0€0€ €pfam07566, DUF1543, Domain of Unknown Function (DUF1543). This domain is found as 1-2 copies in a small family of proteins of unknown function.¡€0€ª€0€ €CDD¡€ €E¶¢€0€0€ €‚Opfam07568, HisKA_2, Histidine kinase. This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with pfam00512 and pfam07536. It is usually found adjacent to a C-terminal ATPase domain (pfam02518). This domain is found in a wide range of Bacteria and also several Archaea.¡€0€ª€0€ €CDD¡€ €XÞ¢€0€0€ €Æpfam07569, Hira, TUP1-like enhancer of split. The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain pfam00400.¡€0€ª€0€ €CDD¡€ €ÀË¢€0€0€ €‚;pfam07571, TAF6_C, TAF6 C-terminal HEAT repeat domain. TAF6_C is the C-terminal domain of the TAF6 subunit of the general transcription factor TFIID. The crystal structure reveals the presence of five conserved HEAT repeats. This region is necessary for the complexing together of the subunits TAF5, TAF6 and TAF9.¡€0€ª€0€ €CDD¡€ €ÀÌ¢€0€0€ €‚Npfam07572, BCNT, Bucentaur or craniofacial development. Bucentaur or craniofacial development protein 1 (BCNT) in ruminents has a different domain architecture to that in mouse and human. For this reason it has been used as a model for molecular evolution. Both bovine and human BCNTs are phosphorylated by casein kinase II in vitro.¡€0€ª€0€ €CDD¡€ €ÀÍ¢€0€0€ €ßpfam07573, AreA_N, Nitrogen regulatory protein AreA N terminus. The AreA nitrogen regulatory protein proteins (which are GATA type transcription factors) share a highly conserved N terminus and pfam00320 at the C terminus.¡€0€ª€0€ €CDD¡€ €À΢€0€0€ €‚¯pfam07574, SMC_Nse1, Nse1 non-SMC component of SMC5-6 complex. S. cerevisiae Nse1 forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism. It is conserved in eukaryotes from yeast to human. This domain lies immediatley up-stream of the DNA-binding zinc-finger domain, zf-RING-like pfam08746.¡€0€ª€0€ €CDD¡€ €ÀÏ¢€0€0€ €‚Êpfam07575, Nucleopor_Nup85, Nup85 Nucleoporin. A family of nucleoporins conserved from yeast to human. THe nuclear pore complex is a large assembly composed of two essential complexes: the heptameric Nup84 complex and the heteromeric Nic96-containing complex. The Nup84 complex is composed of one copy each of Nup84, Nup85, Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure of a complex of Nup85 and Seh1 was solved. The N-terminus of Nup85 is inserted and forms a three-stranded blade that completes the Seh1 6-bladed beta-propeller in trans. Following its N-terminal insertion blade, Nup85 forms a compact cuboid structure composed of 20 helices, with two distinct modules, referred to as crown and trunk.¡€0€ª€0€ €CDD¡€ €ÀТ€0€0€ €‚;pfam07576, BRAP2, BRCA1-associated protein 2. These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localization signals (NLSs) in vitro and in yeast two-hybrid screening. These proteins share a region of sequence similarity at their N terminus. They also have pfam02148 at the C terminus.¡€0€ª€0€ €CDD¡€ €ÀÑ¢€0€0€ €‡pfam07577, DUF1547, Domain of Unknown Function (DUF1547). This family appears to be found only in a small family of Chlamydia species.¡€0€ª€0€ €CDD¡€ €X梀0€0€ €ápfam07578, LAB_N, Lipid A Biosynthesis N-terminal domain. This family is found at the N-terminus of a group of Chlamydial Lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function.¡€0€ª€0€ €CDD¡€ €ÀÒ¢€0€0€ €ˆpfam07579, DUF1548, Domain of Unknown Function (DUF1548). This family appears to be found only in a small family of Chlamydia proteins.¡€0€ª€0€ €CDD¡€ €ÀÓ¢€0€0€ €øpfam07580, Peptidase_M26_C, M26 IgA1-specific Metallo-endopeptidase C-terminal region. These peptidases, which cleave mammalian IgA, are found in Gram-positive bacteria. Often found associated with pfam00746, they may be attached to the cell wall.¡€0€ª€0€ €CDD¡€ €ÀÔ¢€0€0€ €‚‹pfam07581, Glug, The GLUG motif. This family is found in the IgA1 (M26) peptidases, which attached to the cell wall peptidoglycan by an amide bond. IgA1 protease selectively cleaves human IgA1 and is likely to be a pathogenicity factor in some pathogens. This family is also found in various other contexts, including with pfam05860. It is named GLUG after the mostly conserved G-L-any-G motif.¡€0€ª€0€ €CDD¡€ €ÀÕ¢€0€0€ €ûpfam07582, AP_endonuc_2_N, AP endonuclease family 2 C terminus. This highly-conserved sequence is found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases. in a range of Gram-positive and Gram-negative bacteria. See also pfam01261.¡€0€ª€0€ €CDD¡€ €ÀÖ¢€0€0€ €fpfam07583, PSCyt2, Protein of unknown function (DUF1549). A family of paralogues in the planctomyces.¡€0€ª€0€ €CDD¡€ €À×¢€0€0€ €‚cpfam07584, BatA, Aerotolerance regulator N-terminal. These proteins share a highly-conserved sequence at their N-terminus. They include several proteins from Rhodopirellula baltica and also several from proteobacteria. The proteins are produced by the Batl operon which appears to be important in pathogenicity and aerotolerance. This family is the conserved N-terminus, but the full length proteins carry multiple membrane-spanning domains. BatA ensures bacterial survival in the early stages of the infection process, when the infected sites are aerobic, and is produced under conditions of oxidative stress.¡€0€ª€0€ €CDD¡€ €ÀØ¢€0€0€ €¥pfam07585, BBP7, Putative beta barrel porin-7 (BBP7). This is a family of putative beta barrel porin-7 BBP7 proteins identified initially in Rhodopirellula baltica.¡€0€ª€0€ €CDD¡€ €Xí¢€0€0€ €upfam07586, HXXSHH, Protein of unknown function (DUF1552). A family of proteins identified in Rhodopirellula baltica.¡€0€ª€0€ €CDD¡€ €ÀÙ¢€0€0€ €npfam07587, PSD1, Protein of unknown function (DUF1553). A family of proteins found in Rhodopirellula baltica.¡€0€ª€0€ €CDD¡€ €ÀÚ¢€0€0€ €vpfam07588, DUF1554, Protein of unknown function (DUF1554). A family of proteins identified in Leptospira interrogans.¡€0€ª€0€ €CDD¡€ €Xð¢€0€0€ €‚pfam07589, VPEP, PEP-CTERM motif. This motif has been identified in a wide range of bacteria at their C-terminus. It has been suggested that this is a protein sorting signal. Based on phylogenetic profiling it has been suggested that the EpsH family of proteins mediate this function.¡€0€ª€0€ €CDD¡€ €ÀÛ¢€0€0€ € 2 HSO3- + 2 H2S + 2 H+.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚Ópfam07683, CobW_C, Cobalamin synthesis protein cobW C-terminal domain. This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚jpfam07684, NODP, NOTCH protein. NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be elucidated.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €Hpfam07685, GATase_3, CobB/CobQ-like glutamine amidotransferase domain. ¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €ˆpfam07686, V-set, Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.¡€0€ª€0€ €CDD¡€ €Á ¢€0€0€ €‚™pfam07687, M20_dimer, Peptidase dimerisation domain. This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the M20 family of peptidases. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases.¡€0€ª€0€ €CDD¡€ €Á ¢€0€0€ €‚pfam07688, KaiA, KaiA C-terminal domain. The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. The overall fold of the KaiA C-terminal domain is that of a four-helix bundle, which forms a dimer in the known structure.¡€0€ª€0€ €CDD¡€ €Á ¢€0€0€ €‚0pfam07689, KaiB, KaiB domain. The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and is found to be a dimer.¡€0€ª€0€ €CDD¡€ €Y@¢€0€0€ €2pfam07690, MFS_1, Major Facilitator Superfamily. ¡€0€ª€0€ €CDD¡€ €Á ¢€0€0€ €‚Ðpfam07691, PA14, PA14 domain. This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding.¡€0€ª€0€ €CDD¡€ €Á ¢€0€0€ €‚Vpfam07692, Fea1, Low iron-inducible periplasmic protein. In Chlamydomonas reinhardtii, the gene encoding Fe-assimilating protein 1 is induced by iron deficiency. In green algae, this protein is periplasmic. The two paralogues FEA1 and FEA2 are the major proteins secreted by iron-deficient Chlamydomonas reinhardtii, and both are up-regulated in response to iron deficiency. FEA1 but not FEA2 is up-regulated by high CO2 concentration. Both FEA1 and FEA2 are secreted into the periplasmic space and genetic evidence confirms that their association with the cell is required for growth in low iron.¡€0€ª€0€ €CDD¡€ €ᚢ€0€0€ €‚bpfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side.¡€0€ª€0€ €CDD¡€ €YC¢€0€0€ €pfam07694, 5TM-5TMR_LYT, 5TMR of 5TMR-LYT. This entry represents the transmembrane region of the 5TM-LYT (5TM Receptors of the LytS-YhcK type).¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €¾pfam07695, 7TMR-DISM_7TM, 7TM diverse intracellular signalling. This entry represents the transmembrane region of the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules).¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚kpfam07696, 7TMR-DISMED2, 7TMR-DISM extracellular 2. This entry represents one of two distinct types of extracellular domain found in the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules) bacterial transmembrane proteins. It is possible that this domain adopts a jelly roll fold and acts as a receptor for carbohydrates and their derivatives.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €Œpfam07697, 7TMR-HDED, 7TM-HD extracellular. This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase).¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚ pfam07698, 7TM-7TMR_HD, 7TM receptor with intracellular HD hydrolase. These bacterial 7TM receptor proteins have an intracellular pfam01966. This entry corresponds to the 7 helix transmembrane domain. These proteins also contain an N-terminal extracellular domain.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €rpfam07699, Ephrin_rec_like, Putative ephrin-receptor like. This family has repeats of a region rich in cysteines.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚’pfam07700, HNOB, Haem-NO-binding. The HNOB (Haem NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. It is a haem protein sensor (SONO) that displays femtomolar affinity for nitrous oxide, NO. It is predicted to function as a haem-dependent sensor for gaseous ligands and to transduce diverse downstream signals in both bacteria and animals.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚Dpfam07701, HNOBA, Heme NO binding associated. The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚pfam07702, UTRA, UTRA domain. The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to pfam04345. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‡pfam07703, A2M_N_2, Alpha-2-macroglobulin family N-terminal region. This family includes a region of the alpha-2-macroglobulin family.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €¢pfam07704, PSK_trans_fac, Rv0623-like transcription factor. This entry represents the Rv0623-like family of transcription factors associated with the PSK operon.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €Ipfam07705, CARDB, CARDB. Cell adhesion related domain found in bacteria.¡€0€ª€0€ €CDD¡€ €YO¢€0€0€ €‚5pfam07706, TAT_ubiq, Aminotransferase ubiquitination site. This segment contains a probable site of ubiquitination that ensures rapid degradation of tyrosine aminotransferase in rats. The half life of the enzyme in vivo is about 2-4 hours. In addition, unpublished information identifies at least 2 phosphorylation sites including CAPK at Ser29 and, at the other end of the protein, a casein kinase II site at S*QEECDK. This region of TAT is probably primarily related to regulatory events. Most other transaminases are much more stable and are not phosphorylated.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚.pfam07707, BACK, BTB And C-terminal Kelch. This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation).¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚pfam07708, Tash_PEST, Tash protein PEST motif. This motif is found in the Tash AT-hook proteins of Theileria annulata. These proteins are transported to the hosts nucleus and are likely to be involved in pathogenesis. It is also often found in conjunction with pfam04385. It is suggested that they may be 'part of PEST motifs' (a signal for rapid proteolytic degradation) in, though this is not definite. This motif is also found in other T. annulata proteins, which have no other known domains in (unpublished data: C Yeats).¡€0€ª€0€ €CDD¡€ €YR¢€0€0€ €ƒpfam07709, SRR, Seven Residue Repeat. Associated with pfam02969 in This repeat is found in some Plasmodium and Theileria proteins.¡€0€ª€0€ €CDD¡€ €Æc¢€0€0€ €5pfam07710, P53_tetramer, P53 tetramerisation motif. ¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚*pfam07711, RabGGT_insert, Rab geranylgeranyl transferase alpha-subunit, insert domain. Rab geranylgeranyl transferase (RabGGT) catalyzes the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. This domain is inserted between pfam01239 repeats. This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €2pfam07712, SURNod19, Stress up-regulated Nod 19. ¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‘pfam07713, DUF1604, Protein of unknown function (DUF1604). This family is found at the N-terminus of several eukaryotic RNA processing proteins.¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €2pfam07714, Pkinase_Tyr, Protein tyrosine kinase. ¡€0€ª€0€ €CDD¡€ €Á¢€0€0€ €‚8pfam07715, Plug, TonB-dependent Receptor Plug Domain. The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors. It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel.¡€0€ª€0€ €CDD¡€ €Á ¢€0€0€ €1pfam07716, bZIP_2, Basic region leucine zipper. ¡€0€ª€0€ €CDD¡€ €Á!¢€0€0€ €‚upfam07717, OB_NTP_bind, Oligonucleotide/oligosaccharide-binding (OB)-fold. This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself. The structure Structure 3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.¡€0€ª€0€ €CDD¡€ €Á"¢€0€0€ €øpfam07718, Coatamer_beta_C, Coatomer beta C-terminal region. This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). This C-terminal domain probably adapts the function of the N-terminal pfam01602 domain.¡€0€ª€0€ €CDD¡€ €Á#¢€0€0€ €–pfam07719, TPR_2, Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.¡€0€ª€0€ €CDD¡€ €Á$¢€0€0€ €Œpfam07720, TPR_3, Tetratricopeptide repeat. This Pfam entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones.¡€0€ª€0€ €CDD¡€ €Á%¢€0€0€ €£pfam07721, TPR_4, Tetratricopeptide repeat. This Pfam entry includes tetratricopeptide-like repeats not detected by the pfam00515, pfam07719 and pfam07720 models.¡€0€ª€0€ €CDD¡€ €Á&¢€0€0€ €‚+pfam07722, Peptidase_C26, Peptidase C26. These peptidases have gamma-glutamyl hydrolase activity; that is they catalyze the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to pfam00117, but contain extensions in four loops and at the C terminus.¡€0€ª€0€ €CDD¡€ €Á'¢€0€0€ €}pfam07723, LRR_2, Leucine Rich Repeat. This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model.