clan contains families that are involved in intracellular transport and signalling.\t\t    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 16:50:29	2005-04-25 16:18:47	15	139	503	762	16842	1	1
CL0146	Herpes_glyco	NULL	Herpes glycoprotein	Mistry J	anon	This clan contains herpes envelope glycoproteins [1][2].	2008-09-03 16:50:29	2005-04-25 16:48:44	12	0	3	14	14	1	1
CL0147	Traffic	NULL	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 16:50:29	2005-04-26 10:46:36	11	7	75	804	4932	1	1
CL0148	Viral_Gag	NULL	Viral Gag protein	Mistry J	anon	This clan contains Gag proteins which are involved in viral assembly and replication [1][2].  	2008-09-03 16:50:29	2005-04-27 12:13:23	11	1904	267	121	3125	1	1
CL0149	CoA-acyltrans	NULL	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 16:50:29	2005-04-27 14:03:23	12	269	2496	4196	50452	1	1
CL0151	PK_TIM	NULL	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 16:50:29	2005-05-03 14:40:00	12	722	281	5249	41416	1	1
CL0153	dUTPase	NULL	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 16:50:29	2005-05-04 09:16:52	11	383	53	4712	7477	1	1
CL0154	C2		C2 superfamily	Bateman A	anon	This superfamily includes C2 domains and C2-like domains.	2008-09-03 16:50:29	2005-05-04 15:46:49	11	421	1921	1400	65835	1	1
CL0155	CBM_14_19	NULL	Carbohydrate binding domain 14/19 clan	Bateman A	anon	This clan includes two different carbohydrate binding modules.	2008-09-03 16:50:29	2005-05-04 15:50:34	11	8	239	330	10213	1	1
CL0156	Nucleocapsid	NULL	Mononegaviral nucleocapsid superfamily	Bateman A	anon	This clan contains paramyxoviral and ebola type virus nucleocapsid proteins.	2008-09-03 16:50:29	2005-05-04 16:11:33	11	53	2	9	11	1	1
CL0157	Kleisin	NULL	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 16:50:29	2005-05-04 16:26:02	11	11	25	3954	4659	1	1
CL0158	GH_CE	NULL	Glycoside hydrolase/deacetylase superfamily	Bateman A	anon	This superfamily contains diverse enzymes that act on carbohydrates including both hydrolases and deacetylases.	2008-09-03 16:50:29	2005-05-04 16:44:41	12	167	461	4780	25873	1	1
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	16	2024	15952	5124	321167	1	1
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 16:50:29	2005-05-09 16:58:23	11	71	55	4128	12576	1	1
CL0161	GAF	NULL	GAF domain-like	Finn RD	anon	A clan of related transcriptional regulator domains.	2008-09-03 16:50:29	2005-05-09 18:32:14	12	364	4970	4912	55180	1	1
CL0162	FBA	NULL	F-box associated	Finn RD	anon	Clan containing related F-box associated families.	2008-09-03 16:50:29	2005-05-09 18:41:19	11	0	109	52	4671	1	1
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 16:50:29	2005-05-10 16:59:39	11	469	1207	5262	68859	1	1
CL0164	CUB	NULL	CUB clan	Bateman A	anon	This clan contains the CUB domain [1,2].	2008-09-03 16:50:29	2005-05-10 17:23:26	13	46	1398	340	22621	1	1
CL0165	Cache	NULL	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 16:50:29	2005-05-10 17:26:33	11	115	1784	3432	23803	1	1
CL0166	PRD	NULL	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 16:50:29	2005-05-11 14:46:29	12	9	128	877	6052	1	1
CL0167	Zn_Beta_Ribbon		Zinc beta-ribbon	Finn RD	anon	A clan of zinc-binding ribbon domains.	2008-09-03 16:50:29	2005-05-11 16:19:40	15	2457	2720	5482	162614	1	1
CL0168	PAN	NULL	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 16:50:29	2005-05-11 16:56:50	15	164	857	739	13340	1	1
CL0169	Rep	NULL	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 16:50:29	2005-05-13 18:23:32	11	119	83	1838	5066	1	1
CL0170	Peptidase_MD	NULL	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 16:50:29	2005-05-19 09:30:19	11	88	200	3053	6913	1	1
CL0171	Phospoesterase	NULL	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 16:50:29	2005-05-19 17:12:45	11	372	126	4448	17145	1	1
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 16:50:29	2005-05-20 15:54:37	17	3591	2187	5439	186913	1	1
CL0173	STIR	NULL	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 16:50:29	2005-08-11 10:18:06	11	50	1080	1691	12172	1	1
CL0174	TetR_C	NULL	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 16:50:29	2005-08-11 10:47:22	10	355	75	2771	18308	1	1
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 16:50:29	2005-08-15 13:59:13	11	215	554	2918	23436	1	1
CL0176	Chemosens_recp	NULL	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 16:50:29	2005-08-15 14:20:45	10	0	100	81	6083	1	1
CL0177	PBP	NULL	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 16:50:29	2005-08-22 13:15:50	16	2876	1362	5332	233285	1	1
CL0178	PUA	NULL	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 16:50:29	2005-08-22 16:11:13	16	236	346	5083	25469	1	1
CL0179	ATP-grasp	NULL	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 16:50:29	2005-08-23 14:07:58	14	605	866	5318	75551	1	1
CL0181	ABC-2	NULL	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 16:50:29	2005-08-23 16:06:40	10	7	465	5090	60619	1	1
CL0182	IT	NULL	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 16:50:29	2005-08-23 18:40:04	13	10	220	4763	41951	1	1
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 16:50:29	2005-08-24 15:20:49	14	552	12088	4635	113389	1	1
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 16:50:29	2005-08-25 11:36:38	11	36	586	5239	115135	1	1
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 16:50:29	2005-08-26 09:32:54	14	1985	15098	5018	654484	1	1
CL0187	LysM	NULL	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 16:50:29	2005-08-26 09:44:43	11	110	818	4614	29949	1	1
CL0188	CH	NULL	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 16:50:29	2005-08-30 18:32:49	10	153	1007	818	23716	1	1
CL0189	Endonuclease	NULL	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 16:50:29	2005-08-31 14:14:38	10	26	47	4546	5502	1	1
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 16:50:29	2005-09-01 14:25:02	12	335	306	4309	20468	1	1
CL0191	POTRA	NULL	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 16:50:29	2005-09-01 14:31:22	11	40	85	3915	17230	1	1
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 16:50:29	2005-09-02 12:58:56	13	566	1971	4217	124484	1	1
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 16:50:29	2005-09-05 10:13:31	14	678	1312	3148	97834	1	1
CL0194	DNA_pol_B-like	NULL	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 16:50:29	2005-09-05 13:42:41	10	256	153	1501	7133	1	1
CL0195	DBL	NULL	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 16:50:29	2005-09-05 15:25:46	10	34	163	18	3692	1	1
CL0196	DSRM	NULL	DSRM-like clan	Bateman A	anon	This clan contains RNA-binding domains.	2008-09-03 16:50:29	2005-09-08 18:03:50	12	781	406	5382	22210	1	1
CL0197	GME	NULL	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 16:50:29	2005-09-15 15:15:35	10	171	60	3560	7498	1	1
CL0198	HHH		Helix-hairpin-helix superfamily	Bateman A	anon	This superfamily includes Helix-hairpin-helix DNA-binding domains.	2008-09-03 16:50:29	2005-09-16 17:04:15	16	1050	819	5427	77391	1	1
CL0199	DPBB	NULL	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 16:50:29	2005-09-16 17:23:52	12	61	141	3009	10129	1	1
CL0200	Prefoldin	NULL	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 16:50:29	2005-09-19 13:51:59	10	9	113	1015	6156	1	1
CL0201	Peptidase_SH	NULL	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 16:50:29	2005-09-20 12:38:50	10	59	15	892	1169	1	1
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 16:50:29	2005-09-20 16:50:13	11	1350	5108	4050	61721	1	1
CL0203	CBD	NULL	Carbohydrate binding domain superfamily	Bateman A	anon	This superfamily includes several carbohydrate binding domains. These domains have a beta sandwich structure.	2008-09-03 16:50:29	2005-09-21 11:02:43	12	116	518	942	4137	1	1
CL0204	Adhesin	NULL	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 16:50:29	2005-09-21 11:17:50	11	326	135	2231	7571	1	1
CL0205	Di-copper	NULL	Di-copper centre-containing domain	Bateman A	anon	This superfamily includes tyrosinases and hemocyanins that share a di-copper centre [1].	2008-09-03 16:50:29	2005-09-23 12:59:27	11	193	159	855	4909	1	1
CL0206	TRB	NULL	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 16:50:29	2005-09-23 14:02:56	11	139	47	3941	8124	1	1
CL0207	Rhomboid-like	NULL	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 16:50:29	2005-12-01 11:27:30	10	29	185	4055	13592	1	1
CL0208	UBC	NULL	Ubiquitin conjugating enzyme like superfamily	Bateman A	anon	This superfamily includes a diverse set of proteins that bind to ubiquitin [1].	2008-09-03 16:50:29	2005-12-02 15:22:57	11	406	590	1188	27481	1	1
CL0209	Bet_V_1_like	NULL	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	11	692	435	3789	37376	1	1
CL0210	HNOX-like	NULL	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.\t      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 16:50:29	2005-12-06 09:55:10	11	157	135	1723	5080	1	1
CL0212	SNARE	NULL	SNARE-like superfamily	Bateman A	anon	This clan includes part of the SNARE like superfamily.	2008-09-03 16:50:29	2005-12-08 17:07:43	9	74	196	821	11136	1	1
CL0213	ShK-like	NULL	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 16:50:29	2006-01-03 16:32:02	9	30	254	291	7399	1	1
CL0214	UBA	NULL	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 16:50:29	2006-01-05 15:54:42	13	196	692	4657	24290	1	1
CL0217	Rotavirus_VP7	NULL	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 16:50:29	2006-01-24 14:08:46	9	29	2	3	3	1	1
CL0218	ox_reductase_C	NULL	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 16:50:29	2006-01-26 11:16:09	12	229	75	3324	12818	1	1
CL0219	RNase_H	NULL	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 16:50:29	2006-01-31 17:56:29	14	1719	3468	5545	174117	1	1
CL0220	EF_hand	NULL	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 16:50:29	2006-02-01 09:23:33	12	1814	4767	1996	123493	1	1
CL0221	RRM	NULL	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 16:50:29	2006-03-05 12:30:44	11	761	2065	3868	152096	1	1