¡€0€ª€0€ €CDD¡€ €Á(¢€0€0€ €‡pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.¡€0€ª€0€ €CDD¡€ €Á)¢€0€0€ €{pfam07725, LRR_3, Leucine Rich Repeat. This Pfam entry includes some LRRs that fail to be detected by the pfam00560 model.¡€0€ª€0€ €CDD¡€ €Yb¢€0€0€ €ªpfam07726, AAA_3, ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.¡€0€ª€0€ €CDD¡€ €Yc¢€0€0€ €‚¿pfam07727, RVT_2, Reverse transcriptase (RNA-dependent DNA polymerase). A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.¡€0€ª€0€ €CDD¡€ €Á*¢€0€0€ €pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.¡€0€ª€0€ €CDD¡€ €Á+¢€0€0€ €‚)pfam07729, FCD, FCD domain. This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392. This domain is found in Escherichia coli NanR and DgoR that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain).¡€0€ª€0€ €CDD¡€ €Á,¢€0€0€ €¼pfam07730, HisKA_3, Histidine kinase. This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with pfam00512 and pfam07536.¡€0€ª€0€ €CDD¡€ €Á-¢€0€0€ €pfam07731, Cu-oxidase_2, Multicopper oxidase. This entry contains many divergent copper oxidase-like domains that are not recognized by the pfam00394 model.¡€0€ª€0€ €CDD¡€ €Á.¢€0€0€ €pfam07732, Cu-oxidase_3, Multicopper oxidase. This entry contains many divergent copper oxidase-like domains that are not recognized by the pfam00394 model.¡€0€ª€0€ €CDD¡€ €Á/¢€0€0€ €Hpfam07733, DNA_pol3_alpha, Bacterial DNA polymerase III alpha subunit. ¡€0€ª€0€ €CDD¡€ €Á0¢€0€0€ €Ÿpfam07734, FBA_1, F-box associated. Most of these proteins contain pfam00646 at the N terminus, suggesting that they are effectors linked with ubiquitination.¡€0€ª€0€ €CDD¡€ €Ả€0€0€ €Ÿpfam07735, FBA_2, F-box associated. Most of these proteins contain pfam00646 at the N terminus, suggesting that they are effectors linked with ubiquitination.¡€0€ª€0€ €CDD¡€ €Á1¢€0€0€ €‚pfam07736, CM_1, Chorismate mutase type I. Chorismate mutase EC:5.4.99.5 catalyzes the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine.¡€0€ª€0€ €CDD¡€ €Á2¢€0€0€ €¹pfam07737, ATLF, Anthrax toxin lethal factor, N- and C-terminal domain. The C-terminal domain is the catalytically active domain whereas the N-terminal domain is likely to be inactive.¡€0€ª€0€ €CDD¡€ €Ym¢€0€0€ €‚èpfam07738, Sad1_UNC, Sad1 / UNC-like C-terminal. The C. elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development. The S. pombe Sad1 protein localizes at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2. The SUN domain of Sun2 has been demonstrated to be in the periplasm.¡€0€ª€0€ €CDD¡€ €Á3¢€0€0€ €‚pfam07739, TipAS, TipAS antibiotic-recognition domain. This domain is found at the C-terminus of some MerR family transcription factors. The domain has an alpha-helical globin-like fold. The family includes Mta a central regulator of multidrug resistance in Bacillus subtilis.¡€0€ª€0€ €CDD¡€ €Á4¢€0€0€ €‚"pfam07740, Toxin_12, Ion channel inhibitory toxin. This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses. Huwentoxin-IV, from the Chinese bird spider, is a highly potent neurotoxin that specifically inhibits the neuronal tetrodotoxin-sensitive voltage-gated sodium channel in rat dorsal root ganglion neurons. Hainantoxin-4, from the venom of spider Selenocosmia hainana, adopts an inhibitor cystine knot structural motif like huwentoin-IV, and is a potent antagonist that acts at site 1 on tetrodotoxin-sensitive (TTX-S) sodium channels. Study of the molecular nature of toxin-receptor interactions has helped elucidate the functioning of many ion-channels.¡€0€ª€0€ €CDD¡€ €Á5¢€0€0€ €¥pfam07741, BRF1, Brf1-like TBP-binding domain. This region covers both the Brf homology II and III regions. This region is involved in binding TATA binding protein.¡€0€ª€0€ €CDD¡€ €Á6¢€0€0€ €pfam07742, BTG, BTG family. ¡€0€ª€0€ €CDD¡€ €Á7¢€0€0€ €œpfam07743, HSCB_C, HSCB C-terminal oligomerization domain. This domain is the HSCB C-terminal oligomerization domain and is found on co-chaperone proteins.¡€0€ª€0€ €CDD¡€ €Á8¢€0€0€ €‚pfam07744, SPOC, SPOC domain. The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.¡€0€ª€0€ €CDD¡€ €Á9¢€0€0€ €‚pfam07745, Glyco_hydro_53, Glycosyl hydrolase family 53. This domain belongs to family 53 of the glycosyl hydrolase classification. These enzymes are enzymes are endo-1,4- beta-galactanases (EC:3.2.1.89). The structure of this domain is known and has a TIM barrel fold.¡€0€ª€0€ €CDD¡€ €Á:¢€0€0€ €Òpfam07746, LigA, Aromatic-ring-opening dioxygenase LigAB, LigA subunit. This is a family of aromatic ring opening dioxygenases which catalyze the ring-opening reaction of protocatechuate and related compounds.¡€0€ª€0€ €CDD¡€ €Á;¢€0€0€ €Mpfam07747, MTH865, MTH865-like family. This domain has an EF-hand like fold.¡€0€ª€0€ €CDD¡€ €Á<¢€0€0€ €pfam07748, Glyco_hydro_38C, Glycosyl hydrolases family 38 C-terminal domain. Glycosyl hydrolases are key enzymes of carbohydrate metabolism.¡€0€ª€0€ €CDD¡€ €Á=¢€0€0€ €‚@pfam07749, ERp29, Endoplasmic reticulum protein ERp29, C-terminal domain. ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals. ERp29 is comprised of two domains. This domain, the C-terminal domain, has an all helical fold. ERp29 is thought to form part of the thyroglobulin folding complex.¡€0€ª€0€ €CDD¡€ €Á>¢€0€0€ €‚Hpfam07750, GcrA, GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.¡€0€ª€0€ €CDD¡€ €áÄ¢€0€0€ €‚„pfam07751, Abi_2, Abi-like protein. This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins, which are involved in bacteriophage resistance mediated by abortive infection in Lactococcus species. The proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function.¡€0€ª€0€ €CDD¡€ €Á?¢€0€0€ €epfam07752, S-layer, S-layer protein. Archaeal S-layer proteins consist of two copies of this domain.¡€0€ª€0€ €CDD¡€ €Á@¢€0€0€ €‚pfam07753, DUF1609, Protein of unknown function (DUF1609). This region is found in a number of hypothetical proteins thought to be expressed by the eukaryote Encephalitozoon cuniculi, an obligate intracellular microsporidial parasite. It is approximately 200 residues long.¡€0€ª€0€ €CDD¡€ €Y{¢€0€0€ €¹pfam07754, DUF1610, Domain of unknown function (DUF1610). This zinc ribbon domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.¡€0€ª€0€ €CDD¡€ €Y|¢€0€0€ €‚Tpfam07755, DUF1611, Protein of unknown function (DUF1611). This region is found in a number of hypothetical bacterial and archaeal proteins. The region is approximately 350 residues long. A member of this family is thought to associate with another subunit to form an H+-transporting ATPase, but no evidence has been found to support this.¡€0€ª€0€ €CDD¡€ €ÁA¢€0€0€ €‚¶pfam07756, DUF1612, Protein of unknown function (DUF1612). This family includes sequences of largely unknown function but which share a number of features in common. They are expressed by bacterial species, and in many cases these bacteria are known to associate symbiotically with plants. Moreover, the majority are coded for by plasmids, which in many cases are known to confer on the organism the ability to interact symbiotically with leguminous plants. An example of such a plasmid is NGR234, which encodes Y4CF, a protein of unknown function that is a member of this family. Other members of this family are expressed by organisms with a documented genomic similarity to plant symbionts.¡€0€ª€0€ €CDD¡€ €Y~¢€0€0€ €§pfam07757, AdoMet_MTase, Predicted AdoMet-dependent methyltransferase. Proteins in this family have been predicted to function as AdoMet-dependent methyltransferases.¡€0€ª€0€ €CDD¡€ €áÉ¢€0€0€ €©pfam07758, DUF1614, Protein of unknown function (DUF1614). This is a family of sequences coming from hypothetical proteins found in both bacterial and archaeal species.¡€0€ª€0€ €CDD¡€ €ÁB¢€0€0€ €‚pfam07759, DUF1615, Protein of unknown function (DUF1615). This is a family of proteins of unknown function expressed by various bacterial species. Some members of this family are thought to be lipoproteins. Another member of this family is thought to be involved in photosynthesis.¡€0€ª€0€ €CDD¡€ €ÁC¢€0€0€ €Äpfam07760, DUF1616, Protein of unknown function (DUF1616). This is a family of sequences from hypothetical archaeal proteins. The region in question is approximately 330 amino acid residues long.¡€0€ª€0€ €CDD¡€ €ÁD¢€0€0€ €úpfam07761, DUF1617, Protein of unknown function (DUF1617). This is a family of sequences from hypothetical bacterial and bacteriophage proteins. The region in question is approximately 150 residues long and is highly conserved throughout the family.¡€0€ª€0€ €CDD¡€ €Y‚¢€0€0€ €’pfam07762, DUF1618, Protein of unknown function (DUF1618). The members of this family are mainly hypothetical proteins expressed by Oryza sativa.¡€0€ª€0€ €CDD¡€ €ÁE¢€0€0€ €‚èpfam07763, FEZ, FEZ-like protein. This is a family of eukaryotic proteins thought to be involved in axonal outgrowth and fasciculation. The N-terminal regions of these sequences are less conserved than the C-terminal regions, and are highly acidic. The C. elegans homolog, UNC-76, may play structural and signalling roles in the control of axonal extension and adhesion (particularly in the presence of adjacent neuronal cells) and these roles have also been postulated for other FEZ family proteins. Certain homologs have been definitively found to interact with the N-terminal variable region (V1) of PKC-zeta, and this interaction causes cytoplasmic translocation of the FEZ family protein in mammalian neuronal cells. The C-terminal region probably participates in the association with the regulatory domain of PKC-zeta. The members of this family are predicted to form coiled-coil structures, which may interact with members of the RhoA family of signalling proteins, but are not thought to contain other characteristic protein motifs. Certain members of this family are expressed almost exclusively in the brain, whereas others (such as FEZ2) are expressed in other tissues, and are thought to perform similar but unknown functions in these tissues.¡€0€ª€0€ €CDD¡€ €ÁF¢€0€0€ €‚pfam07764, Omega_Repress, Omega Transcriptional Repressor. The omega transcriptional repressor regulates expression of involved in copy number control and stable maintenance of plasmids. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA.¡€0€ª€0€ €CDD¡€ €ÁG¢€0€0€ €‚Åpfam07765, KIP1, KIP1-like protein. This is a family of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions. It has also been suggested that the protein's coiled- coils allow it to dimerize in vivo.¡€0€ª€0€ €CDD¡€ €ÁH¢€0€0€ €‚pfam07766, LETM1, LETM1-like protein. Members of this family are inner mitochondrial membrane proteins which play a role in potassium and hydrogen ion exchange. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans.¡€0€ª€0€ €CDD¡€ €ÁI¢€0€0€ €‚°pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumor suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins.¡€0€ª€0€ €CDD¡€ €ÁJ¢€0€0€ €‚Õpfam07768, PVL_ORF50, PVL ORF-50-like family. This is a family of sequences found in both bacteria and bacteriophages. This region is approximately 130 residues long and in some cases is found as part of the PVL (Panton-Valentine leukocidin) group of genes, which encode a member of the leukocidin group of bacterial toxins that kill leukocytes by creation of pores in the cell membrane. PVL appears to be a virulence factor associated with a number of human diseases.¡€0€ª€0€ €CDD¡€ €Y‰¢€0€0€ €‚"pfam07769, PsiF_repeat, psiF repeat. This region is approximately 35 residues long. It is found repeated in a number of putative phosphate starvation- inducible proteins expressed by various bacterial species. psiF is known to be an example of such phosphate starvation-inducible proteins.¡€0€ª€0€ €CDD¡€ €ÁK¢€0€0€ €‚Qpfam07771, TSGP1, Tick salivary peptide group 1. This contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis. Also present are peptides from a related tick species, Ixodes ricinus. They are characterized by a putative signal peptide indicative of secretion and conserved cysteine residues.¡€0€ª€0€ €CDD¡€ €ÁL¢€0€0€ €êpfam07773, DUF1619, Protein of unknown function (DUF1619). This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.¡€0€ª€0€ €CDD¡€ €ÁM¢€0€0€ €‚pfam07774, DUF1620, Protein of unknown function (DUF1620). These sequences are mainly derived from predicted eukaryotic proteins. The region in question lies towards the C-terminus of these large proteins and is approximately 300 amino acid residues long.¡€0€ª€0€ €CDD¡€ €ÁN¢€0€0€ €‚Ypfam07775, PaRep2b, PaRep2b protein. This is a family of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer functional.¡€0€ª€0€ €CDD¡€ €YŽ¢€0€0€ €þpfam07776, zf-AD, Zinc-finger associated domain (zf-AD). The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA.¡€0€ª€0€ €CDD¡€ €ÁO¢€0€0€ €‚?pfam07777, MFMR, G-box binding protein MFMR. This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localization signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals.¡€0€ª€0€ €CDD¡€ €ÁP¢€0€0€ €‚0pfam07778, CENP-I, Mis6. Mis6 is an essential centromere connector protein acting during G1-S phase of the cell cycle. Mis6 is thought to be required for recruiting CENP-A, the centromere- specific histone H3 variant, an important event for centromere function and chromosome segregation during mitosis.¡€0€ª€0€ €CDD¡€ €ÁQ¢€0€0€ €‚.pfam07779, Cas1_AcylT, 10 TM Acyl Transferase domain found in Cas1p. Cas1p protein of Cryptococcus neoformans is required for the synthesis of O-acetylated glucuronoxylomannans, a consitutent of the capsule, and is critical for its virulence. The multi TM domain of the Cas1p was unified with the 10 TM Sugar Acyltransferase superfamily. This superfamily is comprised of members from the OatA, MdoC, OpgC, NolL and GumG families in addition to the Cas1p family. The Cas1p protein has a N terminal PC-Esterase domain with the opposing Acyl esterase activity.¡€0€ª€0€ €CDD¡€ €ÁR¢€0€0€ €Épfam07780, Spb1_C, Spb1 C-terminal domain. This presumed domain is found at the C-terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis.¡€0€ª€0€ €CDD¡€ €ÁS¢€0€0€ €‚pfam07781, Reovirus_Mu2, Reovirus minor core protein Mu-2. This family represents the Reovirus core protein Mu-2. Mu-2 is a microtubule associated protein and is thought to play a key role in the formation and structural organisation of reovirus inclusion bodies.¡€0€ª€0€ €CDD¡€ €Y”¢€0€0€ €‚Cpfam07782, DC_STAMP, DC-STAMP-like protein. This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family.¡€0€ª€0€ €CDD¡€ €ÁT¢€0€0€ €»pfam07784, DUF1622, Protein of unknown function (DUF1622). This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species.¡€0€ª€0€ €CDD¡€ €ÁU¢€0€0€ €Ípfam07785, DUF1623, Protein of unknown function (DUF1623). The members of this family are all derived from relatively short hypothetical proteins thought to be expressed by various Nucleopolyhedroviruses.¡€0€ª€0€ €CDD¡€ €Y—¢€0€0€ €êpfam07786, DUF1624, Protein of unknown function (DUF1624). These sequences are found in hypothetical proteins of unknown function expressed by bacterial and archaeal species. The region in question is approximately 230 residues long.¡€0€ª€0€ €CDD¡€ €ÁV¢€0€0€ €°pfam07787, TMEM43, Transmembrane protein 43. This entry represents the transmembrane protein 43 family of proteins, which may function as tetraspanin-like membrane organisers.¡€0€ª€0€ €CDD¡€ €ÁW¢€0€0€ €‚¥pfam07788, PDDEXK_10, PD-(D/E)XK nuclease superfamily. This family is found to carry modified motifs characteristic of PD-(D/E)XK endonuclease superfamily. These are the conserved Glu of motif I, the Asp surreounded by hydrophobics of motif II, EIKS of motif III, and the lysine of mmotif IV has migrated to an alpha-helix following the third core beta-strand. The conserved patch of positively charged lysine and arginine residues in the motif IV apha-helix might be involved in substrate-binding or be contributing to active site formation. Members with an additional N-terminal coi9led-coil domain, are annotated as tropomyosin, coiled-coil or microtubule binding proteins.¡€0€ª€0€ €CDD¡€ €Yš¢€0€0€ €ùpfam07789, DUF1627, Protein of unknown function (DUF1627). This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.¡€0€ª€0€ €CDD¡€ €Ƴ¢€0€0€ €‚pfam07790, Pilin_N, Archaeal Type IV pilin, N-terminal. This entry represents the N-terminal domain of archaeal pilins, which play important roles in surface adhesion and twitching motility. This domain contains an conserved N- terminal hydrophobic motif.¡€0€ª€0€ €CDD¡€ €ÁX¢€0€0€ €ñpfam07791, DUF1629, Protein of unknown function (DUF1629). This family consists of sequences from hypothetical proteins thought to be expressed by two members of the Xanthomonas genus. The region in question is 125 amino acid residues long.¡€0€ª€0€ €CDD¡€ €ÁY¢€0€0€ €‚~pfam07792, Afi1, Docking domain of Afi1 for Arf3 in vesicle trafficking. This domain occurs at the N-terminal of Afi1, an Arf3p-interacting protein, is a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3, the highly conserved small GTPases (ADP-ribosylation factors). Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homolog of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalization. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localization and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth.¡€0€ª€0€ €CDD¡€ €ÁZ¢€0€0€ €‚pfam07793, DUF1631, Protein of unknown function (DUF1631). The members of this family are sequences derived from a group of hypothetical proteins expressed by certain bacterial species. The region concerned is approximately 440 amino acid residues in length.¡€0€ª€0€ €CDD¡€ €Á[¢€0€0€ €‚pfam07794, DUF1633, Protein of unknown function (DUF1633). This family contains sequences derived from a group of hypothetical proteins expressed by Arabidopsis thaliana. These sequences are highly similar and the region concerned is about 100 residues long.¡€0€ª€0€ €CDD¡€ €Ƹ¢€0€0€ €âpfam07795, DUF1635, Protein of unknown function (DUF1635). The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.¡€0€ª€0€ €CDD¡€ €Á\¢€0€0€ €þpfam07796, DUF1638, Protein of unknown function (DUF1638). This family contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins. These proteins are expressed by archaeal species of the Methanosarcina genus.¡€0€ª€0€ €CDD¡€ €Á]¢€0€0€ €ùpfam07797, DUF1639, Protein of unknown function (DUF1639). This approximately 50 residue region is found in a number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre.¡€0€ª€0€ €CDD¡€ €Á^¢€0€0€ €Çpfam07798, DUF1640, Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.¡€0€ª€0€ €CDD¡€ €Á_¢€0€0€ €ìpfam07799, DUF1643, Protein of unknown function (DUF1643). The members of this family are all sequences found within hypothetical proteins expressed by various bacterial species. The region concerned is approximately 150 residues long.¡€0€ª€0€ €CDD¡€ €Á`¢€0€0€ €‚Bpfam07800, DUF1644, Protein of unknown function (DUF1644). This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, and is probably a zinc-binding domain.¡€0€ª€0€ €CDD¡€ €Áa¢€0€0€ €‚zpfam07801, DUF1647, Protein of unknown function (DUF1647). The sequences making up this family are all derived from hypothetical proteins expressed by C. elegans. The region in question is approximately 160 amino acids long. The GO annotation for this protein indicates the protein to be involved in nematode larval development and to have a positive regulation on growth rate.¡€0€ª€0€ €CDD¡€ €Áb¢€0€0€ €‚pfam07802, GCK, GCK domain. This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as pfam00071) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family; this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.¡€0€ª€0€ €CDD¡€ €Ác¢€0€0€ €‚jpfam07803, GSG-1, GSG1-like protein. This family contains sequences bearing similarity to a region of GSG1, a protein specifically expressed in testicular germ cells. It is possible that overexpression of the human homolog may be involved in tumorigenesis of human testicular germ cell tumors. The region in question has four highly-conserved cysteine residues.¡€0€ª€0€ €CDD¡€ €Ád¢€0€0€ €‚tpfam07804, HipA_C, HipA-like C-terminal domain. The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species. This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells, but it is usually tightly associated with HipB, and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products.¡€0€ª€0€ €CDD¡€ €Áe¢€0€0€ €‚tpfam07805, HipA_N, HipA-like N-terminal domain. The members of this family are similar to a region close to the N-terminus of the HipA protein expressed by various bacterial species. This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells, but it is usually tightly associated with HipB, and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products.¡€0€ª€0€ €CDD¡€ €Áf¢€0€0€ €‚Åpfam07806, Nod_GRP, Nodule-specific GRP repeat. The region featured in this family is found repeated in a number of plant proteins, some of which are expressed specifically in nodules formed during symbiotic interactions with certain bacterial species. Some of these proteins are also termed glycine-rich proteins (GRPs), due to the presence of a glycine-rich C-terminal region in their structures. Bacterial infection is required for the induction of nodule-specific GRP genes, and it is thought that nodule-specific GRPs may play non-redundant roles required at specific stages of nodule development. Members of this group of proteins may be cytosolic, whereas others are thought to be membrane-associated.¡€0€ª€0€ €CDD¡€ €ÆÄ¢€0€0€ €‚,pfam07807, RED_C, RED-like protein C-terminal region. This family contains sequences that are similar to the C-terminal region of Red protein. This and related proteins are thought to be localized to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated or that the protein self-aggregates extremely efficiently.¡€0€ª€0€ €CDD¡€ €Ág¢€0€0€ €‚dpfam07808, RED_N, RED-like protein N-terminal region. This family contains sequences that are similar to the N-terminal region of Red protein. This and related proteins contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences and a putative trimeric coiled-coil region, suggesting that these proteins are expressed in the nucleus. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated of that the protein self-aggregates extremely efficiently.¡€0€ª€0€ €CDD¡€ €Áh¢€0€0€ €‚¹pfam07809, RTP801_C, RTP801 C-terminal region. The members of this family are sequences similar to the C-terminal region of RTP801, the protein product of a hypoxia-inducible factor 1 (HIF-1)- responsive gene. Two members of this family expressed by Drosophila melanogaster, Scylla and Charybde, are designated by the GenBank as Hox targets. RTP801 is thought to be involved in various cellular processes. Its overexpression caused the apoptosis- resistant phenotype in cycling cells, and apoptosis sensitivity in growth arrested cells. Moreover, the protein product of the mouse homolog of RTP801 (dig2) is thought to be induced by diverse apoptotic signals, and also by dexamethasone treatment.¡€0€ª€0€ €CDD¡€ €Ái¢€0€0€ €‚ópfam07810, TMC, TMC domain. These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters.¡€0€ª€0€ €CDD¡€ €Áj¢€0€0€ €‚Qpfam07811, TadE, TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues.¡€0€ª€0€ €CDD¡€ €Ák¢€0€0€ €‚fpfam07812, TfuA, TfuA-like protein. This family consists of a group of sequences that are similar to a region of TfuA protein. This protein is involved in the production of trifolitoxin (TFX), an gene-encoded, post-translationally modified peptide antibiotic. The role of TfuA in TFX synthesis is unknown, and it may be involved in other cellular processes.¡€0€ª€0€ €CDD¡€ €Ál¢€0€0€ €‚.pfam07813, LTXXQ, LTXXQ motif family protein. This protein family includes two copies of a five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP. This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH. Another member of this family, Spy, is also a periplasmic protein that may be involved in the response to stress. The homology between CpxP and Spy may indicate that these two proteins are functionally related.¡€0€ª€0€ €CDD¡€ €Y°¢€0€0€ €‚Opfam07814, WAPL, Wings apart-like protein regulation of heterochromatin. This family contains sequences expressed in eukaryotic organisms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure. hWAPL, the human homolog, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death.¡€0€ª€0€ €CDD¡€ €Ám¢€0€0€ €‚Úpfam07815, Abi_HHR, Abl-interactor HHR. The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases. More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins. Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganisation, but their precise role remains unclear.¡€0€ª€0€ €CDD¡€ €Án¢€0€0€ €‚Epfam07816, DUF1645, Protein of unknown function (DUF1645). These sequences are derived from a number of hypothetical plant proteins. The region in question is approximately 270 amino acids long. Some members of this family are annotated as yeast pheromone receptor proteins AR781 but no literature was found to support this.¡€0€ª€0€ €CDD¡€ €Áo¢€0€0€ €èpfam07817, GLE1, GLE1-like protein. The members of this family are sequences that are similar to the human protein GLE1. This protein is localized at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm.¡€0€ª€0€ €CDD¡€ €Áp¢€0€0€ €‚pfam07818, HCNGP, HCNGP-like protein. This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP. This protein is localized to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.¡€0€ª€0€ €CDD¡€ €Áq¢€0€0€ €‚–pfam07819, PGAP1, PGAP1-like protein. The sequences found in this family are similar to PGAP1. This is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body.¡€0€ª€0€ €CDD¡€ €Ár¢€0€0€ €‚ƒpfam07820, TraC, TraC-like protein. The members of this family are sequences that are similar to TraC. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli CFN42 that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42a, which is also known as plasmid pSym as it carries most of the genes required for nodulation and nitrogen fixation by the symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58.¡€0€ª€0€ €CDD¡€ €Y·¢€0€0€ €Åpfam07821, Alpha-amyl_C2, Alpha-amylase C-terminal beta-sheet domain. This domain is organised as a five-stranded anti-parallel beta-sheet. It is the probable result of a decay of the common-fold.¡€0€ª€0€ €CDD¡€ €Ás¢€0€0€ €‚¦pfam07822, Toxin_13, Neurotoxin B-IV-like protein. The members of this family resemble neurotoxin B-IV, which is a crustacean-selective neurotoxin produced by the marine worm Cerebratulus lacteus. This highly cationic peptide is approximately 55 residues and is arranged to form two antiparallel helices connected by a well-defined loop in a hairpin structure. The branches of the hairpin are linked by four disulphide bonds. Three residues identified as being important for activity, namely Arg-17, -25 and -34, are found on the same face of the molecule, while another residue important for activity, Trp30, is on the opposite side. The protein's mode of action is not entirely understood, but it may act on voltage-gated sodium channels, possibly by binding to an as yet uncharacterized site on these proteins. Its site of interaction may also be less specific, for example it may interact with negatively charged membrane lipids.¡€0€ª€0€ €CDD¡€ €Át¢€0€0€ €‚çpfam07823, CPDase, Cyclic phosphodiesterase-like protein. Cyclic phosphodiesterase (CPDase) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft. Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site.¡€0€ª€0€ €CDD¡€ €Áu¢€0€0€ €‚5pfam07824, Chaperone_III, Type III secretion chaperone domain. Type III secretion chaperones are involved in delivering virulence effector proteins from bacterial pathogens directly into eukaryotic cells. The chaperones may prevent aggregation and degradation of their substrates, may target the effector to the secretion apparatus, and may ensure a secretion-component unfolded confirmation of their specific substrate. One member of this family, SigE forms homodimers in crystal. The monomers have a novel fold with an alpha-beta(3)-alpha-beta(2)-alpha topology.¡€0€ª€0€ €CDD¡€ €Yº¢€0€0€ €‚pfam07825, Exc, Excisionase-like protein. The phage-encoded excisionase protein (Xis) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha helices are packed against two extended strands. Also present in the structure is a two-stranded anti-parallel beta-sheet, whose strands are connected by a four-residue 'wing'. During interaction with DNA, helix alpha2 is thought to insert into the major groove, while the wing contacts the adjacent minor groove or phosphodiester backbone. The C-terminal region of Xis is involved in interaction with phage-encoded integrase (Int), and a putative C-terminal alpha helix may fold upon interaction with Int and/or DNA.¡€0€ª€0€ €CDD¡€ €Æ×¢€0€0€ €‚³pfam07826, IMP_cyclohyd, IMP cyclohydrolase-like protein. This enzyme (PurO) may catalyze the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to inosine monophosphate (IMP), a reaction which is important in de novo purine biosynthesis in archaeal species. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family.¡€0€ª€0€ €CDD¡€ €Áv¢€0€0€ €‚pfam07827, KNTase_C, KNTase C-terminal domain. Kanamycin nucleotidyltransferase (KNTase) is involved in conferring resistance to aminoglycoside antibiotics and catalyzes the transfer of a nucleoside monophosphate group from a nucleotide to kanamycin. This enzyme is dimeric with each subunit being composed of two domains. The C-terminal domain contains five alpha helices, four of which are organised into an up-and-down alpha helical bundle. Residues found in this domain may contribute to this enzyme's active site.