CL0222	MviN_MATE	NULL	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 16:50:29	2006-03-05 13:21:19	8	19	209	5246	60167	1	1
CL0223	MACRO	NULL	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 16:50:29	2006-03-06 10:58:15	8	289	221	4085	10278	1	1
CL0224	DHQS	NULL	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 16:50:29	2006-03-06 13:57:58	8	148	105	4688	15839	1	1
CL0225	FtsL	NULL	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 16:50:29	2006-03-06 15:46:31	8	4	8	3656	5053	1	1
CL0226	M6PR	NULL	Mannose 6-phosphate receptor	Bateman A	anon	This clan includes cation dependent and independent mannose 6-phosphate receptors.	2008-09-03 16:50:29	2006-03-06 16:32:14	9	59	134	761	5199	1	1
CL0227	Enolase_N	NULL	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 16:50:29	2006-03-06 16:37:34	9	1127	70	5085	14579	1	1
CL0228	Acyltransferase		Acyltransferase clan	Bateman A	anon	This clan includes several families of related acyltransferases.	2008-09-03 16:50:29	2006-03-06 16:43:34	8	15	310	4812	29201	1	1
CL0229	RING	NULL	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 16:50:29	2006-03-06 16:54:46	11	343	4002	1374	118732	1	1
CL0230	HO	NULL	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 16:50:29	2006-03-06 16:57:26	8	245	75	2734	5899	1	1
CL0231	MazG	NULL	all-alpha NTP pyrophosphohydrolase superfamily	Bateman A	anon	This superfamily includes MazG, HisE and dimeric dUTPases (Not yet in Pfam) [1].	2008-09-03 16:50:29	2006-03-06 17:03:44	9	148	71	4596	12510	1	1
CL0232	NifU	NULL	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 16:50:29	2006-03-06 17:10:22	8	31	80	4482	11466	1	1
CL0233	SufE_NifU	NULL	SufE/NifU superfamily	Bateman A	anon	This clan includes iron sulfur cluster assembly proteins.	2008-09-03 16:50:29	2006-03-06 17:18:24	8	218	154	5023	13329	1	1
CL0234	CTPT	NULL	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 16:50:29	2006-03-06 17:30:58	8	4	30	4812	6016	1	1
CL0235	PspA	NULL	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 16:50:29	2006-03-07 09:10:43	9	66	106	2467	9050	1	1
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 15:09:06	2006-03-07 10:09:50	17	985	1210	5479	78963	1	1
CL0237	HD_PDEase	NULL	HD/PDEase superfamily	Bateman A	anon	This clan includes a range of phosphohydrolase enzymes with a common helical fold.	2008-09-03 16:50:29	2006-03-07 17:08:35	8	877	975	5350	50920	1	1
CL0238	PP2C	NULL	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 16:50:29	2006-03-08 17:11:21	8	111	970	4089	33097	1	1
CL0239	Insulin	NULL	Insulin-like superfamily	Bateman A	anon	This superfamily includes the insulin like hormones.	2008-09-03 16:50:29	2006-03-09 13:10:30	8	1314	13	191	1094	1	1
CL0240	PFK	NULL	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 16:50:29	2006-03-09 16:35:37	8	250	275	5022	25773	1	1
CL0241	ABC_membrane	NULL	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 16:50:29	2006-03-09 17:38:52	8	107	484	5048	69512	1	1
CL0242	DNA_primase_lrg	NULL	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 16:50:29	2006-04-21 14:57:17	9	29	24	957	1237	1	1
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 16:50:29	2006-04-24 16:40:55	10	22	29	1161	1332	1	1
CL0244	PGBD	NULL	PGBD superfamily	Bateman A	anon	This clan consists of small putative peptidoglycan binding domains composed of three alpha helices.	2008-09-03 16:50:29	2006-05-16 17:51:06	9	56	577	3341	14746	1	1
CL0245	EDD	NULL	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 16:50:29	2006-05-17 09:35:18	9	124	87	3450	12398	1	1
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 16:50:29	2006-05-17 13:20:27	8	401	304	5019	48439	1	1
CL0247	2H	NULL	2H phosphoesterase superfamily	Bateman A	anon	This clan includes a number of phosphoesterases that contain an internal duplication.	2008-09-03 16:50:29	2006-05-17 15:53:15	9	63	147	3332	7006	1	1
CL0248	ParBc	NULL	ParB-like superfamily	Bateman A	anon	This superfamily includes nucleases related to ParB as well as uncharacterised proteins.	2008-09-03 16:50:29	2006-06-02 16:12:35	8	39	106	4599	12983	1	1
CL0249	Phage_tail_L	NULL	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 16:50:29	2006-06-02 18:35:28	8	0	7	174	237	1	1
CL0250	GAD	NULL	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 16:50:29	2006-07-27 15:00:10	7	29	34	4056	4435	1	1
CL0251	MORN	NULL	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).\tA MORN-repeat protein has been identified in the parasite Toxoplasma gondiis as dynamic component of cell division apparatus [1].\tIt has been hypothesised to function as a linker protein between certain membrane regions and the parasite's cytoskeleton [1].	2008-09-03 16:50:29	2006-07-31 12:59:47	8	41	552	1448	47284	1	1
CL0252	NfeD-like	NULL	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 16:50:29	2006-07-31 13:35:37	7	4	12	3013	3879	1	1
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 16:50:29	2006-07-31 17:23:48	9	848	502	5337	97642	1	1
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 16:50:29	2006-08-01 13:45:46	9	104	144	5039	17025	1	1
CL0256	Enolase_TIM	NULL	Enolase like TIM barrel	Mistry J	anon	This clan contains enzymes which adopt a TIM barrel fold.	2008-09-03 16:50:29	2006-08-01 15:00:35	7	1249	110	5125	17001	1	1
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 16:50:29	2006-08-02 14:16:08	9	1152	1790	5325	146995	1	1
CL0258	DALR	NULL	DALR superfamily	Bateman A	anon	Members of this family are anticodon binding domains from various tRNA synthetases.	2008-09-03 16:50:29	2006-08-17 18:00:51	7	84	319	5396	32031	1	1
CL0259	OstA	NULL	OstA superfamily	Bateman A	anon	This superfamily includes the OstA family as well as a large family of uncharacterised proteins.	2008-09-03 16:50:29	2006-08-22 10:05:45	7	16	30	2147	5075	1	1
CL0260	NTP_transf	NULL	Nucleotidyltransferase superfamily	Bateman A	anon	This clan contains a diverse set of nucleotidyltransferase enzymes.	2008-09-03 16:50:29	2006-08-22 16:46:46	8	736	948	5432	58469	1	1
CL0261	NUDIX		NUDIX superfamily	Bateman A	anon	This superfamily contains the NUDIX family and one related family.	2008-09-03 16:50:29	2006-08-24 18:58:30	7	516	637	5315	53479	1	1
CL0262	Trigger_C	NULL	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 16:50:29	2006-08-30 10:54:44	7	19	79	4295	9077	1	1
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 16:50:29	2006-09-06 17:41:01	8	171	576	4615	22238	1	1
CL0264	SGNH_hydrolase	NULL	SGNH hydrolase superfamily	Bateman A	anon	This superfamily contains a diversity of hydrolytic enzyme activities.	2008-09-03 16:50:29	2006-09-07 09:23:58	7	223	711	4352	34183	1	1
CL0265	HIT	NULL	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 16:50:29	2006-11-09 16:05:44	7	222	229	5228	18356	1	1
CL0266	PH	NULL	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 16:50:29	2006-11-10 10:42:30	9	819	3422	3540	95282	1	1
CL0267	S11_L18p	NULL	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 16:50:29	2006-11-10 14:46:27	8	1302	122	5357	14931	1	1
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 16:50:29	2006-11-10 15:10:57	7	318	2043	3706	44878	1	1
CL0269	Maf	NULL	Maf/Ham1 superfamily	Bateman A	anon	This superfamily includes the Maf-like proteins and ITPases related to YjjX [1].	2008-09-03 16:50:29	2006-11-10 17:10:08	8	90	97	5058	11910	1	1
CL0270	Iso_DH	NULL	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 16:50:29	2006-11-10 17:50:17	7	415	134	4942	25515	1	1
CL0271	F-box	NULL	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 16:50:29	2006-11-22 13:28:07	7	38	1489	845	56272	1	1
CL0272	RGS	NULL	RGS-like superfamily	Bateman A	anon	This clan includes RGS domains that possess an alpha helical fold.	2008-09-03 16:50:29	2006-11-27 17:23:03	7	122	258	689	8588	1	1
CL0273	CYTH	NULL	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 16:50:29	2006-12-05 13:50:23	7	117	95	3532	7004	1	1
CL0274	WRKY-GCM1	NULL	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 16:50:29	2006-12-05 13:57:43	8	9	290	579	12673	1	1
CL0275	HAS-barrel	NULL	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 16:50:29	2006-12-06 11:13:24	9	657	108	5102	15058	1	1
CL0276	Nucleot_cyclase	NULL	Nucleotide cyclase superfamily	Bateman A	anon	This superfamily includes adenylyl cyclase and the GGDEF domain [1].	2008-09-03 16:50:29	2006-12-06 14:41:38	8	299	3922	4058	82763	1	1
CL0277	FAD-oxidase_C	NULL	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 16:50:29	2006-12-07 10:48:02	7	255	286	3935	20818	1	1
CL0278	AIG2	NULL	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.\tConservation 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 16:50:29	2006-12-12 14:39:36	8	20	103	2505	5849	1	1
CL0279	GatB_YqeY	NULL	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 16:50:29	2007-01-24 12:42:11	7	42	35	4846	8183	1	1
CL0280	PIN	NULL	PIN domain superfamily	Bateman A	anon	This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.	2008-09-03 16:50:29	2007-01-25 17:50:12	7	219	442	5371	40988	1	1
CL0281	CCT	NULL	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 16:50:29	2007-01-29 13:51:28	7	25	48	98	3629	1	1
CL0282	Serum_albumin	NULL	Serum albumin superfamily	Bateman A	anon	This superfamily includes serum albumin and related families.	2008-09-03 16:50:29	2007-01-30 15:32:33	7	181	11	92	964	1	1
CL0283	LigB	NULL	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 16:50:29	2007-02-12 17:08:37	7	49	48	2872	5219	1	1
CL0284	Allatostatin	NULL	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 16:50:29	2007-05-04 14:22:41	6	2	9	27	168	1	1
CL0285	YycI_YycH	NULL	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 16:50:29	2007-05-14 11:16:06	7	13	4	438	813	1	1
CL0286	GCS	NULL	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 16:50:29	2007-08-10 14:04:49	6	604	179	5270	25264	1	1
CL0287	Transthyretin	NULL	Transthyretin superfamily	Bateman A	anon	This clan unifies several SCOP superfamilies that all share a 7 stranded beta sandwich fold.	2008-09-03 16:50:29	2007-08-14 16:23:44	7	1245	1713	4053	44463	1	1
CL0288	DAP_epimerase	NULL	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 16:50:29	2007-08-17 11:58:37	6	91	91	4226	14743	1	1
CL0289	FBD	NULL	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 16:50:29	2007-08-17 13:17:41	6	71	124	4694	14328	1	1
CL0290	EPT_RTPC	NULL	EPT/RTPC-like superfamily	Bateman A	anon	This superfamily includes Enolpyruvate transferase (EPT) and RNA 3'-terminal phosphate cyclase (RTPC).	2008-09-03 16:50:29	2007-08-17 13:33:07	6	240	99	5184	12011	1	1
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 16:50:29	2007-08-20 15:49:55	7	39	119	3412	12140	1	1
CL0292	LysE		LysE transporter superfamily	Bateman A	anon	This clan includes a diverse range of transporter families [1].	2008-09-03 16:50:29	2007-10-04 12:03:53	6	0	187	5228	59302	1	1
CL0293	CDC	NULL	Cholesterol-dependent cytolysin superfamily	Bateman A	anon	This superfamily includes the MACPF domain as well as the Cholesterol-dependent cytolysins [1].	2008-09-03 16:50:29	2007-10-19 12:42:17	6	378	168	800	5819	1	1
CL0294	Sec10	NULL	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 16:50:29	2007-11-20 17:02:32	6	0	79	781	3118	1	1
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 16:50:29	2007-11-20 17:11:52	7	21	340	824	17528	1	1
CL0296	GroES	NULL	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 16:50:29	2008-02-08 16:40:31	5	930	840	5161	63559	1	1
CL0297	PhoU	NULL	PhoU-like superfamily	Bateman A	anon	This superfamily includes PhoU and its relatives that contain a three helical bundle domain structure.	2008-09-03 16:50:29	2008-02-08 17:40:34	5	32	36	3761	12404	1	1
CL0298	tRNA_bind_arm		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.	2015-08-25 08:54:17	2008-02-12 16:57:18	5	67	61	5180	13560	1	1
CL0299	Peptidase_SF	NULL	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 16:50:29	2008-02-25 12:55:51	5	74	135	5187	20014	1	1
CL0300	TAT	NULL	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 16:50:29	2008-02-29 15:32:23	5	125	266	2631	4575	1	1
CL0301	PA14	NULL	PA14 superfamily	Bateman A	anon	This clan includes the PA14 domain and related families.	2008-09-03 16:50:29	2008-03-03 17:31:48	6	60	554	1305	3959	1	1
CL0302	Arginase	NULL	Arginase/deacetylase superfamily	Bateman A	anon	This superfamily includes arginase enzymes as well as histone deacetylases and related enzymes [1].	2008-09-03 16:50:29	2008-04-30 14:26:28	6	664	192	3988	17604	1	1
CL0303	H2TH	NULL	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 16:50:29	2008-05-28 16:24:30	5	748	98	5319	14369	1	1
CL0304	CheY	NULL	CheY-like superfamily	Bateman A	anon	This clan includes the CheY-like response regulators from bacteria [1-2].	2008-09-03 16:50:29	2008-06-04 14:50:30	5	641	5806	5239	187083	1	1
CL0305	PTH2	NULL	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 16:50:29	2008-06-05 14:00:28	5	24	40	1600	2445	1	1
CL0306	HeH	NULL	LEM/SAP HeH motif	Bateman A	anon	This superfamily includes protein domains with the helix-extended loop-helix (HeH) structure.	2008-09-03 16:50:29	2008-09-03 10:49:37	4	96	366	4028	10137	1	1
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 14:12:16	2008-09-05 14:12:16	4	0	133	2962	11890	1	1
CL0308	DMSO_reductase	NULL	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 16:56:29	2008-09-23 16:56:29	4	8	17	1227	2378	1	1
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 13:01:30	2008-10-08 13:01:30	4	48	113	2743	14064	1	1
CL0311	SCP2	NULL	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 15:19:21	2008-10-13 15:19:21	4	112	116	2977	6752	1	1
CL0312	HemS_ChuX	NULL	Heme iron utilization protein-like superfamily	Bateman A	anon	This superfamily includes HemS and ChuX like protein families.	2008-10-22 17:49:13	2008-10-22 17:49:13	4	20	14	633	1124	1	1
CL0314	PP-binding	NULL	ACP-like superfamily	Bateman A	anon	NULL	2008-11-19 12:30:53	2008-11-19 12:30:53	4	209	4087	4724	47941	1	1
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	4	34	180	3448	14147	1	1
CL0316	Acyl_transf_3	NULL	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	4	0	121	4133	19419	1	1
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	4	309	396	2088	9666	1	1
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	4	848	585	3468	34005	1	1
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	4	345	140	4736	13156	1	1
CL0320	PepSY	NULL	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	4	73	114	2465	6611	1	1
CL0321	PLAT	NULL	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	4	103	289	418	5974	1	1
CL0322	RND_permease	NULL	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	4	197	263	4956	47832	1	1
CL0323	Patatin	NULL	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	4	122	2199	4661	33939	1	1
CL0324	Homing_endonuc	NULL	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	4	187	335	2272	5129	1	1
CL0325	Form_Glyc_dh	NULL	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	4	532	255	5081	32252	1	1
CL0326	Reo_sigma	NULL	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	4	193	7	9	9	1	1
CL0327	Pilus	NULL	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	4	127	50	1409	6071	1	1
CL0328	2heme_cytochrom		Transmembrane di-heme cytochrome superfamily	Bateman A	anon	This superfamily includes a variety of different heme binding cytochromes.	2009-05-08 20:48:23	NULL	4	135	439	4084	31119	1	1
CL0329	S5	NULL	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 20:52:37	NULL	4	2189	771	5441	100766	1	1
CL0330	AVL9		Late secretory pathway transport machinery	Bateman A	anon	Members of this clan are involved in vesicle formation/trafficking.	2009-05-08 20:52:58	NULL	4	2	219	804	6885	1	1
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 20:53:19	NULL	4	58	24	1670	4349	1	1
CL0332	AcetylDC-like		Acetyl-decarboxylase like superfamily	Coggill P	anon	These families are double psi-beta barrel structures.	2009-05-08 20:53:39	NULL	4	409	176	4071	15469	1	1
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 20:54:54	NULL	4	87	91	472	5017	1	1
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 20:57:58	NULL	4	536	93	4456	18260	1	1
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 20:58:20	NULL	4	210	39	2986	6421	1	1
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 20:58:45	NULL	4	317	243	4675	30318	1	1
CL0337	RF	NULL	Release factor superfamily	Coggill P	anon	These families are peptide chain release factors.	2009-05-08 20:59:09	NULL	4	49	72	5106	13810	1	1
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 20:59:52	NULL	4	232	166	5158	16037	1	1
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 21:00:18	NULL	4	29	164	2754	9325	1	1
CL0341	LDH_C	NULL	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 21:00:39	NULL	4	736	50	4330	10318	1	1
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 21:00:59	NULL	4	114	100	2051	6354	1	1
CL0343	MHC		MHC antigen-recognition domain	Coggill P	anon	This superfamily includes all the Class I-related antigen-recognition domain families.	2009-05-08 21:01:29	NULL	4	1797	58	94	3282	1	1
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 21:01:52	NULL	4	579	2767	5175	120789	1	1
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 21:02:15	NULL	4	76	20	171	320	1	1
CL0346	Ribo_L29	NULL	Ribosomal protein L29, L29p, superfamily	Coggill P	anon	Superfamily includes Ribosomal protein L29 family and its corresponding mitochondrial ribosomal family, L47.	2009-05-08 21:02:37	NULL	4	636	32	5126	6224	1	1
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 21:04:53	NULL	4	18	131	577	9631	1	1
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 21:05:12	NULL	4	1	14	1010	1743	1	1
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 21:05:29	NULL	4	71	77	4698	11883	1	1
CL0350	PRC-barrel	NULL	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 21:05:48	NULL	4	141	65	3741	8754	1	1
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 21:06:07	NULL	4	91	117	792	6950	1	1
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 21:06:25	NULL	4	96	83	759	5041	1	1
CL0353	TIMP-like	NULL	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 21:06:43	NULL	4	96	115	266	2512	1	1
CL0354	bBprotInhib	NULL	beta-Barrel protease inhibitors	Coggill P	anon	Superfamily consists of both metalloprotease- inhibitors and staphostatins.	2009-05-08 21:07:02	NULL	4	11	5	183	279	1	1
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 21:07:19	NULL	4	39	37	1746	4850	1	1
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 21:07:37	NULL	4	133	131	4802	14745	1	1
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 21:07:54	NULL	4	189	773	2977	22785	1	1
CL0359	Intron-mat_II	NULL	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 21:08:30	NULL	4	1	29	974	2642	1	1
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 21:08:47	NULL	4	35	16	1752	2129	1	1
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 21:09:05	NULL	4	352	8541	1352	420550	1	1
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 21:09:23	NULL	4	170	32	1567	5826	1	1
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 21:09:41	NULL	4	91	765	1731	5099	1	1
CL0364	Leu-IlvD	NULL	LeuD/IlvD-like	Bateman A	anon	Superfamily includes LeuD-like, IlvD/EDD C-terminal domain-like, and AF0055-like families.	2009-05-08 21:09:58	NULL	4	324	659	5216	45903	1	1
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 21:10:16	NULL	4	14	37	2548	3625	1	1
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 21:10:33	NULL	4	153	263	4331	14116	1	1
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 21:10:50	NULL	4	70	17	714	1484	1	1
CL0368	PhosC-NucP1	NULL	Phospholipase C/P1 nuclease superfamily	Coggill P	anon	This superfamily includes the Phospholipase C and P1-nuclease families.	2009-05-08 21:11:07	NULL	4	37	44	2881	5399	1	1
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 21:11:24	NULL	4	789	689	3964	30031	1	1
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 21:11:41	NULL	4	12	4	55	344	1	1