¡€0€ª€0€ €CDD¡€ €Y¼¢€0€0€ €‚¢pfam07828, PA-IL, PA-IL-like protein. The members of this family are similar to the galactophilic lectin-1 expressed by P. aeruginosa ((PA-IL). Lectins recognising specific carbohydrates found on the surface of host cells are known to be involved in the initiation of infections by this organism. The protein is thought to be organised into an extensive network of beta-sheets, as is the case with many other lectins.¡€0€ª€0€ €CDD¡€ €ÆÙ¢€0€0€ €‚ëpfam07829, Toxin_14, Alpha-A conotoxin PIVA-like protein. Alpha-A conotoxin PIVA is the major paralytic toxin found in the venom produced by the piscivorous snail Conus purpurascens. This peptide acts by blocking the acetylcholine binding site of the nicotinic acetylcholine receptor at the neuromuscular junction. The overall shape of the peptide is described as an "iron" with a highly charged hydrophilic loop of 15S-19R forming the "handle" domain that is exposed to the exterior of the protein. The stability of the conotoxin is primarily governed by three disulphide bonds. A triangular structural motif formed by residues 19R, 12H and 6Y is thought to constitute a "binding core" that is important in binding to the acetylcholine receptor.¡€0€ª€0€ €CDD¡€ €Áw¢€0€0€ €‚xpfam07830, PP2C_C, Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain.¡€0€ª€0€ €CDD¡€ €Áx¢€0€0€ €‚kpfam07831, PYNP_C, Pyrimidine nucleoside phosphorylase C-terminal domain. This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer.¡€0€ª€0€ €CDD¡€ €Y¾¢€0€0€ €‚Æpfam07832, Bse634I, Cfr10I/Bse634I restriction endonuclease. Cfr10I and Bse634I are two Type II restriction endonucleases. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged 'back-to-back' with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet.The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3.¡€0€ª€0€ €CDD¡€ €áú¢€0€0€ €‚fpfam07833, Cu_amine_oxidN1, Copper amine oxidase N-terminal domain. Copper amine oxidases catalyze the oxidative deamination of primary amines to the corresponding aldehydes, while reducing molecular oxygen to hydrogen peroxide. These enzymes are dimers of identical subunits, each comprising four domains. The N-terminal domain, which is absent in some amine oxidases, consists of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the 'stalk' of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other.¡€0€ª€0€ €CDD¡€ €Áy¢€0€0€ €‚hpfam07834, RanGAP1_C, RanGAP1 C-terminal domain. Ran-GTPase activating protein 1 (RanGAP1) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localization at the vertebrate nuclear pore complex, and is sumoylated by the small ubiquitin-related modifier protein (SUMO-1). This domain is composed almost entirely of helical substructures that are organised into an alpha-alpha superhelix fold, with the exception of the peptide containing the lysine residue required for SUMO-1 conjugation.¡€0€ª€0€ €CDD¡€ €Áz¢€0€0€ €‚ pfam07835, COX4_pro_2, Bacterial aa3 type cytochrome c oxidase subunit IV. Bacterial cytochrome c oxidase is found bound to the to the cell membrane, where it is involved in the generation of the transmembrane proton electrochemical gradient. It is composed of four subunits. Subunit IV consists of one transmembrane helix that does not interact directly with the other subunits, but maintains its position by indirect contacts via phospholipid molecules found in the structure. The function of subunit IV is as yet unknown.¡€0€ª€0€ €CDD¡€ €Á{¢€0€0€ €‚pfam07836, DmpG_comm, DmpG-like communication domain. This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain. The communication domain is thought to play an important role in the heterodimerisation of the enzyme.¡€0€ª€0€ €CDD¡€ €Á|¢€0€0€ €‚ípfam07837, FTCD_N, Formiminotransferase domain, N-terminal subdomain. The formiminotransferase (FT) domain of formiminotransferase- cyclodeaminase (FTCD) forms a homodimer, and each protomer comprises two subdomains. The N-terminal subdomain is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains.¡€0€ª€0€ €CDD¡€ €Á}¢€0€0€ €‚´pfam07839, CaM_binding, Plant calmodulin-binding domain. The sequences featured in this family are found repeated in a number of plant calmodulin-binding proteins, and are thought to constitute the calmodulin-binding domains. Binding of the proteins to calmodulin depends on the presence of calcium ions. These proteins are thought to be involved in various processes, such as plant defense responses and stolonisation or tuberization.¡€0€ª€0€ €CDD¡€ €Á~¢€0€0€ €‚¢€0€0€ €mpfam08146, BP28CT, BP28CT (NUC211) domain. This C terminal domain is found in BAP28-like nucleolar proteins.¡€0€ª€0€ €CDD¡€ €Â?¢€0€0€ €„pfam08147, DBP10CT, DBP10CT (NUC160) domain. This C terminal domain is found in the Dbp10p subfamily of hypothetical RNA helicases.¡€0€ª€0€ €CDD¡€ €Â@¢€0€0€ €tpfam08148, DSHCT, DSHCT (NUC185) domain. This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases.¡€0€ª€0€ €CDD¡€ €ÂA¢€0€0€ €„pfam08149, BING4CT, BING4CT (NUC141) domain. This C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins.¡€0€ª€0€ €CDD¡€ €ÂB¢€0€0€ €bpfam08150, FerB, FerB (NUC096) domain. This is central domain B in proteins of the Ferlin family.¡€0€ª€0€ €CDD¡€ €ÂC¢€0€0€ €Œpfam08151, FerI, FerI (NUC094) domain. This domain is present in proteins of the Ferlin family. It is often located between two C2 domains.¡€0€ª€0€ €CDD¡€ €ÂD¢€0€0€ €wpfam08152, GUCT, GUCT (NUC152) domain. This is the C terminal domain found in the RNA helicase II / Gu protein family.¡€0€ª€0€ €CDD¡€ €ÂE¢€0€0€ € pfam08153, NGP1NT, NGP1NT (NUC091) domain. This N terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1.¡€0€ª€0€ €CDD¡€ €ÂF¢€0€0€ €ªpfam08154, NLE, NLE (NUC135) domain. This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated yeast ribosome biogenesis protein YTM1.¡€0€ª€0€ €CDD¡€ €ÂG¢€0€0€ €pfam08155, NOGCT, NOGCT (NUC087) domain. This C terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins.¡€0€ª€0€ €CDD¡€ €ÂH¢€0€0€ €wpfam08156, NOP5NT, NOP5NT (NUC127) domain. This N terminal domain is found in RNA-binding proteins of the NOP5 family.¡€0€ª€0€ €CDD¡€ €ÂI¢€0€0€ €xpfam08157, NUC129, NUC129 domain. This C terminal domain is found in a novel family of hypothetical nucleolar proteins.¡€0€ª€0€ €CDD¡€ €ÂJ¢€0€0€ €opfam08158, NUC130_3NT, NUC130/3NT domain. This N terminal domain is found in a novel nucleolar protein family.¡€0€ª€0€ €CDD¡€ €ÂK¢€0€0€ €\pfam08159, NUC153, NUC153 domain. This small domain is found in a a novel nucleolar family.¡€0€ª€0€ €CDD¡€ €ÂL¢€0€0€ €tpfam08161, NUC173, NUC173 domain. This is the central domain of of novel family of hypothetical nucleolar proteins.¡€0€ª€0€ €CDD¡€ €ÂM¢€0€0€ €npfam08163, NUC194, NUC194 domain. This is domain B in the catalytic subunit of DNA-dependent protein kinases.¡€0€ª€0€ €CDD¡€ €ÂN¢€0€0€ €‚Epfam08164, TRAUB, Apoptosis-antagonizing transcription factor, C-terminal. This C terminal domain is found in traube proteins. This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcription.¡€0€ª€0€ €CDD¡€ €ÂO¢€0€0€ €bpfam08165, FerA, FerA (NUC095) domain. This is central domain A in proteins of the Ferlin family.¡€0€ª€0€ €CDD¡€ €ÂP¢€0€0€ €`pfam08166, NUC202, NUC202 domain. This domain is found in a novel family of nucleolar proteins.¡€0€ª€0€ €CDD¡€ €G6¢€0€0€ €‚|pfam08167, RIX1, rRNA processing/ribosome biogenesis. Rix1 is a nucleoplasmic particle involved in rRNA processing/ribosome assembly. It associates with two other proteins, Ipi1 and Ipi3, to form the RIX1 complex that allows Rea1 - the AAA ATPase - to associate with the 60S ribosomal subunit. More than 170 assembly factors are involved in the construction and maturation of yeast ribosomes, and after these factors have completed their function they need to be released from the pre-ribosomes. Rea1 induces the release of the assembly protein complex in a mechanical fashion. This family is usually associated with NUC202, pfam08166.¡€0€ª€0€ €CDD¡€ €ÂQ¢€0€0€ €`pfam08168, NUC205, NUC205 domain. This domain is found in a novel family of nucleolar proteins.¡€0€ª€0€ €CDD¡€ €ZÏ¢€0€0€ €­pfam08169, RBB1NT, RBB1NT (NUC162) domain. This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family.¡€0€ª€0€ €CDD¡€ €ÂR¢€0€0€ €_pfam08170, POPLD, POPLD (NUC188) domain. This domain is found in POP1-like nucleolar proteins.¡€0€ª€0€ €CDD¡€ €ÂS¢€0€0€ €‚4pfam08171, Mad3_BUB1_II, Mad3/BUB1 homology region 2. This domain is found in checkpoint proteins which are involved in cell division. This region has been shown to be necessary and sufficient for the binding of MAD3 to BUB3 in Saccharomyces cerevisiae. This domain is present in BUB1 which also binds BUB3.¡€0€ª€0€ €CDD¡€ €ÂT¢€0€0€ €¾pfam08172, CASP_C, CASP C terminal. This domain is the C-terminal region of the CASP family of proteins. It is a Golgi membrane protein which is thought to have a role in vesicle transport.¡€0€ª€0€ €CDD¡€ €ÂU¢€0€0€ €‚™pfam08173, YbgT_YccB, Membrane bound YbgT-like protein. This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in E. coli. Members have a consensus motif (MWYFXW) which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to Proteobacteria.¡€0€ª€0€ €CDD¡€ €ÂV¢€0€0€ €‚Jpfam08174, Anillin, Cell division protein anillin. Anillin is a protein involved in septin organisation during cell division. It is an actin binding protein that is localized to the cleavage furrow, and it maintains the localization of active myosin, which ensures the spatial control of concerted contraction during cytokinesis.¡€0€ª€0€ €CDD¡€ €ÂW¢€0€0€ €‚tpfam08175, SspO, Small acid-soluble spore protein O family. This family consists of the small acid-soluble spore proteins (SASP) O type (sspO). SspO (originally cotK) are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspO is the first gene in a likely operon with sspP and transcription of this gene is primarily by RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspO causes the loss of the SspO from the forespore but had no discernible effect on sporulation, spore properties or spore germination.¡€0€ª€0€ €CDD¡€ €ÂX¢€0€0€ €‚Mpfam08176, SspK, Small acid-soluble spore protein K family. This family consists of the small acid-soluble spore proteins (SASP) belonging to the K type (sspK). The sspK are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspK gene is monocistronic and transcription is primarily by the RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspK results in loss of SspK from the spore but had no discernible effect on sporulation, spore properties or spore germination.¡€0€ª€0€ €CDD¡€ €Z×¢€0€0€ €‚ppfam08177, SspN, Small acid-soluble spore protein N family. This family consists of the small acid-soluble spore protein (SASP) N type (sspN). SspN is a 48 residues protein that is expressed only in the forespore compartment of sporulating Bacillus subtilis. The sspN gene is recognized equally by both sigma-G and sigma-F. The role of SspN is still not well-defined.¡€0€ª€0€ €CDD¡€ €ZØ¢€0€0€ €‚°pfam08178, GnsAB_toxin, GnsA/GnsB toxin of bacterial toxin-antitoxin system. This family consists of the GnsA/GnsB family. GnsA and GnsB are multicopy suppressors of the secG null mutation. These proteins participate in the synthesis of phospholipids, suggesting the functional relationship between SecG and membrane phospholipids. Over-expression of gnsA and gnsB causes a remarkable increase in the unsaturated fatty acid content. However, the gnsA-gnsB double null mutant exhibits no effect. Both proteins are predicted to possess a helix-turn-helix structure. GnsAB is a family of putative bacterial toxins (both GnsA and GnsB) that, are neutralized by the antitoxin YmcE, pfam15939.¡€0€ª€0€ €CDD¡€ €ZÙ¢€0€0€ €‚–pfam08179, SspP, Small acid-soluble spore protein P family. This family consists of the small acid-soluble spore proteins (SASP) P type (sspP). sspP is expressed only in the forespore compartment of the sporulating cell. sspP is also expressed under sigma-G control from the same promoter as sspO. Mutations deleting sspP causes no discernible effect on sporulation, spore properties or spore germination.¡€0€ª€0€ €CDD¡€ €ZÚ¢€0€0€ €‚pfam08252, Leader_CPA1, arg-2/CPA1 leader peptide. In this family there are Leaders Peptides involved in the regulation the glutaminase subunit (small subunit) of arginine-specific carbamoyl phosphate synthetase. In Neurospora crassa it is a small upstream ORF of 24 codon above the arg-2 locus. In yeast it is the leader peptide of the CPA1 gene. The 5' region of CPA1 mRNA contains a 25 codon upstream open reading frame. The leader peptide, the product of the upstream open reading frame, plays an essential, negative role in the specific repression of CPA1 by arginine.¡€0€ª€0€ €CDD¡€ €[¢€0€0€ €µpfam08253, Leader_Erm, Erm Leader peptide. These short proteins are Leader peptides (15-19 amino acids) of erm genes that code for resistance determinants in Staphylococcus aureus.¡€0€ª€0€ €CDD¡€ €[¢€0€0€ €Épfam08254, Leader_Thr, Threonine leader peptide. Threonine leader peptide of the Threonine operon thrA1A2BC. It as been sequenced in different bacteria: E. coli, Serratia marcescens, Salmonella typhi.¡€0€ª€0€ €CDD¡€ €[¢€0€0€ €‚pfam08255, Leader_Trp, Trp-operon Leader Peptide. The tryptophan operon regulatory region of C. freundii's (leader transcript) encodes a 14-residue peptide containing characteristic tandem tryptophan residues. It is about 10 nucleotides shorter than those of E. coli and S. typhimurium.¡€0€ª€0€ €CDD¡€ €[¢€0€0€ €‚Apfam08256, Antimicrobial20, Aurein-like antibiotic peptide. This family of antibacterial peptides are secreted from the granular dorsal glands of the Green and Golden Bell Frog Litoria aurea, Southern Bell Frog L. raniformis, Blue Mountains tree-frog Litoria citropa (genus Litoria) and frogs from genus Uperoleia. They are a part of the FSAP peptide family. Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides.¡€0€ª€0€ €CDD¡€ €Èi¢€0€0€ €‚ñpfam08257, Sulfakinin, Sulfakinin family. The sulfakinin (SK) family of neuropeptides have only been identified in crustaceans and insects. For most species there is the potential for producing two sulfakinin peptides one have a short sulfakinin sequence The function of the sulfakinins is difficult to assess. For the American cockroach, various forms of the endogenous sulfakinins have been shown to be active on the hindgut, and also on the heart. In C. vomitoria the peptides act as neurotransmitters or neuromodulators, linking the brain with all thoracic and abdominal ganglia. In adults of P. monodon they appear to be restricted to a few neurones in the brain with a neural pathway extending along to the ventral thoracic and abdominal ganglia.¡€0€ª€0€ €CDD¡€ €Èj¢€0€0€ €‚Mpfam08258, WWamide, WWamide peptide. This family contain neuropeptides, isolated from ganglia of the African giant snail, Achatina fulica. Each peptide has a Trp residue at both the N- and C-termini. Purified WWamide-1, -2 and -3 showed an inhibitory effect on the phasic contractions of the anterior byssus retractor muscle (ABRM).