CL0371	Inovirus-Coat	NULL	Inovirus (filamentous phage) major coat protein	Coggill P	anon	Superfamily contains a number of filamentous phage coat-protein families.	2009-05-08 21:11:58	NULL	4	61	3	43	51	1	1
CL0372	Hy-ly_N	NULL	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 21:12:16	NULL	4	74	122	1155	2519	1	1
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 21:12:33	NULL	4	141	33	1830	3191	1	1
CL0374	PEP-carboxyk	NULL	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 21:12:50	NULL	4	131	34	4153	6366	1	1
CL0375	Transporter		Transporter superfamily, four TM region	Bateman A	anon	The members of this superfamily are probably all transporter protein domains. All families normally carry four tansmembrane regions, which in many instances associate into hexameric structures.  They are frequently involved in gap-junction formation between cells or in forming pores linking the cytosol with the extracellulare space 1,2]. The clan includes members of the TCDB superfamilies 1.A.24 and 1.A.25.	2014-05-16 12:14:25	NULL	4	52	165	646	15143	1	1
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 21:13:27	NULL	4	10	71	5113	8001	1	1
CL0377	FAH	NULL	Fumarylacetoacetate hydrolase, C-terminal domain, superfamily	Bateman A	anon	Superfamily contains fumarylacetoacetate hydrolase and related enzymes,	2009-05-08 21:13:45	NULL	4	116	125	3727	13430	1	1
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 21:14:02	NULL	4	307	3077	4804	97677	1	1
CL0379	PgaPase	NULL	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 21:14:20	NULL	4	68	27	1356	1674	1	1
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 21:14:37	NULL	4	93	44	1708	3529	1	1
CL0381	Metallo-HOrase	NULL	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 21:14:54	NULL	4	634	593	5393	62884	1	1
CL0382	DNA-mend	NULL	DNA breaking-rejoining enzyme superfamily	Bateman A	anon	This is a superfamily of DNA recombinases, topoisomerases and integrases.	2009-05-08 21:15:13	NULL	4	126	285	5230	37608	1	1
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 21:15:30	NULL	4	42	67	5046	8065	1	1
CL0384	PLC		PLC-like phosphodiesterases	Coggill P	anon	Superfamily consists of Glycerophosphoryl diester phosphodiesterase and phosphatidylinositol-specific phospholipase C families.	2009-05-08 21:15:48	NULL	4	128	516	4075	20075	1	1
CL0385	Hydrophilin	NULL	Hydrophilin-like superfamily	Coggill P	anon	This superfamily includes plant and bacterial hydrophilin families.	2009-05-08 21:16:05	NULL	4	0	27	522	1752	1	1
CL0386	Ant-toxin_C	NULL	Superantigen toxins, C-terminal domain superfamily	Coggill P	anon	Superfamily contains bacterial super-antigen toxins and the MAP family.	2009-05-08 21:16:23	NULL	4	253	6	6	42	1	1
CL0387	DHFred	NULL	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 21:16:40	NULL	4	635	79	4892	13706	1	1
CL0388	FadR-C	NULL	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 21:16:57	NULL	4	41	69	2744	22244	1	1
CL0389	TRAF	NULL	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 21:17:16	NULL	4	68	285	697	9286	1	1
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 21:17:33	NULL	4	235	1885	826	40589	1	1
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 21:17:50	NULL	4	16	62	805	2457	1	1
CL0392	Chaperone-J	NULL	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 21:18:07	NULL	4	79	1110	5193	41677	1	1
CL0393	FucI-AraA_C	NULL	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 21:18:26	NULL	4	54	8	1047	1563	1	1
CL0394	DsrEFH-like	NULL	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 21:18:45	NULL	4	54	21	2272	4955	1	1
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 21:19:04	NULL	4	11	85	1164	5892	1	1
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 21:19:22	NULL	4	0	67	667	6681	1	1
CL0397	TusA-like	SirA-like;	TusA-like superfamily	Bateman A	anon	Member families include sulfurtransferase TusA.	2009-05-08 21:19:39	NULL	4	9	62	2624	4918	1	1
CL0398	RMMBL_DRMBL	NULL	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 21:19:56	NULL	4	63	130	4382	9036	1	1
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 21:20:14	NULL	4	468	98	4964	16919	1	1
CL0400	GG-leader	NULL	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 21:20:32	NULL	4	4	5	52	124	1	1
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 21:20:49	NULL	4	0	71	2257	9380	1	1
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 21:21:06	NULL	4	207	97	1139	4312	1	1
CL0403	ADC-like	NULL	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 21:21:23	NULL	4	36	21	1081	1628	1	1
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 21:21:41	NULL	4	71	236	4587	181085	1	1
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 21:21:58	NULL	4	15	113	112	8101	1	1
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 21:22:16	NULL	4	2	11	1958	3726	1	1
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 21:22:35	NULL	4	171	76	2504	6522	1	1
CL0408	PUP	NULL	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 21:22:53	NULL	4	1163	431	4910	18915	1	1
CL0409	GAP	NULL	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 21:23:11	NULL	4	65	749	821	21128	1	1
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 21:23:28	NULL	4	318	196	5215	7802	1	1
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 21:23:45	NULL	4	0	11	10	2135	1	1
CL0412	Frag1-like	NULL	Frag1 like	Mistry J, Finn RD	anon	This clan contains the Frag1/DRA</Sfk1 Pfam family (Pfam:PF10277) and related families.	2009-05-08 21:24:02	NULL	4	0	41	1326	3128	1	1
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 21:24:21	NULL	4	197	410	5381	29288	1	1
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 18:52:30	NULL	4	5	44	1600	3355	1	1
CL0416	Anoctamin-like	NULL	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 21:25:15	NULL	4	4	167	797	8031	1	1
CL0417	BIR-like	NULL	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 21:25:32	NULL	4	262	83	758	4103	1	1
CL0418	GIY-YIG	NULL	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 21:25:49	NULL	4	39	176	5035	12548	1	1
CL0419	T3SS-Chaperone	NULL	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 21:26:06	NULL	4	3	6	1385	1522	1	1
CL0420	GlpM-like	NULL	Bacterial membrane GlpM-like group	Finn RD, Coggill P	anon	This is a group of membrane proteins of the GlpM type.	2009-05-08 21:26:23	NULL	4	0	4	180	216	1	1
CL0421	LppaM	NULL	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 22:19:03	NULL	4	0	9	451	523	1	1
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 22:19:20	NULL	4	288	352	282	6943	1	1
CL0423	AhpD-like	NULL	AhpD-like superfamily	Bateman A	anon	Superfamily contains CMD-like, and Antioxidant defense protein AhpD families.	2009-05-08 22:19:37	NULL	4	133	76	3583	12365	1	1
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 22:19:55	NULL	4	2	12	3113	4756	1	1
CL0425	ComplexI-N	NULL	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 22:20:12	NULL	4	24	72	3362	16357	1	1
CL0426	HRDC-like	NULL	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 22:20:30	NULL	4	140	171	4078	8830	1	1
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 22:28:43	NULL	4	20	147	2029	7860	1	1
CL0429	UcrQ-like	NULL	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 22:29:01	NULL	4	71	14	626	739	1	1
CL0430	CopD_like		Copper resistance protein D	Mistry J	anon	This clan contains families that are related to the CopD family of proteins.\t    CopD, together with CopC, performs copper uptake into the cytoplasm.	2009-05-08 22:29:20	NULL	4	0	27	2731	4991	1	1
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 22:29:38	NULL	4	131	82	1373	5709	1	1
CL0433	SPFH	NULL	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 10:16:10	NULL	4	45	151	4840	18462	1	1
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 12:40:27	2009-08-03 12:40:27	4	688	375	2255	9072	1	1
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 13:51:07	2009-08-24 13:51:07	4	0	39	658	1959	1	1
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 14:45:28	2009-08-24 14:45:28	4	36	50	3410	10220	1	1
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 16:16:01	2009-08-24 16:16:01	4	198	236	5396	39127	1	1
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 14:27:05	2009-08-25 14:27:05	4	31	51	5101	6566	1	1
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 11:57:56	2009-08-27 11:57:56	4	49	97	2662	5643	1	1
CL0442	Tubulin_C	Tubulin_C; Tubulin-like;	Tubulin, FtsZ and Misato and their C-termini,	Coggill P	pcc	This superfamily is characterised by being at the C-terminus of the GTPase-binding region of tubulins.	2013-08-02 16:31:27	2009-08-28 13:07:36	4	581	124	5015	12569	1	1
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 15:55:14	2009-09-10 15:55:14	4	114	188	837	8965	1	1
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	3	25	20	54	89	1	1
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	3	0	10	1150	1274	1	1
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	3	53	102	808	5553	1	1
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	3	0	242	804	8449	1	1
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	3	34	75	138	1321	1	1
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	3	61	775	248	9797	1	1
CL0452	Tropomyosin-lke		Tropomyosin-like superfamily	Coggill P	pcc		2009-12-18 15:27:21	2009-12-18 15:27:21	3	86	42	626	2564	1	1
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	3	6	44	3578	5976	1	1
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	3	2	23	780	1440	1	1
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	3	0	36	752	1529	1	1
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	3	26	355	1765	7571	1	1
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	3	254	280	5368	25517	1	1
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	3	191	784	4832	18655	1	1
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	3	28	12	219	532	1	1
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	3	11	44	714	1337	1	1
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	3	73	137	5143	10087	1	1
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	3	294	10606	2907	220725	1	1
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	3	941	1345	5157	63282	1	1
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	3	3	367	483	6021	1	1
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	3	35	118	4247	18154	1	1
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	3	0	22	2055	5596	1	1
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	3	5	44	1119	3002	1	1
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	3	4	105	4158	12345	1	1
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	3	0	44	3	816	1	1
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	3	421	381	4867	26678	1	1
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 09:59:45	2010-04-13 09:59:45	3	33	24	833	1249	1	1
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 16:55:02	2010-05-04 16:55:02	3	29	59	2437	7908	1	1
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 13:41:39	2010-05-19 13:41:39	3	0	2	1317	1437	1	1
CL0479	PLD		Phospholipase D superfamily	Bateman A	pcc	This superfamily includes proteins that are related to Phospholiase D.	2010-06-17 10:09:37	2010-06-17 10:09:37	3	112	292	4760	26607	1	1
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 13:33:47	2010-07-13 13:33:47	3	40	51	2081	6178	1	1
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 13:41:48	2010-07-21 13:41:48	3	78	69	59	7198	1	1
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 13:47:06	2010-07-21 13:47:06	3	335	270	5104	24377	1	1
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 13:49:56	2010-07-21 13:49:56	3	0	123	674	2596	1	1
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 12:00:26	2010-07-24 12:00:26	3	488	575	4752	42533	1	1
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 12:45:24	2010-07-25 12:45:24	3	580	452	5322	39865	1	1
CL0488	FixH-like		FixH-like	Coggill P	pcc	This is a superfamily of FixH-like proteins of unknown function.	2010-07-28 14:48:41	2010-07-28 14:48:41	3	0	29	1286	1654	1	1
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 14:32:26	2010-07-29 14:32:26	3	32	48	2976	7500	1	1
CL0490	PepSY_TM-like		PepSY_TM-like	Coggill P	pcc	This is a superfamily of PepSY-transmembrane-like domain families.	2010-08-04 16:51:29	2010-08-04 16:51:29	3	0	26	1583	3879	1	1
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 17:20:34	2010-08-19 17:20:34	3	8	89	774	5532	1	1
CL0492	S4		S4 domain superfamily	Bateman A	agb	This superfamily includes diverse proteins related to the ribosomal S4 protein.	2010-08-27 16:46:09	2010-08-27 16:46:09	3	712	107	5368	34533	1	1
CL0493	PTS_EIIC		Phosphotransferase system, EIIC superfamily	Bateman A	agb		2010-09-02 15:47:12	2010-09-02 15:47:12	3	5	55	1804	9940	1	1
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 13:39:03	2010-09-17 13:39:03	3	12	47	4465	8221	1	1
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 16:11:00	2010-09-28 16:11:00	3	0	36	1507	5188	1	1
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 11:28:59	2010-10-04 11:28:59	3	1286	479	2745	30983	1	1
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 16:46:04	2010-10-07 16:46:04	3	285	38	1547	2121	1	1
CL0499	O-anti_assembly	O-antige_ligase;	O-antigen assembly enzyme superfamily	Coggill P	pcc	This superfamily is characterised by a group of bacterial proteins that lie in the membrane. The families are all enzymes involved in the assembly of O-antigen lipopolysaccharide, and include O-antigen flippase, polymerase and ligase, the flippase being the putative transporter [1].	2015-04-29 11:45:09	2010-10-07 18:04:39	3	0	99	3273	7437	1	1
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 11:24:07	2010-10-14 11:24:07	3	2	83	3147	7216	1	1
CL0502	STAS		STAS domain superfamily	Bateman A	agb	This superfamily includes proteins that have a STAS domain.	2010-10-28 17:36:18	2010-10-28 17:36:18	3	71	254	4115	19476	1	1
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	3	114	14	1149	1545	1	1
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	3	35	120	1690	4268	1	1
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	3	52	720	2499	26968	1	1
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	3	102	129	3980	13595	1	1
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	3	4	1260	390	52592	1	1
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	3	97	125	3210	11656	1	1
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	3	613	90	5225	8273	1	1
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	3	69	1132	844	28450	1	1
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	3	53	293	801	12308	1	1
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	3	1	73	610	2118	1	1
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	3	56	15	1239	1896	1	1
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	3	489	197	3605	18568	1	1
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	3	0	106	2343	8819	1	1
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	3	0	33	63	3041	1	1
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	3	15	90	820	5358	1	1
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 15:50:08	2011-05-13 15:50:08	3	22	13	1835	2318	1	1
CL0523	GAG-polyprotein		LTR-copia-type polyprotein segment	Coggill P	pcc	This superfamily is characterised by family members that are derived from retrotransposons of the copia-type.	2016-09-02 14:44:37	2011-05-13 17:31:38	3	0	805	508	18868	1	1
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 14:54:12	2011-05-23 14:54:12	3	10	30	679	1061	1	1
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 15:59:14	2011-06-02 15:59:14	3	41	232	4733	21259	1	1
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 21:15:40	2011-07-18 21:15:40	3	8	78	1584	3539	1	1
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 06:20:17	2011-09-10 06:20:17	3	1059	285	2812	17620	1	1
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 22:21:03	2011-09-23 22:21:03	3	9	14	725	2685	1	1
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	2	312	172	4543	18410	1	1
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	2	264	635	4674	28459	1	1
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	2	201	1796	4479	52312	1	1
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	2	81	72	711	4298	1	1
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	2	570	236	5285	49320	1	1
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	2	283	121	4386	15478	1	1
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	2	4	100	221	455	1	1
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	2	505	560	5095	69204	1	1
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	2	51	680	827	24950	1	1
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	2	0	45	439	2098	1	1
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	2	74	163	4923	10414	1	1
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	2	5	65	805	4128	1	1
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	2	561	697	771	16603	1	1
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	2	37	242	679	5462	1	1
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	2	257	3	7	7	1	1
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 09:17:33	2012-03-27 09:17:33	2	354	231	3782	38575	1	1
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 14:17:34	2012-04-18 14:17:34	2	38	72	805	3631	1	1
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 15:53:24	2012-04-30 15:53:24	2	172	260	1766	5338	1	1
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 10:19:56	2012-05-01 10:19:56	2	166	179	272	4311	1	1
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 17:00:04	2012-05-01 17:00:04	2	104	23	4139	10552	1	1
CL0550	SRCR		SRCR-like	Eberhardt R	re3		2012-07-11 14:20:22	2012-07-11 14:20:22	2	20	493	280	12312	1	1
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 15:55:14	2012-08-31 15:55:14	2	403	68	767	3391	1	1
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 16:42:50	2012-09-07 16:42:50	2	40	473	825	10648	1	1
CL0556	PapD-like		PapD-like superfamily,immunoglobulin-like beta sandwich	Coggill P	pcc	This superfamily is characterised by proteins in families involved in ciliary or flagellar function. The families may be acting as chaperones.	2012-11-14 17:54:36	2012-11-14 17:54:36	2	148	465	1953	9314	1	1
CL0559	CBD9-like		Small molecule-binding and fam 9 carbohydrate-binding module	Coggill P	pcc	This superfamily is characterised by having seven beta strands in 2 sheets in the form of a Greek-key, with an additional strand at the N-terminus. The binding region is defined by a hydrophobic pocket created between the folds.	2013-02-04 10:13:30	2013-02-01 11:57:53	2	22	328	1346	4868	1	1
CL0560	Chalcone-like		Chalcone isomerase-like superfamily	Coggill P	pcc	This superfamily is characterised by a fold that is conserved across plants, bacteria and fungi. However, possible key residues necessary for binding naringenin, 4',5,7-trihydroxyflavanone, are not conserved beyond plants.	2013-02-13 11:12:28	2013-02-13 11:12:28	2	25	29	902	1575	1	1
CL0561	LisH		LisH-like	Eberhardt R	re3	Members of this clan include the LisH dimerisation/tetramerisation domains and the FOP N terminal dimerisation domain.	2013-02-15 11:38:38	2013-02-15 11:38:38	2	22	111	791	3673	1	1
CL0562	Holin-V		Holin superfamily V	Coggill P	pcc	This superfamily is characterised by three-pass transmembrane proteins from Hol44 and Hol118 families of holins.	2013-02-28 13:53:34	2013-02-28 13:53:34	2	0	2	186	248	1	1
CL0563	Holin-II		Bacteriophage holin superfamily II	Coggill P	pcc	This superfamily is characterised by phage holins of one or two transmembrane domains. It includes the P21 Holin S, the T7 Holin, the HP1 Holin and the Pseudomonas phage F116 Holin families.	2013-02-28 14:17:08	2013-02-28 14:17:08	2	0	4	114	158	1	1
CL0564	Holin-III		Holin superfamily III	Coggill P	pcc	This superfamily is characterised by one to three-pass transmembrane proteins from Lambda S, P2, LydA, P35, Hol, Holin-X, D/T-Hol holin families.	2013-03-05 16:16:15	2013-03-05 16:16:15	2	0	5	177	266	1	1