¡€0€ª€0€ €CDD¡€ €Èk¢€0€0€ €¡pfam08259, Periviscerokin, Periviscerokinin family. Abdominal Perisympathetic organs of insects contain Periviscerokinins neuropeptides of about 11 amino acids.¡€0€ª€0€ €CDD¡€ €â㢀0€0€ €‚ÿpfam08260, Kinin, Insect kinin peptide. These neuropeptides are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterized the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. These peptides have length from 6 to 14 amino acids.¡€0€ª€0€ €CDD¡€ €Èm¢€0€0€ €‚"pfam08261, Carcinustatin, Carcinustatin peptide. A total of 20 peptides of the superfamily allostatin were isolated from the shore crab Carcinus maenas. They are named carcinustatin 1 to 20 and their length ranges from 5 to 27 amino acids. This family includes carcinustatin 8,9,15 and 16.¡€0€ª€0€ €CDD¡€ €U±¢€0€0€ €‚€pfam08262, Lem_TRP, Leucophaea maderae tachykinin-related peptide. These peptides are designated Leucophaea maderae tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific. The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae. They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of the Locusta migratoria. They stimulate visceral muscle contractions of the oviduct and the foregut of Locusta migratoria.¡€0€ª€0€ €CDD¡€ €Èn¢€0€0€ €‚Qpfam08263, LRRNT_2, Leucine rich repeat N-terminal domain. Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.¡€0€ª€0€ €CDD¡€ €„¢€0€0€ €£pfam08264, Anticodon_1, Anticodon-binding domain of tRNA. This domain is found mainly hydrophobic tRNA synthetases. The domain binds to the anticodon of the tRNA.¡€0€ª€0€ €CDD¡€ €Â…¢€0€0€ €ýpfam08265, YL1_C, YL1 nuclear protein C-terminal domain. This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins.¡€0€ª€0€ €CDD¡€ €†¢€0€0€ €npfam08266, Cadherin_2, Cadherin-like. This cadherin domain is usually the most N-terminal copy of the domain.¡€0€ª€0€ €CDD¡€ €‡¢€0€0€ €‚•pfam08267, Meth_synt_1, Cobalamin-independent synthase, N-terminal domain. The N-terminal domain and C-terminal domains of cobalamin-independent synthases together 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 stabilize a loop from the C-terminal domain.¡€0€ª€0€ €CDD¡€ €ˆ¢€0€0€ €,pfam08268, FBA_3, F-box associated domain. ¡€0€ª€0€ €CDD¡€ €[¢€0€0€ €…pfam08269, dCache_2, Cache domain. Double Cache domain 2 (dCache_2) may be a result of single Cache domain 2 (sCache_2) duplication.¡€0€ª€0€ €CDD¡€ €‰¢€0€0€ €‚$pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA) PRD domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This corresponds to the PRD like region.¡€0€ª€0€ €CDD¡€ €[¢€0€0€ €‚=pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.¡€0€ª€0€ €CDD¡€ €Š¢€0€0€ €‚%pfam08272, Topo_Zn_Ribbon, Topoisomerase I zinc-ribbon-like. Some Proteobacteria topoisomerase I contain two zinc-ribbon-like domains at the C-terminus that structurally homologous to pfam01396. However, this domain no longer bind zinc. Indeed, only one of the four cysteine residues remains.¡€0€ª€0€ €CDD¡€ €‹¢€0€0€ €Epfam08273, Prim_Zn_Ribbon, Zinc-binding domain of primase-helicase. ¡€0€ª€0€ €CDD¡€ €[!¢€0€0€ €.pfam08274, PhnA_Zn_Ribbon, PhnA Zinc-Ribbon. ¡€0€ª€0€ €CDD¡€ €ÂŒ¢€0€0€ €Epfam08275, Toprim_N, DNA primase catalytic core, N-terminal domain. ¡€0€ª€0€ €CDD¡€ €¢€0€0€ €$pfam08276, PAN_2, PAN-like domain. ¡€0€ª€0€ €CDD¡€ €ÂŽ¢€0€0€ €$pfam08277, PAN_3, PAN-like domain. ¡€0€ª€0€ €CDD¡€ €¢€0€0€ €‚pfam08278, DnaG_DnaB_bind, DNA primase DnaG DnaB-binding. Eubacterial DnaG primases interact with several factors to from the replisome. One of these factors in DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB.¡€0€ª€0€ €CDD¡€ €¢€0€0€ €lpfam08279, HTH_11, HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.¡€0€ª€0€ €CDD¡€ €['¢€0€0€ €ûpfam08280, HTH_Mga, M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions.¡€0€ª€0€ €CDD¡€ €‘¢€0€0€ €§pfam08281, Sigma70_r4_2, Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.¡€0€ª€0€ €CDD¡€ €Â’¢€0€0€ €pfam08282, Hydrolase_3, haloacid dehalogenase-like hydrolase. This family contains haloacid dehalogenase-like hydrolase enzymes.¡€0€ª€0€ €CDD¡€ €“¢€0€0€ €|pfam08283, Gemini_AL1_M, Geminivirus rep protein central domain. This is the cetral domain of the geminivirus rep proteins.¡€0€ª€0€ €CDD¡€ €[+¢€0€0€ €‚ipfam08284, RVP_2, Retroviral aspartyl protease. Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.¡€0€ª€0€ €CDD¡€ €[,¢€0€0€ €‚Žpfam08285, DPM3, Dolichol-phosphate mannosyltransferase subunit 3 (DPM3). This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilizing the dolichol-phosphate mannosyl transferase complex.¡€0€ª€0€ €CDD¡€ €”¢€0€0€ €¯pfam08286, Spc24, Spc24 subunit of Ndc80. Spc24 is a component of the evolutionarily conserved kinetochore-associated Ndc80 complex and is involved in chromosome segregation.¡€0€ª€0€ €CDD¡€ €•¢€0€0€ €Ìpfam08287, DASH_Spc19, Spc19. Spc19 is a component of the DASH complex. The DASH complex associates with the spindle pole body and is important for spindle and kinetochore integrity during cell division.¡€0€ª€0€ €CDD¡€ €–¢€0€0€ €‚ pfam08288, PIGA, PIGA (GPI anchor biosynthesis). This domain is found on phosphatidylinositol n-acetylglucosaminyltransferase proteins. These proteins are involved in GPI anchor biosynthesis and are associated with disease the paroxysmal nocturnal haemoglobinuria.¡€0€ª€0€ €CDD¡€ €—¢€0€0€ €pfam08289, Flu_M1_C, Influenza Matrix protein (M1) C-terminal domain. This region is thought to be a second domain of the M1 matrix protein.¡€0€ª€0€ €CDD¡€ €[0¢€0€0€ €Øpfam08290, Hep_core_N, Hepatitis core protein, putative zinc finger. This short region is found at the N-terminus of some hepatitis core proteins. Its conservation of four cys and his suggests a zinc binding domain.¡€0€ª€0€ €CDD¡€ €[1¢€0€0€ €,pfam08291, Peptidase_M15_3, Peptidase M15. ¡€0€ª€0€ €CDD¡€ €˜¢€0€0€ €‚Ypfam08292, RNA_pol_Rbc25, RNA polymerase III subunit Rpc25. Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III.¡€0€ª€0€ €CDD¡€ €™¢€0€0€ €‚Tpfam08293, MRP-S33, Mitochondrial ribosomal subunit S27. This family of proteins corresponds to mitochondrial ribosomal subunit S27 in prokaryotes and to subunit S33 in humans. It is a small 106 residue protein.The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome.¡€0€ª€0€ €CDD¡€ €š¢€0€0€ € pfam08294, TIM21, TIM21. TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane.¡€0€ª€0€ €CDD¡€ €›¢€0€0€ €špfam08295, Sin3_corepress, Sin3 family co-repressor. This domain is found on transcriptional regulators. It forms interactions with histone deacetylases.¡€0€ª€0€ €CDD¡€ €Âœ¢€0€0€ €±pfam08297, U3_snoRNA_assoc, U3 snoRNA associated. This family of proteins is associated with U3 snoRNA. U3 snoRNA is required for nucleolar processing of pre-18S ribosomal RNA.¡€0€ª€0€ €CDD¡€ €¢€0€0€ €©pfam08298, AAA_PrkA, PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.¡€0€ª€0€ €CDD¡€ €È‘¢€0€0€ €Apfam08299, Bac_DnaA_C, Bacterial dnaA protein helix-turn-helix. ¡€0€ª€0€ €CDD¡€ €ž¢€0€0€ €‚rpfam08300, HCV_NS5a_1a, Hepatitis C virus non-structural 5a zinc finger domain. The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This domain corresponds to the N-terminal zinc binding domain.¡€0€ª€0€ €CDD¡€ €Ÿ¢€0€0€ €‚Tpfam08301, HCV_NS5a_1b, Hepatitis C virus non-structural 5a domain 1b. The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.¡€0€ª€0€ €CDD¡€ €G†¢€0€0€ €‚pfam08302, tRNA_lig_CPD, Fungal tRNA ligase phosphodiesterase domain. This domain is found in fungal tRNA ligases and has cyclic phosphodiesterase activity. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns.¡€0€ª€0€ €CDD¡€ € ¢€0€0€ €‚pfam08303, tRNA_lig_kinase, tRNA ligase kinase domain. This domain is found in fungal tRNA ligases and has kinase activity. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. This family contains a P-loop motif.¡€0€ª€0€ €CDD¡€ €[;¢€0€0€ €‚^pfam08305, NPCBM, NPCBM/NEW2 domain. This novel putative carbohydrate binding module (NPCBM) domain is found at the N-terminus of glycosyl hydrolase family 98 proteins. This domain has also been called the NEW2 domain (Naumoff DG. Phylogenetic analysis of alpha-galactosidases of the GH27 family. Molecular Biology (Engl Transl). (2004)38:388-399.).¡€0€ª€0€ €CDD¡€ €¡¢€0€0€ €‘pfam08306, Glyco_hydro_98M, Glycosyl hydrolase family 98. This domain is the putative catalytic domain of glycosyl hydrolase family 98 proteins.¡€0€ª€0€ €CDD¡€ €¢¢€0€0€ €êpfam08307, Glyco_hydro_98C, Glycosyl hydrolase family 98 C-terminal domain. This putative domain is found at the C-terminus of glycosyl hydrolase family 98 proteins. This domain is not expected to form part of the catalytic activity.¡€0€ª€0€ €CDD¡€ €[>¢€0€0€ €‚apfam08308, PEGA, PEGA domain. This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins. It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16].¡€0€ª€0€ €CDD¡€ €[?¢€0€0€ €‚„pfam08309, LVIVD, LVIVD repeat. This repeat is found in bacterial and archaeal cell surface proteins, many of which are hypothetical. The secondary structure corresponding to this repeat is predicted to comprise from 1-7 of 4-beta-strands which may associate to form a beta-propeller. The repeat copy number varies from 3-29. This repeat is sometimes found with the PKD domain pfam00801.¡€0€ª€0€ €CDD¡€ €[@¢€0€0€ €‚³pfam08310, LGFP, LGFP repeat. This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from C.glutamicum and C.efficiens along with PS1 protein contain this repeat region. The N-terminus region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminus region consists of 4 tandem LGFP repeats. It is hypothesized that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. Deletion of Corynebacterium glutamicum csp1 protein results in a 10-fold increase in the cell volume of the organism and infers the corresponding proteins involvement in the cell shape formation. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix [Adindla et al. 2004].¡€0€ª€0€ €CDD¡€ €£¢€0€0€ €îpfam08311, Mad3_BUB1_I, Mad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.¡€0€ª€0€ €CDD¡€ €¤¢€0€0€ €‚§pfam08312, cwf21, cwf21 domain. The cwf21 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe. The function of the cwf21 domain is to bind directly to the spliceosomal protein Prp8. Mutations in the cwf21 domain prevent Prp8 from binding. The structure of this domain has recently been solved which shows this domain to be composed of two alpha helices.¡€0€ª€0€ €CDD¡€ €Â¥¢€0€0€ €‚Cpfam08313, SCA7, SCA7, zinc-binding domain. This domain is found in the protein Sgf73/Sca7 which is a component of the multihistone acetyltransferase complexes SAGA and SILK. This domain is also found in Ataxin-7, a human protein which in its polyglutamine expanded pathological form, is responsible for the neurodegenerative disease spinocerebellar ataxia 7 (SCA7). Ataxin-7 is an integral component of the mammalian SAGA-like complexes, the TATA-binding protein-free TAF-containing complex (TFTC) and the SPT3/TAF9/GCN5 acetyltransferase complex (STAGA). This domain is a minimal domain in ataxin-7-like proteins that is required for interaction with TFTC/STAGA subunits and is conserved highly through evolution. The domain contains a conserved Cys(3)His motif that binds zinc, thus indicating this to be a new zinc-binding domain.¡€0€ª€0€ €CDD¡€ €¦¢€0€0€ €‚6pfam08314, Sec39, Secretory pathway protein Sec39. Mnaimneh et al identified Sec39p as a protein involved in ER-Golgi transport in a large scale promoter shut down analysis of essential yeast genes. Kraynack et al. (2005) showed that Sec39p (Dsl3p) is required for Golgi-ER retrograde transport and is part of a very stable protein complex that also includes Dsl1p (in mammals ZW10), Tip20p (Rint-1) and the ER localized Q-SNARE proteins Ufe1p (syntaxin-18), Sec20p and Use1p. This was confirmed in a genome-wide analysis of protein complexes by Gavin et al (2006).¡€0€ª€0€ €CDD¡€ €§¢€0€0€ €¶pfam08315, cwf18, cwf18 pre-mRNA splicing factor. The cwf18 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe.¡€0€ª€0€ €CDD¡€ €¨¢€0€0€ €‚Qpfam08316, Pal1, Pal1 cell morphology protein. Pal1 is a membrane associated protein that is involved in the maintenance of cylindrical cellular morphology. It localizes to sites of active growth. Pal1 physically interacts and displays overlapping localization with the Huntingtin-interacting-protein (Hip1)-related protein Sla2p/End4p.¡€0€ª€0€ €CDD¡€ €©¢€0€0€ €’pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.¡€0€ª€0€ €CDD¡€ €ª¢€0€0€ €§pfam08318, COG4, COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi an intra Golgi transport.¡€0€ª€0€ €CDD¡€ €«¢€0€0€ €Îpfam08320, PIG-X, PIG-X / PBN1. Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I. These enzymes are involved in the transfer of sugar molecules.¡€0€ª€0€ €CDD¡€ €¬¢€0€0€ €’pfam08321, PPP5, PPP5 TPR repeat region. This region is specific to the PPP5 subfamily of serine/threonine phosphatases and contains TPR repeats.¡€0€ª€0€ €CDD¡€ €­¢€0€0€ €>pfam08323, Glyco_transf_5, Starch synthase catalytic domain. ¡€0€ª€0€ €CDD¡€ €®¢€0€0€ €Òpfam08324, PUL, PUL domain. The PUL (PLAP, Ufd3p and Lub1p) domain is a novel alpha-helical Ub-associated domain. It directly binds to Cdc48, a chaperone-like AAA ATPase that collects ubiquitylated substrates.¡€0€ª€0€ €CDD¡€ €¯¢€0€0€ €‚=pfam08325, WLM, WLM domain. This is a predicted metallopeptidase domain called WLM (Wss1p-like metalloproteases). These are linked to the Ub-system by virtue of fusions with the UB-binding PUG (PUB), Ub-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation.¡€0€ª€0€ €CDD¡€ €°¢€0€0€ €‚Tpfam08326, ACC_central, Acetyl-CoA carboxylase, central region. The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyzes the rate-limiting step in this process.¡€0€ª€0€ €CDD¡€ €±¢€0€0€ €‚ðpfam08327, AHSA1, Activator of Hsp90 ATPase homolog 1-like protein. This family includes eukaryotic, prokaryotic and archaeal proteins that bear similarity to a C-terminal region of human activator of 90 kDa heat shock protein ATPase homolog 1 (AHSA1/p38). This protein is known to interact with the middle domain of Hsp90, and stimulate its ATPase activity. It is probably a general upregulator of Hsp90 function, particularly contributing to its efficiency in conditions of increased stress. p38 is also known to interact with the cytoplasmic domain of the VSV G protein, and may thus be involved in protein transport. It has also been reported as being underexpressed in Down's syndrome. This region is found repeated in two members of this family.