CL0565	GHKL		ATPase domain of HSP90, DNA topoisomerase II and histidine kinase 	Coggill P	pcc	The GHKL (gyrase, Hsp90, histidine kinase, MutL) superfamily is characterised by an eight-stranded mixed beta-sheet in two layers - alpha/beta. This is the unconventional Bergerat ATP-binding fold and is thus the most singular unifying feature of this superfamily.	2013-05-24 16:47:12	2013-05-24 16:47:12	2	4	50	1041	1923	1	1
CL0566	Tubulin		Tubulin nucleotide-binding domain-like, GTPase	Coggill P	pcc	The characteristic families of this clan are the tubulin GTPase domain and the alpha and beta tubulin subunits. 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].	2013-08-02 16:33:39	2013-08-02 15:19:51	2	616	193	5068	15511	1	1
CL0567	Phage_TACs		Phage tail assembly chaperone	Davidson A, Coggill P	pcc	This superfamily is characterised by only distantly related families of tail assembly chaperones or TACs. Most bacteriophages possess a long tail that is either contractile as in the Siphoviridae family or contractile as in the Myoviridae family. TACs are required for the morphogenesis of all long-tailed phages.  All the studied TACs form spiral quaternary rings that have arisen through diverging sequences and oligomerisation mechanisms. The proposed function in all cases, however, is for the TAC to coat the tape-measure protein to prevent it from forming unproductive complexes or precipitating before the tail tube protein has been incorporated [1,2].	2013-08-29 14:35:23	2013-08-29 14:35:23	2	3	22	938	1614	1	1
CL0568	Man_lectin		Mannoase-binding lectin superfamily	Eberhardt RY	re3	This familu of lectins has a beta-prism fold [1-2].	2013-08-30 08:56:00	2013-08-30 08:56:00	2	259	131	399	3225	1	1
CL0569	Phage_TTPs		Phage tail tube proteins superfamily	Coggill P	pcc	This superfamily represents families of phage tail tube proteins TTPs. Most bacteriophages possess a long tail that is either non-contractile as in the Siphoviridae family or contractile as in the Myoviridae family. These multi-component structures are assembled in regulated pathways that commence with the formation of the tail tip. Tail tip complexes, also referred to as baseplates in some phages, vary considerably in size and protein composition, but all probably serve as the initiator of tail tube protein polymerisation. The tube protein in each case is a long tubular strucutre through which the viral DNA passes during infection. The tube is created by polymerisation of the tube single tube protein. Contractile tails include a central tail tube protein (TTP) that is surrounded by a tail sheath protein (TSP). On infection, the tail sheath contracts and the TTP penetrates the outer cell membrane and cell wall [1,2,3].	2013-08-30 13:11:01	2013-08-30 13:11:01	2	35	28	1311	2289	1	1
CL0570	PPP-I		Protease propeptides/inhibitors	Coggill P	pcc	This superfamily is characterised by families of short N-terminal domains such as the pancreatic carboxypeptidase activation domain, the subtilase propeptides/inhibitors, the prohormone convertase 1 pro-domain, and the peptidase- S8 pro-domain.  All families exbhibit an alpha+beta sandwich with antiparallel beta-sheets in a (beta-alpha-beta)x2 conformation.	2013-12-03 14:56:52	2013-12-03 14:56:52	2	67	329	1486	11633	1	1
CL0571	30K_movement		30 kDa viral movement proteins superfamily	Karlin D, Coggill P	pcc	The 30K superfamily comprises several large families of viral movement proteins which include Pfam families: 3A, MP, Bromo_MP, TBSV_P22, Tenui_NS4, Gemini_BL1, and Emaravirus_P4. They are all related to the 30 kDa ('30K') movement protein of tobacco mosaic virus [1].	2014-01-03 13:28:37	2014-01-03 13:28:37	2	0	15	54	248	1	1
CL0572	TIKI		Tiki-like, or EreA-ChaN-like 2His 2Glu metallopreotease SF	Coggill P	pcc	TIKI superfamily proteins carry a core fold contributing to the enzymic activity, that ranges from metalloprotease, erythromycin esterase and bacterial toinosis as in the MARTX and dermonecrotic toxin families, amongst others. All superfamily members carry the active site residues of two histidines and two glutamates [1]. Tiki proteins themselves antagonize Wnt activity upstream of its receptor.	2014-02-05 16:41:18	2014-02-05 16:41:18	2	5	60	2425	4464	1	1
CL0573	KA1-like		Kinase associated domain 1-like	Coggill P	pcc	This superfamily is characterised by small adenylate-sensing domains at the C-terminus of molecules such as AMP-Activated Protein Kinases an SNF1-like protein kinases [1].	2014-02-17 10:01:29	2014-02-17 10:01:29	2	48	76	724	4422	1	1
CL0575	EFTPs		Translation proteins of Elongation Factors superfamily	Coggill P	pcc	This superfamily is characterised ba a barrel that is formed as a greek-key. It is found as the second domain in many elongation factor proteins, as well as in an elaborated from in two ribosomal proteins and in some other N-terminal domains, eg of AlaX and Gar1 and RimM protein famlies.	2014-03-25 13:51:49	2014-03-25 13:51:49	2	1133	423	5411	44473	1	1
CL0576	STARBD		Starch-binding domain like superfamily	Coggill P	pcc	This is a superfamily of starch-binding domains thta are distinct from the CBM, carbohydrate-binding superfamily. STARBD ares characterised by a beta-sandwich arranged as a greek key, of seven betA-strands in two sheets, with some members having additionlly one or two strands.	2014-03-26 16:45:55	2014-03-26 16:45:55	2	32	171	929	2591	1	1
CL0577	Paramyxovirin_C		C protein of Paramyovirinae families	Coggill P	pcc	C proteins of the Paramyxovirinae families are one of several genes transcribed from overlapping frames of the phosphoprotein (P) gene. The C proteins cluster in three groups, which are made up of measles, Nipah, and Sendai viruses.  All C proteins have a similar organisation which consists of a variable, disordered N-terminus and a conserved, alpha-helical C-terminus [1].	2014-04-03 16:26:21	2014-04-03 16:26:21	2	1	3	3	3	1	1
CL0578	AbiEI		Antitoxin of Type IV toxin-antitoxin, Abi system	Coggill P	pcc	AbiEI is a famaily of bacterial toxins that are both the cognate antitoxins of the bacterial toxin-antitoxin system of type IV and part of the innate immunity system against phage infection. Bacterial abortive infection (Abi) systems are the apoptosis sytems of bacteria that ensue after phage infection to prevent further viral replication.  This superfamily of antitoxins are derived from the orthologous clusters COG5340 and COG4861.  They all appear to be transcriptional regulators and in each case their cognate toxin is the nucleotidyal transferase, AbiEii, Pfam:PF08843, derived from COG2253 and COG4849. Each has an N-terminal winged-helix-turn-helix domain required for repression of abiE transcription (these may or ay not be modelled in the families), and an uncharacterized bi-functional C-terminal domain that is necessary for transcriptional repression and is sufficient for neutralising the toxin [1].	2014-04-22 13:58:39	2014-04-22 13:58:39	2	2	10	534	641	1	1
CL0580	YqgF		YqgF-like family	Eberhardt RY	ruthe	This clain contains the bacterial YqgF family [1-2] and homologous domains in bacterial Tex proteins [3], involved in transcriptional processes, and eukaryotic transcription elongation factor SPT6 [4-5].	2014-05-14 15:53:25	2014-05-14 15:53:25	2	13	79	4814	8063	1	1
CL0582	TrkA_C		TrkA C-terminal domain-like	Coggill P	pcc	This superfamily is characterised by families that form part of voltage-gated ion channels found in a wide range of bacteria, archaea, eukaryotes and viruses.	2014-06-03 10:54:53	2014-06-03 10:54:53	2	150	116	4144	16670	1	1
CL0584	FF		FF domain	Eberhardt R	ruthe	This superfamily contains FF domains.	2014-11-28 12:22:48	2014-11-28 12:22:48	2	19	84	761	6090	1	1
CL0585	Nucleoporin_A		Nucleoporin superfamily	Coggill P	ruthe	This is a superfamily of nucleoporins. Nucleoporins are all-beta structures that form part of the nuclear-pore complex.	2014-11-28 13:06:10	2014-11-28 13:06:10	2	15	46	703	1825	1	1
CL0586	CTC1		CST, telomere maintenance, complex subunit CTC1	Eberhardt R	ruthe	This clan contains CST telomere maintenance proteins.	2014-11-28 13:09:26	2014-11-28 13:09:26	2	0	8	162	259	1	1
CL0587	STAND_N		N-terminal of fungal STAND proteins superfamily	Coggill P	pcc	This superfamily is characterised by proteins from various fungal STAND proteins [1].	2015-01-19 14:02:00	2015-01-19 14:02:00	2	0	292	199	1506	1	1
CL0588	Ribos_L15p_L18e		Ribosomal proteins L15 bacteria, L18e archaea	Coggill P	pcc	This superfamily is characterised by ribisomol proteins from varied phyla and cellular organelles.	2015-03-06 13:41:02	2015-03-06 13:41:02	2	766	60	5246	7745	1	1
CL0589	KIX_like		Kix domain of CBP (creb binding protein) and MED13/15	Coggill P	pcc	This superfamily is characterised by structures with three helices in a partly opened bundle bundle. There are both creb-binding proteins and activator-binding proteins on mediator subunits, such as higher eukaryotic 13 and fungal 15.	2015-03-20 17:47:28	2015-03-20 17:47:28	2	11	73	455	1103	1	1
CL0590	OML_zippers		Major outer membrane lipoprotein zipper superfamily	Coggill P	pcc	This is a superfamily of short outer membrane lipoporteins that are coiled-coils of alpha-helices. The families included are both leucine and alanine zippers. A zipper motif is a heptad or seven-residue repeat, represented by X..X...X..X...X..X...X..X...X..X, etc, where the X is hydrophobic residue, usually a leucine or alanine, and the intermediate residues are largely polar or hydrophilic; that is, the responsible residues occur at positions 1 and 4 in the heptad. Monomers combine together into dimers and higher order structures. Coiled-coil motifs are ubiquitous mediators of specific protein-protein interactions, in this case outer membrane 'tubes', by forming interlocking hydrophobic seams between the alpha-helical chains [1].	2015-04-08 13:00:00	2015-04-08 13:00:00	2	20	15	332	366	1	1
CL0591	TKC_like		Transketolase C-terminal domain-like superfamily	Coggill P	pcc	This superfamily is coposed of three branches that include the true C-terminal domains of transketolases, the C-terminal domain of the beta-subunit of branched-chain alpha-keto acid dehydrogenase, and domain II of pyruvate-ferredoxin oxidoreductase, PFOR, family.	2015-04-13 12:51:41	2015-04-13 12:51:41	2	261	214	5272	27995	1	1
CL0592	beta_Roll		beta-strand roll of R-module,  superfamily	Coggill P	pcc	This superfamily is characterised by families of a short nonarepeat unit. The beta-roll is made up of a super-helix of beta-strand-turns of two short strands each, and the loops are stabilised by Ca2+ ions. The region of a protein with this beta-roll is often termed the R-module, and it can frequently be found in metalloproteases of the serralysin type and in epimerases [1].  The nonarepeat is also found multiple times in haemolysins, where the structure is again stabilised by binding Ca2+ ions.	2015-04-24 13:51:51	2015-04-24 13:51:51	2	45	1517	945	62472	1	1
CL0593	G5		B region of SasG biofilm-forming surface protein	Bateman A, Coggill P	pcc	This superfamily is characterised by repeating domains, G5 and SasG-E, where the SasG-E domain is a truncated form of the G5 domain.  Member domains are composed of triple-stranded single-layer beta-sheets connected by an intertwined motif, which leads to a strand switch [1]. These domain-members occur on extracellular proteins which, in Staphylococcus spp, form biofilms.	2015-06-12 11:23:49	2015-06-11 16:52:10	2	16	143	1174	2507	1	1
CL0594	DUF1735		DUF1735-like superfamily	Bateman A	agb	This superfamily includes a number of families that are related to the domain of unknown function DUF1735.  These proteins have a beta-sandwich fold.	2015-08-19 15:04:25	2015-08-19 15:04:25	2	14	35	177	861	1	1
CL0595	Fusion_gly		Fusion glycoprotein superfamily	Bateman A	agb	This superfamily includes several families of viral glycoproteins that mediate fusion with target membranes.	2015-08-24 11:42:44	2015-08-24 11:42:44	2	226	33	51	269	1	1
CL0596	VPS23_C		Endosomal sorting complex assembly domain	Bateman A	agb		2015-08-25 09:59:17	2015-08-25 09:59:17	2	31	55	758	2679	1	1
CL0597	Post-HMGL		Post-HMGL domain-like superfamily	Bateman A	agb		2015-08-25 10:16:31	2015-08-25 10:16:31	2	97	46	2985	3989	1	1
CL0598	B_GA		Bacterial immunoglobulin/albumin-binding domain superfamily	Bateman A	agb		2015-08-25 10:31:58	2015-08-25 10:31:58	2	106	544	271	2991	1	1
CL0599	GH57_38_middle		Families 57/38 glycoside transferase middle domain superfamily	Bateman A	agb		2015-08-25 10:36:38	2015-08-25 10:36:38	2	77	75	1831	3860	1	1
CL0600	S15_NS1		S15/NS1 RNA-binding domain superfamily	Bateman A	agb		2015-08-25 10:57:17	2015-08-25 10:57:17	2	761	165	5191	8200	1	1
CL0601	Cob_adeno_trans		Cobalamin adenosyltransferase-like superfamily	Bateman A	agb	This superfamily includes cobalamin adenosyltransferase enzymes as well as the uncharacterised protein family DUF1940.	2015-08-25 11:55:14	2015-08-25 11:55:14	2	67	16	2633	2989	1	1
CL0602	Kringle		Kringle/FnII superfamily	Bateman A	agb	This superfamily includes both Kringle domains and fibronectin type II domains.	2015-08-31 18:34:21	2015-08-31 18:34:21	2	181	454	294	6271	1	1
CL0603	AA_dh_N		Aminoacid dehydrogenase-like, N-terminal domain superfamily	Bateman A	agb	According to SCOP this superfamilies core fold has 3 layers in an alpha/beta/alpha configuration. Its central parallel beta sheet of four stands has the order 2134. In amino acid dehydrogenases this domain participates in dimerisation. This superfamily also  includes domains from tetrahydrofolate dehydrogenase/cyclohydrolase,  methylene-tetrahydromethanopterin dehydrogenase and shikimate dehydrogenase.	2015-09-15 15:54:56	2015-09-15 15:54:56	2	535	261	5247	27539	1	1
CL0604	post-AAA		post-AAA+ oligomerization domain-like superfamily	Bateman A	agb	According to SCOP this superfamily contains a 5 helical bundle domain that is found to the C-terminus of a P-loop AAA domain.	2015-09-15 16:20:25	2015-09-15 16:20:25	2	101	117	5152	12709	1	1
CL0605	ssDNA_NP_VP		ssDNA viruses Nucleoplasmin-like/VP coat superfamily	Bateman A	agb	According to SCOP this superfamily includes proteins that have a beta sandwich fold with two sheets in a jelly roll topology. Families in this superfamily belong to various ssDNA viruses.	2015-09-15 16:26:44	2015-09-15 16:26:44	2	253	14	98	222	1	1
CL0606	Phage_fibre		Phage fibre superfamily	Bateman A	agb	According to SCOP this superfamily includes phage tail fibre proteins that form homotrimers with each chain donating 3 beta-strands per turn of the helix	2015-09-15 16:33:02	2015-09-15 16:33:02	2	128	13	104	180	1	1
CL0607	TNF_receptor		TNF receptor-like superfamily	Bateman A	agb		2015-09-15 16:39:48	2015-09-15 16:39:48	2	184	159	276	7500	1	1
CL0608	Reductase_C		FAD/NAD-linked reductase C-terminal domain superfamily	Bateman A	agb	This domain is found at the C-terminus of a variety of FAD/NAD-linked reductases.	2015-09-16 11:56:07	2015-09-16 11:56:07	2	449	143	4644	20135	1	1
CL0609	sPC4_like		PC4-like superfamily	Bateman A	agb	According to SCOP this superfamily contains a helix-swapped dimer of beta(4)-alpha motifs. Members of this superfamily are ssDNA binding domains found transcriptional regulators.	2015-09-16 12:02:23	2015-09-16 12:02:23	2	99	51	1694	3661	1	1
CL0610	ETAP		Electron transport accessory protein superfamily	Bateman A	agb	According to SCOP the domains in this superfamily have an SH3 like barrel fold.	2015-09-16 13:10:31	2015-09-16 13:10:31	2	167	17	484	1115	1	1
CL0611	Hexon		Hexon-like superfamily	Bateman A	agb	This superfamily includes beta-sandwich viral coat proteins.	2015-09-16 13:16:13	2015-09-16 13:16:13	2	155	7	25	42	1	1
CL0612	PHM_PNGase_F		PHM/PNGase F superfamily	Bateman A	agb	Members of this superfamily adopt a beta-sandwich fold. With two adjacent domains in a protein interacting in the same way as nucleoplasmins that share the same fold. This superfamily includes the Peptide-N-glycosidase F enzymes and the peptidylglycine alpha-hydroxylating monooxygenase enzymes.	2015-11-12 18:41:11	2015-11-12 18:41:11	1	38	68	427	2242	1	1
CL0613	Terp_synthase		Terpenoid synthases superfamily	Bateman A	agb	This superfamily includes a diverse range of terpene synthase enzymes which share an alpha helical core.	2015-11-13 14:59:08	2015-11-13 14:59:08	1	723	267	5029	34690	1	1
CL0614	L27		L27 domain superfamily	Bateman A	agb		2015-11-13 15:02:59	2015-11-13 15:02:59	1	29	108	238	2436	1	1
CL0615	ALDC		ALDC superfamily	Bateman A	agb	This superfamiy includes the enzyme acetolactate decarboxylase as well as s number of other uncharacterised presumed enzymes. The core of this superfamily is an alpha/beta domain with a highly curved beta sheet that often has a zinc cordination site with three histidine residues.	2015-11-18 11:56:23	2015-11-18 11:56:23	1	29	42	1529	3849	1	1
CL0616	SPOC		SPOC domain-like superfamily	Bateman A	agb	The crystal structure of the SPOC domain [3] showed it has similarity  with the beta barrel domain of the Ku proteins. These domains share a 7 stranded beta barrel. In the Ku proteins this domain interacts DNA, whereas the SPOC domain mediates protein binding.	2015-11-18 12:17:33	2015-11-18 12:17:33	1	15	128	1958	5139	1	1
CL0617	Peroxidase		Heme-dependent peroxidases superfamily	Bateman A	agb	This superfamily includes two families of heme-dependent peroxidases that have an all alpha helical fold.	2015-11-18 12:43:32	2015-11-18 12:43:32	1	867	399	2323	18770	1	1
CL0618	MCR		Methyl-coenzyme M reductase subunit superfamily	Bateman A	agb	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial  formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02745), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites. The N-terminal domain has a ferredoxin-like fold.	2015-11-19 17:30:02	2015-11-19 17:30:02	1	123	4	66	238	1	1
CL0619	Mog1p_PsbP		Mog1p/PsbP-like superfamily	Bateman A	agb	Members of this superfamily have a 7 stranded antiparallel beta sheet. The family includes the Mog1p protein and the PsbP proteins.	2015-11-19 18:00:45	2015-11-19 18:00:45	1	22	48	1056	2775	1	1
CL0620	Antihemostatic		Leech antihemostatic protein superfamily	Bateman A	agb	This superfamily includes three families of leech antihemostatic proteins that have a knokttin fold.	2015-11-19 18:06:55	2015-11-19 18:06:55	1	14	134	202	974	1	1
CL0621	Colipase		Colipase-like superfamily	Bateman A	agb	This superfamily includes the two subdomains of colipase along with the black mamba Intestinal toxin 1 [1]. This superfamily has a knottin fold.	2015-11-19 18:15:15	2015-11-19 18:15:15	1	9	8	109	402	1	1
CL0622	Acylphosphatase		Acylphosphatase/BLUF domain-like superfamily	Bateman A	agb	This superfamily has a ferredoxin fold. It contains the BLUF domain and the acylphosphatase family.	2015-11-19 18:28:03	2015-11-19 18:28:03	1	142	99	3654	6496	1	1
CL0623	SRP9_14		SRP alu RNA binding heterodimer, SRP9/14 superfamily	Bateman A	agb	This superfamily represents both the 9 kDa SRP9 and the 14 kDa SRP14 components. Both SRP9 and SRP14 have the same  (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP.	2015-11-20 10:10:15	2015-11-20 10:10:15	1	23	33	719	1396	1	1
CL0624	CcdB_PemK		Cell growth inhibitor/plasmid maintenance toxic component superfamily	Bateman A	agb	This superfamily includes cell growth inhibitors and toxin components. These proteins share an SH3-like barrel structure.	2015-11-20 10:25:15	2015-11-20 10:25:15	1	98	22	2339	4573	1	1
CL0625	eIF4e		eIF4e-like superfamily	Bateman A	agb	This superfamily includes eIF4e as well as the family that includes BLES03 [1].	2015-11-20 10:33:55	2015-11-20 10:33:55	1	116	59	865	3296	1	1