¡€0€ª€0€ €CDD¡€ €²¢€0€0€ €‚½pfam08328, ASL_C, Adenylosuccinate lyase C-terminal. This domain is found at the C-terminus of adenylosuccinate lyase(ASL; PurB in E. coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain pfam00206. ASL catalyzes the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚pfam08329, ChitinaseA_N, Chitinase A, N-terminal domain. This domain is found in a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin. It is separated by a hinge region from the catalytic domain (pfam00704); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €¾pfam08331, DUF1730, Domain of unknown function (DUF1730). This domain of unknown function occurs in Iron-sulfur cluster-binding proteins together with the 4Fe-4S binding domain (pfam00037).¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚™pfam08332, CaMKII_AD, Calcium/calmodulin dependent protein kinase II association domain. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.¡€0€ª€0€ €CDD¡€ €[T¢€0€0€ €‚.pfam08333, DUF1725, Protein of unknown function (DUF1725). This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚±pfam08334, T2SSG, Type II secretion system (T2SS), protein G. The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. The T2SG family includes proteins such as EpsG (P45773) in Vibrio cholera, XcpT also called PddA (Q00514) in Pseudomonas aeruginosa or PulG (P15746)in Klebsiella pneumoniae. The PulG is thought to be anchored in the inner membrane with its C-terminus directed towards the periplasme. Together with other members of the Type II secretion machinery, it is thought to assemble into a pilus-like structure that may function as a dynamic mechanism to push secreted proteins out of the cell. The polypeptide is organized into a long N-terminal alpha-helix followed by a loop region that separates it from a C-terminal anti-parallel beta-sheet.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚+pfam08335, GlnD_UR_UTase, GlnD PII-uridylyltransferase. This is a family of bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD) that are responsible for the modification (EC:2.7.7.59) of the regulatory protein P-II, or GlnB (pfam00543). In response to nitrogen limitation, these transferases catalyze the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA). Deadenylylated glutamine synthetase is the more active form of the enzyme. Moreover, uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes. It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species. The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain (pfam01909), and N-terminal to an HD domain (pfam01966) and two ACT domains (pfam01842).¡€0€ª€0€ €CDD¡€ €¸¢€0€0€ €‚0pfam08336, P4Ha_N, Prolyl 4-Hydroxylase alpha-subunit, N-terminal region. The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known.¡€0€ª€0€ €CDD¡€ €¹¢€0€0€ €‚ pfam08337, Plexin_cytopl, Plexin cytoplasmic RasGAP domain. This family features the C-terminal regions of various plexins. Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels. The cytoplasmic region, which has been called a SEX domain in some members of this family, is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins. This domain acts as a RasGAP domain.¡€0€ª€0€ €CDD¡€ €º¢€0€0€ €‚¢€0€0€ €‚¿pfam08517, AXH, Ataxin-1 and HBP1 module (AXH). AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1). ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression.¡€0€ª€0€ €CDD¡€ €Ã?¢€0€0€ €‚Öpfam08518, GIT_SHD, Spa2 homology domain (SHD) of GIT. GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase.¡€0€ª€0€ €CDD¡€ €Ã@¢€0€0€ €‚%pfam08519, RFC1, Replication factor RFC1 C terminal domain. This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.¡€0€ª€0€ €CDD¡€ €ÃA¢€0€0€ €{pfam08520, DUF1748, Fungal protein of unknown function (DUF1748). This is a family of fungal proteins of unknown function.¡€0€ª€0€ €CDD¡€ €ÃB¢€0€0€ €’pfam08521, 2CSK_N, Two-component sensor kinase N-terminal. This domain is found in bacterial two-component sensor kinases towards the N-terminus.¡€0€ª€0€ €CDD¡€ €ÃC¢€0€0€ €Öpfam08522, DUF1735, Domain of unknown function (DUF1735). This domain of unknown function is found in a number of bacterial proteins including acylhydrolases. The structure of this domain has a beta-sandwich fold.¡€0€ª€0€ €CDD¡€ €ÃD¢€0€0€ €‚’pfam08523, MBF1, Multiprotein bridging factor 1. This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilizing the Ftz-F1-DNA complex. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (pfam01381) is found to its C-terminus.¡€0€ª€0€ €CDD¡€ €ÃE¢€0€0€ €‚Rpfam08524, rRNA_processing, rRNA processing. This is a family of proteins that are involved in rRNA processing. In a localization study they were found to localize to the nucleus and nucleolus. The family also includes other metazoa members from plants to mammals where the protein has been named BR22 and is associated with TTF-1, thyroid transcription factor 1. In the lungs, the family binds TTF-1 to form a complex which influences the expression of the key lung surfactant protein-B (SP-B) and -C (SP-C), the small hydrophobic surfactant proteins that maintain surface tension in alveoli.¡€0€ª€0€ €CDD¡€ €ÃF¢€0€0€ €‚pfam08525, OapA_N, Opacity-associated protein A N-terminal motif. This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation. This motif occurs at the N-terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues.¡€0€ª€0€ €CDD¡€ €ÃG¢€0€0€ €Èpfam08526, PAD_N, Protein-arginine deiminase (PAD) N-terminal domain. This family represents the N-terminal non-catalytic domain of protein-arginine deiminase. This domain has a cupredoxin-like fold.¡€0€ª€0€ €CDD¡€ €ÃH¢€0€0€ €Æpfam08527, PAD_M, Protein-arginine deiminase (PAD) middle domain. This family represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold.¡€0€ª€0€ €CDD¡€ €ÃI¢€0€0€ €‚ 2-dehydropantoate + NADPH. AbpA catalyzes the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway. ApbA and PanE are allelic. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway.¡€0€ª€0€ €CDD¡€ €ÃV¢€0€0€ €‚×pfam08547, CIA30, Complex I intermediate-associated protein 30 (CIA30). This protein is associated with mitochondrial Complex I intermediate-associated protein 30 (CIA30) in human and mouse. The family is also present in Schizosaccharomyces pombe which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits. This means it is possible that this family of protein may not be directly involved in oxidative phosphorylation.¡€0€ª€0€ €CDD¡€ €ÃW¢€0€0€ €‚’pfam08548, Peptidase_M10_C, Peptidase M10 serralysin C terminal. Serralysins are peptidases related to mammalian matrix metallopeptidases (MMPs). The peptidase unit is found at the N terminal while this domain at the C terminal forms a corkscrew and is thought to be important for secretion of the protein through the bacterial cell wall. This domain contains the calcium ion binding domain pfam00353.¡€0€ª€0€ €CDD¡€ €\¢€0€0€ €spfam08549, SWI-SNF_Ssr4, Fungal domain of unknown function (DUF1750). This is a fungal domain of unknown function.¡€0€ª€0€ €CDD¡€ €ÃX¢€0€0€ €‚¦pfam08550, DUF1752, Fungal protein of unknown function (DUF1752). This is a family of fungal proteins of unknown function. This short section domain is bounded by two highly conserved tryptophans. The family contains MKS1 that is thought to be a negative regulator of RAS-cAMP pathway in S.cerevisiae. the Sch.pombe member is a GAF1 transcription factor that is also associated with the zinc finger family GATA pfam00320.¡€0€ª€0€ €CDD¡€ €ÃY¢€0€0€ €Ýpfam08551, DUF1751, Eukaryotic integral membrane protein (DUF1751). This domain is found in eukaryotic integral membrane proteins. YOL107W, a Saccharomyces cerervisiae protein, has been shown to localize COP II vesicles.¡€0€ª€0€ €CDD¡€ €\¢€0€0€ €‚Npfam08552, Kei1, Inositolphosphorylceramide synthase subunit Kei1. Kei1 is a subunit of Saccharomyces cerevisiae inositol phosphorylceramide (IPC) synthase. It is localized to the Golgi and is cleaved by the late Golgi processing endopeptidase Kex2. Kei1 is essential for both the activity and the Golgi localization of IPC synthase.¡€0€ª€0€ €CDD¡€ €ÃZ¢€0€0€ €àpfam08553, VID27, VID27 cytoplasmic protein. This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation.¡€0€ª€0€ €CDD¡€ €Ã[¢€0€0€ €~pfam08555, DUF1754, Eukaryotic family of unknown function (DUF1754). This is a eukaryotic protein family of unknown function.¡€0€ª€0€ €CDD¡€ €Ã\¢€0€0€ €‚‡pfam08557, Lipid_DES, Sphingolipid Delta4-desaturase (DES). Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyzes the formation of (E)-sphing-4-enine. Some proteins in this family have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis. This small domain associates with FA_desaturase pfam00487 and appears to be specific to sphingolipid delta 4-desaturase.¡€0€ª€0€ €CDD¡€ €Ã]¢€0€0€ €‚¶pfam08558, TRF, Telomere repeat binding factor (TRF). Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain pfam00249 at the carboxy terminus. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres. This domain is composed of multiple alpha helices arranged in a solenoid conformation similar to TPR repeats. The fungal members have now also been found to carry two double strand telomeric repeat binding factors.¡€0€ª€0€ €CDD¡€ €Ã^¢€0€0€ €‚…pfam08559, Cut8, Cut8, nuclear proteasome tether protein. In Schizosaccharomyces pombe, Cut8 is a nuclear envelope protein that physically interacts with and tethers 26S proteasome in the nucleus resulting in the nuclear accumulation of proteasome. Cut8 comprises three functional domains. An N-terminal lysine-rich segment which binds to the proteasome when ubiquitinated, a central dimerisation domain and a C-terminal nine-helix, Structure 3q5w, bundle which shows structural similarity to 14-3-3 phosphoprotein-binding domains. The helical bundle is necessary for liposome and cholesterol binding. Cut8 is a proteasome substrate and the N-terminal segment is polyubiquitinated and functions as a degron tag. Ubiquitination of the amino N-terminal segment is essential for the function of Cut8. Lysine residues in the N-terminal segment of Cut8 are required for physical interaction with proteasome. In fission yeast the function of Cut8 has been demonstrated to be regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating enzymes Ubr1. Cut8 homologs have been identified in Drosophila melanogaster, Anopheles gambiae and Dictyostelium discoideum.¡€0€ª€0€ €CDD¡€ €Ã_¢€0€0€ €“pfam08560, DUF1757, Protein of unknown function (DUF1757). This family of proteins are about 150 amino acids in length and have no known function.¡€0€ª€0€ €CDD¡€ €Ã`¢€0€0€ €„pfam08561, Ribosomal_L37, Mitochondrial ribosomal protein L37. This family includes yeast MRPL37 a mitochondrial ribosomal protein.¡€0€ª€0€ €CDD¡€ €Ãa¢€0€0€ €‚§pfam08562, Crisp, Crisp. This domain is found on Crisp proteins which contain pfam00188 and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling. It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK.¡€0€ª€0€ €CDD¡€ €Ãb¢€0€0€ €‚pfam08563, P53_TAD, P53 transactivation motif. The binding of the p53 transactivation domain by regulatory proteins regulates p53 transcription activation. This motif is comprised of a single amphipathic alpha helix and contains a highly conserved sequence.¡€0€ª€0€ €CDD¡€ €Ãc¢€0€0€ €‚mpfam08564, CDC37_C, Cdc37 C terminal domain. Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the C terminal domain whose function is unclear. It is found C terminal to the Hsp90 chaperone (Heat shocked protein 90) binding domain pfam08565 and the N terminal kinase binding domain of Cdc37 pfam03234.¡€0€ª€0€ €CDD¡€ €Ãd¢€0€0€ €‚ªpfam08565, CDC37_M, Cdc37 Hsp90 binding domain. Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the Hsp90 chaperone (Heat shocked protein 90) binding domain of Cdc37. It is found between the N terminal Cdc37 domain pfam03234, which is predominantly involved in kinase binding, and the C terminal domain of Cdc37 pfam08564 whose function is unclear.¡€0€ª€0€ €CDD¡€ €Ãe¢€0€0€ €‚Ãpfam08566, Pam17, Mitochondrial import protein Pam17. The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins.¡€0€ª€0€ €CDD¡€ €Ãf¢€0€0€ €‚ôpfam08567, PH_TFIIH, TFIIH p62 subunit, N-terminal domain. The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal domain reveals that it adopts a pleckstrin homology (PH) fold. This PH-type domain has been shown to bind to a mono-phosphorylated inositide.¡€0€ª€0€ €CDD¡€ €Ãg¢€0€0€ €‚lpfam08568, Kinetochor_Ybp2, Uncharacterized protein family, YAP/Alf4/glomulin. This entry contains a number of protein families with apparently unrelated functions. These include the YAP binding proteins of yeasts. These are stress response and redox homeostasis proteins, induced by hydrogen peroxide or induced in response to alkylating agent methyl methanesulphonate (MMS). The family includes Aberrant root formation protein 4 (Alf4) of Arabidopsis thaliana (Mouse-ear cress), which is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation. The family includes glomulin (FAP68), which is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12.¡€0€ª€0€ €CDD¡€ €Ãh¢€0€0€ €îpfam08569, Mo25, Mo25-like. Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localized alternately to the spindle pole body and to the site cell division in a cell cycle dependent manner.¡€0€ª€0€ €CDD¡€ €Ãi¢€0€0€ €pfam08570, DUF1761, Protein of unknown function (DUF1761). Family of conserved fungal and bacterial membrane proteins with unknown function.¡€0€ª€0€ €CDD¡€ €Ãj¢€0€0€ €Öpfam08571, Yos1, Yos1-like. In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Yos1 appears to be conserved in eukaryotes.¡€0€ª€0€ €CDD¡€ €Ãk¢€0€0€ €Çpfam08572, PRP3, pre-mRNA processing factor 3 (PRP3). Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa.¡€0€ª€0€ €CDD¡€ €Ãl¢€0€0€ €‚@pfam08573, SAE2, DNA repair protein endonuclease SAE2/CtIP C-terminus. SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. It is now known to be an endonuclease. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions.¡€0€ª€0€ €CDD¡€ €Ãm¢€0€0€ €ôpfam08574, Iwr1, Transcription factor Iwr1. Iwr1 is involved in transcription from polymerase II promoters; it interacts with with most of the polymerase II subunits. Deletion of this protein results in hypersensitivity to the K1 killer toxin.¡€0€ª€0€ €CDD¡€ €Ãn¢€0€0€ €´pfam08576, DUF1764, Eukaryotic protein of unknown function (DUF1764). This is a family of eukaryotic proteins of unknown function. This family contains many hypothetical proteins.¡€0€ª€0€ €CDD¡€ €Ão¢€0€0€ €—pfam08577, PI31_Prot_C, PI31 proteasome regulator. PI31 is a cellular regulator of proteasome formation and of proteasome-mediated antigen processing.¡€0€ª€0€ €CDD¡€ €Ãp¢€0€0€ €¬pfam08578, DUF1765, Protein of unknown function (DUF1765). This region represents a conserved region found in hypothetical proteins from fungi, mycetozoa and entamoebidae.¡€0€ª€0€ €CDD¡€ €Ãq¢€0€0€ €‚Œpfam08579, RPM2, Mitochondrial ribonuclease P subunit (RPM2). Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends. RPM2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as transcriptional activator in the nucleus where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components.¡€0€ª€0€ €CDD¡€ €HM¢€0€0€ €‚Hpfam08580, KAR9, Yeast cortical protein KAR9. The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.¡€0€ª€0€ €CDD¡€ €Ãr¢€0€0€ €’pfam08581, Tup_N, Tup N-terminal. The N-terminal domain of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor.¡€0€ª€0€ €CDD¡€ €Ãs¢€0€0€ €‚¼pfam08583, Cmc1, Cytochrome c oxidase biogenesis protein Cmc1 like. Cmc1 is a metallo-chaperone like protein which is known to localize to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.¡€0€ª€0€ €CDD¡€ €Ãt¢€0€0€ €‚Tpfam08584, Ribonuc_P_40, Ribonuclease P 40kDa (Rpp40) subunit. The tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule and at least eight protein subunits. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 (this entry) are involved in extensive, but weak, protein-protein interactions in the holoenzyme complex.¡€0€ª€0€ €CDD¡€ €Ãu¢€0€0€ €‚pfam08585, RMI1_N, RecQ mediated genome instability protein. RMI1_N is an N-terminal family of eukaryotic proteins. The domain probably carries an oligo-nucleotide-binding domain or OB-fold, and forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha.¡€0€ª€0€ €CDD¡€ €Ãv¢€0€0€ €‚'pfam08586, Rsc14, RSC complex, Rsc14/Ldb7 subunit. RSC is an ATP-dependent chromatin remodelling complex found in yeast. The RSC components Rsc7/Npl6 and Rsc14/Ldb7 interact physically and/or functionally with Rsc3, Rsc30, and Htl1 to form a module important for a broad range of RSC functions.¡€0€ª€0€ €CDD¡€ €Ãw¢€0€0€ €–pfam08587, UBA_2, Ubiquitin associated domain (UBA). This is a UBA (ubiquitin associated) domain. Ubiquitin is involved in intracellular proteolysis.¡€0€ª€0€ €CDD¡€ €Ãx¢€0€0€ €kpfam08588, DUF1769, Protein of unknown function (DUF1769). Family of fungal protein with unknown function.¡€0€ª€0€ €CDD¡€ €Ãy¢€0€0€ €Çpfam08589, DUF1770, Fungal protein of unknown function (DUF1770). The function of this family is unknown. These proteins are rather dissimilar except for a single strongly conserved motif (PDLRFEQ).¡€0€ª€0€ €CDD¡€ €Ãz¢€0€0€ €mpfam08590, DUF1771, Domain of unknown function (DUF1771). This domain is always found adjacent to pfam01713.¡€0€ª€0€ €CDD¡€ €Ã{¢€0€0€ €¨pfam08591, RNR_inhib, Ribonucleotide reductase inhibitor. This family includes S. pombe Spd1. Spd1p inhibits fission yeast RNR activity by interacting with the Cdc22p.¡€0€ª€0€ €CDD¡€ €Ã|¢€0€0€ €^pfam08592, DUF1772, Domain of unknown function (DUF1772). This domain is of unknown function.¡€0€ª€0€ €CDD¡€ €Ã}¢€0€0€ €òpfam08593, DUF1773, Domain of unknown function. This is the C-terminal part of some meiotically up-regulated gene products from fission yeast. The actual function is not yet known but the proteins are likely to be cell-surface glycoproteins.¡€0€ª€0€ €CDD¡€ €Ã~¢€0€0€ €ypfam08594, UPF0300, Uncharacterized protein family (UPF0300). This family of proteins appear to be specific to S. pombe.¡€0€ª€0€ €CDD¡€ €Ã¢€0€0€ €‚3pfam08595, RXT2_N, RXT2-like, N-terminal. The family represents the N-terminal region of RXT2-like proteins. In S. cerevisiae, RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth. A high throughput localization study has localized RXT2 to the nucleus.¡€0€ª€0€ €CDD¡€ €À¢€0€0€ €‚£pfam08596, Lgl_C, Lethal giant larvae(Lgl) like, C-terminal. The Lethal giant larvae (Lgl) tumor suppressor family is conserved from yeast to mammals. The Lgl family functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface. The N-terminal half of Lgl members contains WD40 repeats (see pfam00400), while the C-terminal half appears specific to the family.¡€0€ª€0€ €CDD¡€ €â€0€0€ €‚kpfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit. This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein HCR1 has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.¡€0€ª€0€ €CDD¡€ €¢€0€0€ €‚£pfam08598, Sds3, Sds3-like. Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins. This family represents the conserved region found in Sds3, Dep1 and BRMS1-homolog p40 proteins.¡€0€ª€0€ €CDD¡€ €â€0€0€ €·pfam08599, Nbs1_C, DNA damage repair protein Nbs1. This C terminal region of the DNA damage repair protein Nbs1 has been identified to be necessary for the binding of Mre11 and Tel1.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €Xpfam08600, Rsm1, Rsm1-like. Rsm1 is a protein involved in mRNA export from the nucleus.¡€0€ª€0€ €CDD¡€ €Ã…¢€0€0€ €‚ƒpfam08601, PAP1, Transcription factor PAP1. The transcription factor Pap1 regulates antioxidant-gene transcription in response to H2O2. This region is cysteine rich. Alkylation of cysteine residues following treatment with a cysteine alkylating agent can mask the accessibility of the nuclear exporter Crm1, triggering nuclear accumulation and Pap1 dependent transcriptional expression.¡€0€ª€0€ €CDD¡€ €Æ¢€0€0€ €‚5pfam08602, Mgr1, Mgr1-like, i-AAA protease complex subunit. The S. cerevisiae Mgr1 protein has been shown to be required for mitochondrial viability in yeast lacking mitochondrial DNA. It is a mitochondrial inner membrane protein, which interacts with Yme1 and is a new subunit of the i-AAA protease complex.¡€0€ª€0€ €CDD¡€ €Ç¢€0€0€ €Bpfam08603, CAP_C, Adenylate cyclase associated (CAP) C terminal. ¡€0€ª€0€ €CDD¡€ €È¢€0€0€ €Ãpfam08604, Nup153, Nucleoporin Nup153-like. This family contains both the nucleoporin Nup153 from human and Nup154 from fission yeast. These have been demonstrated to be functionally equivalent.¡€0€ª€0€ €CDD¡€ €É¢€0€0€ €‚rpfam08605, Rad9_Rad53_bind, Fungal Rad9-like Rad53-binding. In Saccharomyces cerevisiae the Rad9 a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via Rad53 pfam00498 domains. This region is structurally composed of a pair of TUDOR domains.¡€0€ª€0€ €CDD¡€ €ãâ€0€0€ €‚"pfam08606, Prp19, Prp19/Pso4-like. This regions is found specifically in PRP19-like protein. The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly.¡€0€ª€0€ €CDD¡€ €Ê¢€0€0€ €‚ pfam08608, Wyosine_form, Wyosine base formation. Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.¡€0€ª€0€ €CDD¡€ €Ë¢€0€0€ €‚pfam08609, Fes1, Nucleotide exchange factor Fes1. Fes1 is a cytosolic homolog of Sls1, an ER protein which has nucleotide exchange factor activity. Fes1 in yeast has been shown to bind to the molecular chaperone Hsp70 and has adenyl-nucleotide exchange factor activity.¡€0€ª€0€ €CDD¡€ €ÃŒ¢€0€0€ €Žpfam08610, Pex16, Peroxisomal membrane protein (Pex16). Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane.¡€0€ª€0€ €CDD¡€ €â€0€0€ €opfam08611, DUF1774, Fungal protein of unknown function (DUF1774). This is a fungal family of unknown function.¡€0€ª€0€ €CDD¡€ €ÃŽ¢€0€0€ €‚Ópfam08612, Med20, TATA-binding related factor (TRF) of subunit 20 of Mediator complex. This family of proteins is related to TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex. Human TRF has been shown to associate with an RNA polymerase II-SRB complex. This Med20 subunit of Mediator is found in the non-essential part of the head.¡€0€ª€0€ €CDD¡€ €â€0€0€ €¬pfam08613, Cyclin, Cyclin. This family includes many different cyclin proteins. Members include the G1/S-specific cyclin pas1, and the phosphate system cyclin PHO80/PHO85.¡€0€ª€0€ €CDD¡€ €\Q¢€0€0€ €‚‹pfam08614, ATG16, Autophagy protein 16 (ATG16). Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway.¡€0€ª€0€ €CDD¡€ €â€0€0€ €‚=pfam08615, RNase_H2_suC, Ribonuclease H2 non-catalytic subunit (Ylr154p-like). This entry represents the non-catalytic subunit of RNase H2, which in S. cerevisiae is Ylr154p/Rnh203p. Whereas bacterial and archaeal RNases H2 are active as single polypeptides, the Saccharomyces cerevisiae homolog, Rnh2Ap, when expressed in Escherichia coli, fails to produce an active RNase H2. For RNase H2 activity three proteins are required [Rnh2Ap (Rnh201p), Ydr279p (Rnh202p) and Ylr154p (Rnh203p)]. Deletion of any one of the proteins or mutations in the catalytic site in Rnh2A leads to loss of RNase H2 activity. RNase H2 ia an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication.¡€0€ª€0€ €CDD¡€ €Ñ¢€0€0€ €‚Dpfam08616, SPA, Stabilization of polarity axis. Yeast AFI1 has been shown to interact with the outer plaque of the spindle pole body. In Aspergillus nidulans the protein member is necessary for stabilization of the polarity axes during septation. and in S. cerevisiae it functions as a polarisation-specific docking factor.¡€0€ª€0€ €CDD¡€ €Ã’¢€0€0€ €‚pfam08617, CGI-121, Kinase binding protein CGI-121. CGI-121 has been shown to bind to the p53-related protein kinase (PRPK). PRPK is a novel protein kinase which binds to and induces phosphorylation of the tumor suppressor protein p53. CGI-121 is part of a conserved protein complex, KEOPS. The KEOPS complex is involved in telomere uncapping and telomere elongation. Interestingly this family also include archaeal homologs, formerly in the DUF509 family. A structure for these proteins has been solved by structural genomics.¡€0€ª€0€ €CDD¡€ €Ó¢€0€0€ €‚kpfam08618, Opi1, Transcription factor Opi1. Opi1 is a leucine zipper containing yeast transcription factor that negatively regulates phospholipid biosynthesis. It represses the expression of several UAS(INO) cis acting element containing genes and its activity is mediated by phosphorylations catalyzed by protein kinase A, protein kinase C and casein kinase II.¡€0€ª€0€ €CDD¡€ €Ô¢€0€0€ €‚#pfam08619, Nha1_C, Alkali metal cation/H+ antiporter Nha1 C terminus. The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an execessive loss of ions and water. This domain is found with pfam00999.¡€0€ª€0€ €CDD¡€ €Õ¢€0€0€ €‚Wpfam08620, RPAP1_C, RPAP1-like, C-terminal. Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.¡€0€ª€0€ €CDD¡€ €Ö¢€0€0€ €‚;pfam08621, RPAP1_N, RPAP1-like, N-terminal. Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.¡€0€ª€0€ €CDD¡€ €×¢€0€0€ €Çpfam08622, Svf1, Svf1-like N-terminal lipocalin domain. Family of proteins that are involved in survival during oxidative stress. This entry corresponds to the N-terminal lipocalin domain of a pair.¡€0€ª€0€ €CDD¡€ €Ø¢€0€0€ €×pfam08623, TIP120, TATA-binding protein interacting (TIP20). TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription.¡€0€ª€0€ €CDD¡€ €Ù¢€0€0€ €‚Tpfam08624, CRC_subunit, Chromatin remodelling complex Rsc7/Swp82 subunit. This family has been identified as a subunit of chromatin remodelling complexes. Saccharomyces cerevisiae NPL6 and its paralogue SWP82 have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively.¡€0€ª€0€ €CDD¡€ €Ú¢€0€0€ €‚epfam08625, Utp13, Utp13 specific WD40 associated domain. Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome. Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end.¡€0€ª€0€ €CDD¡€ €Û¢€0€0€ €‚npfam08626, TRAPPC9-Trs120, Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit. This region is found at the N terminal of Saccharomyces cerevisiae Trs120 protein. Trs120 is a subunit of the multiprotein complex TRAPP (transport particle protein) which functions in ER to Golgi traffic. Trs120 is specific to the larger TRAPP complex, TRAPP II, along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way. It is likely that there is a complex function for TRAPP II in multiple pathways.¡€0€ª€0€ €CDD¡€ €Ãœ¢€0€0€ €´pfam08627, CRT-like, CRT-like, chloroquine-resistance transporter-like. This region is found in proteins related to Plasmodium falciparum chloroquine resistance transporter (CRT).¡€0€ª€0€ €CDD¡€ €â€0€0€ €½pfam08628, Nexin_C, Sorting nexin C terminal. This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787.¡€0€ª€0€ €CDD¡€ €Þ¢€0€0€ €‹pfam08629, PDE8, PDE8 phosphodiesterase. This region is found in members of the PDE8 phosphodiesterase family. It is found with pfam00233.¡€0€ª€0€ €CDD¡€ €\a¢€0€0€ €õpfam08630, Dfp1_Him1_M, Dfp1/Him1, central region. This is the middle regions described by Ogino et al. This region, together with the C-terminal zinc finger (pfam07535) is essential for the mitotic and kinase activation functions of Dfp1/Him1.¡€0€ª€0€ €CDD¡€ €ߢ€0€0€ €àpfam08631, SPO22, Meiosis protein SPO22/ZIP4 like. SPO22/ZIP4 in yeast is a meiosis specific protein involved in sporulation. It has been shown to regulate crossover distribution by promoting synaptonemal complex formation.¡€0€ª€0€ €CDD¡€ €ࢀ0€0€ €‚(pfam08632, Zds_C, Activator of mitotic machinery Cdc14 phosphatase activation C-term. This region of the Zds1 protein is critical for sporulation and has also been shown to suppress the calcium sensitivity of Zds1 deletions. The C-terminal motif is common to both Zds1 and Zds2 proteins, both of which are putative interactors of Cdc55 and are required for the completion of mitotic exit and cytokinesis. They both contribute to timely Cdc14 activation during mitotic exit and are required downstream of separase to facilitate nucleolar Cdc14 release.¡€0€ª€0€ €CDD¡€ €ᢀ0€0€ €pfam08633, Rox3, Rox3 mediator complex subunit. The mediator complex is part of the RNA polymerase II holoenzyme. Rox3 is a subunit of the mediator complex.¡€0€ª€0€ €CDD¡€ €⢀0€0€ €‚pfam08634, Pet127, Mitochondrial protein Pet127. Pet127 has been implicated in mitochondrial RNA stability and/or processing and is localized to the mitochondrial membrane. The Pet127 family is part of the PD-(D/E)XK nuclease superfamily including a full set of active site residues.¡€0€ª€0€ €CDD¡€ €㢀0€0€ €pfam08635, ox_reductase_C, Putative oxidoreductase C terminal. This is the C terminal of a family of putative oxidoreductases.¡€0€ª€0€ €CDD¡€ €ÉØ¢€0€0€ €apfam08636, Pkr1, ER protein Pkr1. Pkr1 has been identified as an ER protein of unknown function.¡€0€ª€0€ €CDD¡€ €䢀0€0€ €³pfam08637, NCA2, ATP synthase regulation protein NCA2. NCA2 has been shown to be required for the regulation of ATP synthase subunits Atp6p and Atp8p in Saccharomyces cerevisiae.¡€0€ª€0€ €CDD¡€ €Ã¥¢€0€0€ €‚²pfam08638, Med14, Mediator complex subunit MED14. Saccharomyces cerevisiae RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes and sporulation, required for glucose repression, HO repression, RME1 repression and sporulation. This subunit is also found in higher eukaryotes and Med14 is the agreed unified nomenclature for this subunit. Med14 is found in the tail region of Mediator.¡€0€ª€0€ €CDD¡€ €梀0€0€ €ªpfam08639, SLD3, DNA replication regulator SLD3. The SLD3 DNA replication regulator is required for loading and maintenance of Cdc45 on chromatin during DNA replication.¡€0€ª€0€ €CDD¡€ €碀0€0€ €Âpfam08640, U3_assoc_6, U3 small nucleolar RNA-associated protein 6. This is a family of U3 nucleolar RNA-associated proteins which are involved in nucleolar processing of pre-18S ribosomal RNA.¡€0€ª€0€ €CDD¡€ €袀0€0€ €™pfam08641, Mis14, Kinetochore protein Mis14 like. Mis14 is a kinetochore protein which is known to be recruited to kinetochores independently of CENP-A.