CL0626	Levi_coat		RNA bacteriophage capsid protein superfamily	Bateman A	agb	This superfamily includes coat proteins from Leviviruses.	2015-11-20 10:49:00	2015-11-20 10:49:00	1	276	2	2	3	1	1
CL0627	Antibiotic_NAT		DUF436/YokD-like superfamily	Bateman A	agb	This superfamily includes a family of N-acetyl transferases as well as the DUF436 family.	2015-11-20 11:34:12	2015-11-20 11:34:12	1	39	10	907	1104	1	1
CL0628	EspA_CesA		EspA/CesA-like superfamily	Bateman A	agb	This superfamily includes the two components of the heterodimeric CesA/EspA complex which form a coiled-coil interacting structure [1].	2015-11-20 12:45:22	2015-11-20 12:45:22	1	4	3	20	41	1	1
CL0629	PLA2		Phospholipase A2 superfamily	Bateman A	agb		2015-11-24 12:40:40	2015-11-24 12:40:40	1	472	54	505	2405	1	1
CL0630	PSI		Plexin fold superfamily	Bateman A	agb	This superfamily includes a disulphide rich domain found in Plexins, semaphorins and some integrin protein. According to SCOP the common core is alpha+beta with two conserved disulfides.	2015-11-26 12:02:29	2015-11-26 12:02:29	1	179	482	294	6020	1	1
CL0631	YgaC_TfoX-N		YgaC/TfoX-N like superfamily	Bateman A	agb	This superfamily includes the YgaC (DUF2002) family and the  TfoX-N domain.	2015-12-03 16:21:35	2015-12-03 16:21:35	1	3	9	1041	1254	1	1
CL0632	FERM_M		FERM middle domain superfamily	Bateman A	agb		2015-12-03 16:32:24	2015-12-03 16:32:24	1	159	633	1128	11535	1	1
CL0633	NusB		NusB-like superfamily	Bateman A	agb		2015-12-03 16:38:50	2015-12-03 16:38:50	1	33	17	4280	7287	1	1
CL0634	CheY-binding		CheY-binding domain of CheA superfamily	Bateman A	agb		2015-12-03 16:43:53	2015-12-03 16:43:53	1	15	29	723	864	1	1
CL0635	DmpA_ArgJ		DmpA/ArgJ-like superfamily	Bateman A	agb	This superfamily includes the ArgJ protein and members of peptidase family S58. According to SCOP these proteins have a fold which resembles but is unrelated to that of the NTN hydrolases.	2015-12-03 16:49:32	2015-12-03 16:49:32	1	99	20	3350	5094	1	1
CL0636	Leukocidin		Leukocidin-like superfamily	Bateman A	agb	According to SCOP this superfamily contains beta-sandwich of Ig-like (greek-key) topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel.	2015-12-04 13:34:53	2015-12-04 13:34:53	1	162	8	106	419	1	1
CL0637	KaiA_RbsU		KaiA/RbsU domain superfamily	Bateman A	agb	According to SCOP members of this superfamily have a 4 helix bundle with a right-handed twist. The superfamily includes the C-terminal domain of the circadian clock protein KaiA and the N-terminal domain of Phosphoserine phosphatase RsbU.	2015-12-04 13:59:57	2015-12-04 13:59:57	1	24	19	280	281	1	1
CL0638	PAZ		PAZ domain superfamily	Bateman A	agb	This superfamily corresponds to the RNA-binding PAZ domain which has an SH3 like barrel fold.	2015-12-04 14:25:37	2015-12-04 14:25:37	1	71	210	686	4486	1	1
CL0639	Rof		Rof/RNase P subunit-like superfamily	Bateman A	agb	According to SCOP members of this superfamily have an open SH3-like barrel topology.	2015-12-04 14:29:12	2015-12-04 14:29:12	1	10	11	1084	1189	1	1
CL0640	Colicin_D_E5		Colicin D/E5 nuclease domain superfamily	Bateman A	agb	This superfamily includes the nuclease domains from colicins that act up tRNA substrates.	2015-12-04 14:56:23	2015-12-04 14:56:23	1	13	19	45	49	1	1
CL0642	SOCS_box		SOCS-box like superfamily	Bateman A	agb	This superfamily includes the SOCS-box domain and the VHL-box domain [1].	2015-12-09 14:43:39	2015-12-09 14:43:39	1	109	207	238	3908	1	1
CL0643	YqbG		YqbG-like superfamily	Bateman A	agb	This superfamily includes diverse phage proteins. It includes the gp6 head-tail connector proteins from phage HK97 [1]. The clan also includes the P22 accessory factor gp4 [2].	2015-12-09 14:56:15	2015-12-09 14:56:15	1	68	6	775	1099	1	1
CL0644	Fz		Frizzled cysteine-rich domain-related superfamily	Bateman A	agb	This superfamily includes diverse cysteine rich domains identified as being homologous [1].	2015-12-10 12:21:57	2015-12-10 12:21:57	1	116	252	700	6139	1	1
CL0645	Anti-sigma_N		N-terminal, cytoplasmic domain of anti-sigma factor superfamily	Bateman A	agb		2015-12-10 12:38:43	2015-12-10 12:38:43	1	24	75	2004	4309	1	1
CL0646	T3SS		Type III secretion system domain superfamily	Bateman A	agb	This superfamily includes a range of proteins involved in regulation of secretion by type III secretion systems, such as HrpJ, TyeA and YopR.	2015-12-10 15:24:21	2015-12-10 15:24:21	1	21	8	189	336	1	1
CL0647	FG_rpt		Nucleoporin FG repeat	Mistry J	jaina	This clan includes families which contain nucleoporin FG repeats.	2016-03-29 13:31:41	2016-03-29 13:31:41	1	31	134	685	7215	1	1
CL0648	Aha1_BPI		Aha1/BPI domain-like superfamily	Bateman A	agb	This superfamily was defined based on the ECOD resource which combines two SCOP superfamilies.	2016-08-24 15:02:14	2016-08-24 15:02:14	1	52	132	1100	7130	1	1
CL0649	PseudoU_synth		Pseudouridine synthase superfamily	Bateman A	agb	This superfamily was built based on the ECOD classification.	2016-08-24 15:10:15	2016-08-24 15:10:15	1	90	251	5326	47909	1	1
CL0650	AOC_barrel		AOC barrel-like superfamily	Bateman A	agb	This superfamily was built based on the ECOD classification. According to SCOP this superfamily has a beta barrel topology with 8 strands.	2016-08-24 16:09:21	2016-08-24 16:09:21	1	82	68	832	3800	1	1
CL0651	Mad2		Mad2 superfamily	Bateman A	agb		2016-08-24 16:16:35	2016-08-24 16:16:35	1	78	52	794	3799	1	1
CL0652	S24e_L23_L15e		Ribosomal S24e, L23 and L15e superfamily	Bateman A	agb		2016-08-24 16:22:34	2016-08-24 16:22:34	1	873	96	5269	8497	1	1
CL0653	VCCI		VCCI superfamily superfamily	Bateman A	agb	This superfamily is defined by SCOP based on the soluble secreted chemikine inhibitor from cowpox virus. 	2016-08-24 16:29:14	2016-08-24 16:29:14	1	18	6	7	22	1	1
CL0654	WYL		WYL-like superfamily	Richardson L	lornar	Members of this clan all belong to the WYL-like superfamily, and  show structural similarity to the Sm-like SH3 beta-barrel fold. The WYL domain was first named for three conserved amino acids, however this motif was subsequently shown to be found only in a small subset of examples of this clan. The conservation pattern more widely applicable across the clan includes four basic residues and a position often occupied by a cysteine. These residues are predicted  to line a ligand-binding groove similar to that found in Sm-like SH3  beta-barrels. WYL domains often occur in two copies in the same protein, or are encoded alongside neighbouring genes that encode multi-WYL domain proteins, and it has been suggested that they form toroidal multimeric assemblies. WYL domains are often associated with various predicted DNA-binding N-terminal wHTH domains, but may also exist as fusions to several enzymatic domains.	2016-08-31 16:04:18	2016-08-31 15:02:46	1	0	52	2880	8038	1	1
CL0655	PilP		GspC HR domain/PilP-like superfamily	Bateman A	agb		2016-09-09 11:49:18	2016-09-09 11:49:18	1	47	13	830	1495	1	1
CL0656	VSA		Variant surface antigens	El-Gebali S	selgebali	Members of this clan belong to variant surfance antigens (VSA). They are gene products encoded by multi-copy gene families. Four of the largest multi-copy gene families found in the genome of P. falciparum are designated as var, rif (repetitive interspersed family), stevor (subtelomeric variable open reading frame) and pfmc-2tm (P. falciparum Maurerâ€™s clefts 2 transmembrane). They code for variable proteins termed PfEMP1 (P. falciparum erythrocyte membrane protein 1), RIFIN, STEVOR and PfMC-2TM, respectively. All small VSA proteins contain a signal peptide and a PEXEL/HT motif. This characteristic as well as their large number and hypervariability support their suggested role in antigenic variation. Antigenic variation and sequestration are strategies used by the malaria parasite P. falciparum to evade antibody mediated immune recognition and splenic clearance [1].	2016-09-27 15:57:09	2016-09-27 15:57:09	1	0	38	15	1878	1	1
CL0658	OB_enterotoxin		Bacterial enterotoxin OB-fold	Bateman A	agb	This superfamily contains OB-fold domains found within bacterial enterotoxins.  According to the SCOP and ECOD databases these domains are distinct from Clan:CL0021.	2016-10-03 17:02:54	2016-10-03 17:02:54	1	754	8	10	39	1	1
CL0659	CAP		Cysteine-rich secretory proteins	El-Gebali S	selgebali	This is a highly evolutionary diversified protein superfamily whose members share specific sequence motifs. For the mammalian members, roles in reproduction, development, immune function and several pathologies have been proposed. Ant and wasp allergens, snake venom toxins and plant antifungal proteins are included in this superfamily data suggest that CAP proteins participate in various biological activities across phyla. Several signature sequences characterize mammalian members of the superfamily: CAP1-2 and CAP3-4, variable Cys-rich hinge regions and Ct extensions. Mammalian CAPs include nine subfamilies: cysteine rich secretory proteins (CRISPs), glioma pathogenesis related-1 (GLIPR1), glioma pathogenesis related-2 (GLIPR2)/Golgi, associated pathogenesis related-1 (GAPR1), peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), CRISP LCCL domain containing 1 and 2 (CRISPLD1/CAPLD1 and CRISPLD2/CAPLD2), mannose receptor-like/CP domain, CTL domain containing (CAPCL) and the R3H domain-like protein (R3HMDL). CRISP (cysteine rich secretory proteins) proteins (venom-related proteins, and proteins produced by reproductive organs and cells) and plant-derived pathogenesis related proteins are the best characterized. Helminth parasite proteins of this superfamily were first reported in hookworms and later in related nematodes and platyhelminths. While nematodes' CAP proteins are known as Ancylostoma secreted proteins (ASPs), platyhelminths' CAP are known as venom allergen-like (VAL) proteins. Some of these proteins have been studied as vaccine candidates due to their immunogenic and protective properties (e.g. Na-ASP-2, Ov-Asp1, Oo-ASP-1) [1].	2017-01-11 16:08:48	2017-01-11 16:08:48	1	53	362	2863	13877	1	1