¡€0€ª€0€ €CDD¡€ €颀0€0€ €|pfam08642, Rxt3, Histone deacetylation protein Rxt3. Rxt3 has been shown in yeast to be required for histone deacetylation.¡€0€ª€0€ €CDD¡€ €ꢀ0€0€ €¿pfam08643, DUF1776, Fungal family of unknown function (DUF1776). This is a fungal family of unknown function. One of the proteins in this family YSC83 has been localized to the mitochondria.¡€0€ª€0€ €CDD¡€ €뢀0€0€ €öpfam08644, SPT16, FACT complex subunit (SPT16/CDC68). Proteins in this family are subunits the FACT complex. The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin.¡€0€ª€0€ €CDD¡€ €좀0€0€ €×pfam08645, PNK3P, Polynucleotide kinase 3 phosphatase. Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin.¡€0€ª€0€ €CDD¡€ €í¢€0€0€ €÷pfam08646, Rep_fac-A_C, Replication factor-A C terminal domain. This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA.¡€0€ª€0€ €CDD¡€ €0€0€ €«pfam08647, BRE1, BRE1 E3 ubiquitin ligase. BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions.¡€0€ª€0€ €CDD¡€ €0€0€ €Èpfam08648, DUF1777, Protein of unknown function (DUF1777). This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins.¡€0€ª€0€ €CDD¡€ €ð¢€0€0€ €‚6pfam08649, DASH_Dad1, DASH complex subunit Dad1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules. Throughout the cell cycle Dad1 remains bound to kinetochores throughout the cell cycle and its association is dependent on the Mis6 and Mal2.¡€0€ª€0€ €CDD¡€ €ñ¢€0€0€ €‚ pfam08650, DASH_Dad4, DASH complex subunit Dad4. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.¡€0€ª€0€ €CDD¡€ €ò¢€0€0€ €‚ pfam08651, DASH_Duo1, DASH complex subunit Duo1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.¡€0€ª€0€ €CDD¡€ €ó¢€0€0€ €‚„pfam08652, RAI1, RAI1 like PD-(D/E)XK nuclease. RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z and binds to a nuclear exoribonuclease. It is required for 5.8S rRNA processing. Profile-profile comparison tools demonstrate this to be a PD-(D/E)XK nuclease, with a full set of canonical active site signature motifs characteristic to the PD-(D/E)XK nuclease superfamily.¡€0€ª€0€ €CDD¡€ €ô¢€0€0€ €‚¨pfam08653, DASH_Dam1, DASH complex subunit Dam1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules.¡€0€ª€0€ €CDD¡€ €õ¢€0€0€ €‚ pfam08654, DASH_Dad2, DASH complex subunit Dad2. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.¡€0€ª€0€ €CDD¡€ €ö¢€0€0€ €‚¨pfam08655, DASH_Ask1, DASH complex subunit Ask1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules.¡€0€ª€0€ €CDD¡€ €÷¢€0€0€ €‚ pfam08656, DASH_Dad3, DASH complex subunit Dad3. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.¡€0€ª€0€ €CDD¡€ €ø¢€0€0€ €‚ªpfam08657, DASH_Spc34, DASH complex subunit Spc34. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules.¡€0€ª€0€ €CDD¡€ €ù¢€0€0€ €^pfam08658, Rad54_N, Rad54 N terminal. This is the N terminal of the DNA repair protein Rad54.¡€0€ª€0€ €CDD¡€ €ú¢€0€0€ €‚pfam08659, KR, KR domain. This enzymatic domain is part of bacterial polyketide synthases and catalyzes the first step in the reductive modification of the beta-carbonyl centers in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.¡€0€ª€0€ €CDD¡€ €û¢€0€0€ €¾pfam08660, Alg14, Oligosaccharide biosynthesis protein Alg14 like. Alg14 is involved dolichol-linked oligosaccharide biosynthesis and anchors the catalytic subunit Alg13 to the ER membrane.¡€0€ª€0€ €CDD¡€ €ü¢€0€0€ €’pfam08661, Rep_fac-A_3, Replication factor A protein 3. Replication factor A is involved in eukaryotic DNA replication, recombination and repair.¡€0€ª€0€ €CDD¡€ €ý¢€0€0€ €pfam08662, eIF2A, Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.¡€0€ª€0€ €CDD¡€ €\¢€0€0€ €†pfam08663, HalX, HalX domain. HalX is a domain of unknown function, previously (mis)annotated as HoxA-like transcriptional regulator.¡€0€ª€0€ €CDD¡€ €þ¢€0€0€ €¢€0€0€ €spfam08823, PG_binding_2, Putative peptidoglycan binding domain. This family may be a peptidoglycan binding domain.¡€0€ª€0€ €CDD¡€ €äR¢€0€0€ €‚ pfam08824, Serine_rich, Serine rich protein interaction domain. This is a serine rich domain that is found in the docking protein p130(cas) (Crk-associated substrate). This domain folds into a four helix bundle which is associated with protein-protein interactions.¡€0€ª€0€ €CDD¡€ €Ä?¢€0€0€ €‚‚pfam08825, E2_bind, E2 binding domain. E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains.¡€0€ª€0€ €CDD¡€ €Ä@¢€0€0€ €¾pfam08826, DMPK_coil, DMPK coiled coil domain like. This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation.¡€0€ª€0€ €CDD¡€ €Ê”¢€0€0€ €µpfam08827, DUF1805, Domain of unknown function (DUF1805). This domain is found in bacteria and archaea and has an N terminal tetramerisation region that is composed of beta sheets.¡€0€ª€0€ €CDD¡€ €ÄA¢€0€0€ €‚?pfam08828, DSX_dimer, Doublesex dimerisation domain. Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure of this domain has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor.¡€0€ª€0€ €CDD¡€ €ÄB¢€0€0€ €‚¾pfam08829, AlphaC_N, Alpha C protein N terminal. The alpha C protein (ACP) is found in Streptococcus and acts as an invasin which plays a role in the internalisation and translocation of the organism across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. The N terminal of ACP is associated with virulence and forms a beta sandwich and a three helix bundle.¡€0€ª€0€ €CDD¡€ €ÄC¢€0€0€ €ãpfam08830, DUF1806, Protein of unknown function (DUF1806). This is a bacterial family of uncharacterized proteins. The structure of one of the proteins in this family has been solved and it adopts a beta barrel-like structure.¡€0€ª€0€ €CDD¡€ €ÄD¢€0€0€ €‚Èpfam08831, MHCassoc_trimer, Class II MHC-associated invariant chain trimerisation domain. The class II associated invariant chain peptide is required for folding and localization of MHC class II heterodimers. This domain is involved in trimerisation of the ectoderm and interferes with DM/class II binding. The trimeric protein forms a cylindrical shape which is thought to be important for interactions between the invariant chain and class II molecules.¡€0€ª€0€ €CDD¡€ €ÄE¢€0€0€ €ùpfam08832, SRC-1, Steroid receptor coactivator. This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.¡€0€ª€0€ €CDD¡€ €ÄF¢€0€0€ €‚pfam08833, Axin_b-cat_bind, Axin beta-catenin binding domain. This domain is found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex. It competes with the tumor suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin.¡€0€ª€0€ €CDD¡€ €ÄG¢€0€0€ €Üpfam08837, DUF1810, Protein of unknown function (DUF1810). This is a family of uncharacterized proteins. The structure of one of the members in this family has been solved and it adopts a mainly alpha helical structure.¡€0€ª€0€ €CDD¡€ €ÄH¢€0€0€ €‚;pfam08838, DUF1811, Protein of unknown function (DUF1811). This is a bacterial family of uncharacterized proteins. Some of the proteins are annotated as being transcriptional regulators. The structure of one of the proteins in this family has revealed a beta-barrel like structure with helix-turn-helix like motif.¡€0€ª€0€ €CDD¡€ €ÄI¢€0€0€ €‚Ypfam08839, CDT1, DNA replication factor CDT1 like. CDT1 is a component of the replication licensing system and promotes the loading of the mini-chromosome maintenance complex onto chromatin. Geminin is an inhibitor of CDT1 and prevents inappropriate re-initiation of replication on an already fired origin. This region of CDT1 binds to Geminin.¡€0€ª€0€ €CDD¡€ €ÄJ¢€0€0€ €Ïpfam08840, BAAT_C, BAAT / Acyl-CoA thioester hydrolase C terminal. This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT).¡€0€ª€0€ €CDD¡€ €ÄK¢€0€0€ €‚·pfam08841, DDR, Diol dehydratase reactivase ATPase-like domain. Diol dehydratase (DDH, EC:4.2.1.28) and its isofunctional homolog glycerol dehydratase (GDH, EC.4.2.1.30) are enzymes which catalyze the conversion of glycerol 1,2-propanediol, and 1,2-ethanediol to aldehydes. These reactions require coenzyme B12. Cleavage of the Co-C bond of coenzyme B12 by substrates or coenzyme analogues results in inactivation during which coenzyme B12 remains tightly bound to the apoenzyme. This family comprises of the large subunit of the diol dehydratase and glycerol dehydratase reactivating factors whose function is to reactivate the holoenzyme by exchange of a damaged cofactor for intact coenzyme.¡€0€ª€0€ €CDD¡€ €ÄL¢€0€0€ €‚ºpfam08842, Mfa2, Fimbrillin-A associated anchor proteins Mfa1 and Mfa2. This family of proteins may be lipoproteins principally from bacilli. They are between 300 and 400 residues. Many Bacteroides-like bacterial species, including Porphyromonas gingivalis, the causal agent of periodontal infection, carry at least two types of fimbriae, namely FimA and Mfa1 fimbriae, following the names of their major subunit proteins. Normally, FimA fimbriae are long filaments that are easily detached from cells, whereas Mfa1 fimbriae are short filaments that are tightly bound to cells; however, in the absence of Mfa2 protein, the Mfa1 fimbriae are also very long and are not attached. Mfa2 and Mfa1 are associated with each other in whole P. gingivalis cells to the extent that Mfa2 is located on the cell surface and probably associated with Mfa1 fimbriae in such a way that it anchors the Mfa1 fimbriae to the cell surface and regulates Mfa1 filament length.¡€0€ª€0€ €CDD¡€ €ÄM¢€0€0€ €‚7pfam08843, AbiEii, Nucleotidyl transferase AbiEii toxin, Type IV TA system. This family was recently identified as belonging to the nucleotidyltransferase superfamily. AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338.¡€0€ª€0€ €CDD¡€ €ÄN¢€0€0€ €—pfam08844, DUF1815, Domain of unknown function (DUF1815). This presumed domain is about 100 amino acids in length and is functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €]&¢€0€0€ €‚âpfam08845, SymE_toxin, Toxin SymE, type I toxin-antitoxin system. SymE (SOS-induced yjiW gene with similarity to MazE ) is an SOS-induced toxin. It inhibits cell growth, decreases protein synthesis and increases RNA degradation. It may play a role in the recycling of RNAs damaged under SOS response-inducing conditions. It is predicted to have an AbrB fold, similar to that of the antitoxin MazE. Its translation is repressed by the antisense RNA SymR, which acts as an antitoxin.¡€0€ª€0€ €CDD¡€ €ÄO¢€0€0€ €Âpfam08846, DUF1816, Domain of unknown function (DUF1816). Crocosphaera watsonii CpcD is associated with the pfam01383 domain suggesting this presumed domain could have a role in phycobilisomes.¡€0€ª€0€ €CDD¡€ €ÄP¢€0€0€ €spfam08847, DUF1817, Domain of unknown function (DUF1817). Members of this family are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ÄQ¢€0€0€ €¶pfam08848, DUF1818, Domain of unknown function (DUF1818). This presumed domain is found in a small family of cyanobacterial protein. These proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ÄR¢€0€0€ €«pfam08849, DUF1819, Putative inner membrane protein (DUF1819). These proteins are functionally uncharacterized. Several are annotated as putative inner membrane proteins.¡€0€ª€0€ €CDD¡€ €ÄS¢€0€0€ €pfam08850, DUF1820, Domain of unknown function (DUF1820). This family includes small functionally uncharacterized proteins around 100 amino acids in length.¡€0€ª€0€ €CDD¡€ €ÄT¢€0€0€ €upfam08852, DUF1822, Protein of unknown function (DUF1822). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ÄU¢€0€0€ €ppfam08853, DUF1823, Domain of unknown function (DUF1823). This presumed domain is functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ÄV¢€0€0€ €Špfam08854, DUF1824, Domain of unknown function (DUF1824). This uncharacterized family of proteins are principally found in cyanobacteria.¡€0€ª€0€ €CDD¡€ €ÄW¢€0€0€ €Špfam08855, DUF1825, Domain of unknown function (DUF1825). This uncharacterized family of proteins are principally found in cyanobacteria.¡€0€ª€0€ €CDD¡€ €]0¢€0€0€ €lpfam08856, DUF1826, Protein of unknown function (DUF1826). These proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ÄX¢€0€0€ €­pfam08857, ParBc_2, Putative ParB-like nuclease. This domain is probably distantly related to pfam02195. Suggesting these uncharacterized proteins have a nuclease function.¡€0€ª€0€ €CDD¡€ €ÄY¢€0€0€ €ípfam08858, IDEAL, IDEAL domain. This short domain is found at the C-terminus of proteins in the UPF0302 family. The domain is named after the sequence of the most conserved region in some members. The function of this domain is unknown.¡€0€ª€0€ €CDD¡€ €ÄZ¢€0€0€ €æpfam08859, DGC, DGC domain. This domain appears to be a zinc binding domain from the conservation of four potential chelating cysteines. The domain is named after a conserved central motif. The function of this domain is unknown.¡€0€ª€0€ €CDD¡€ €Ä[¢€0€0€ €fpfam08860, DUF1827, Domain of unknown function (DUF1827). This presumed domain has no known function.¡€0€ª€0€ €CDD¡€ €Ä\¢€0€0€ €npfam08861, DUF1828, Domain of unknown function DUF1828. This presumed domain is functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä]¢€0€0€ €ppfam08862, DUF1829, Domain of unknown function DUF1829. This short domain is usually associated with pfam08861.¡€0€ª€0€ €CDD¡€ €Ä^¢€0€0€ €ìpfam08863, YolD, YolD-like protein. Members of this family are functionally uncharacterized. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from gram-negative bacteria.¡€0€ª€0€ €CDD¡€ €Ä_¢€0€0€ €fpfam08864, UPF0302, UPF0302 domain. This family is known as UPF0302. It is currently uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä`¢€0€0€ €ypfam08865, DUF1830, Domain of unknown function (DUF1830). This family of short proteins is functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Äa¢€0€0€ €‚pfam08866, DUF1831, Putative amino acid metabolism. Solution of the structure of the Lactobacillus plantarum protein from this family has indicated a potential new fold with remote similarities to TBP-like (TATA-binding protein) structures. This similarity, in combination with genomic context analysis, leads us to propose an involvement in amino-acid metabolism. The potentially novel fold is an alpha + beta fold comprising two beta sheets packed against a single helix. The enzyme is present in the cytosol.¡€0€ª€0€ €CDD¡€ €Äb¢€0€0€ €„pfam08867, FRG, FRG domain. This presumed domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Äc¢€0€0€ €ypfam08868, YugN, YugN-like family. This family of proteins related to B. subtilis YugN are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Äd¢€0€0€ €ápfam08869, XisI, XisI protein. The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required.¡€0€ª€0€ €CDD¡€ €Äe¢€0€0€ €tpfam08870, DUF1832, Domain of unknown function (DUF1832). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Äf¢€0€0€ €•pfam08872, KGK, KGK domain. This presumed domain is found in one or two copies in cyanobacterial proteins. It is named after a short sequence motif.¡€0€ª€0€ €CDD¡€ €Äg¢€0€0€ €¬pfam08873, DUF1834, Domain of unknown function (DUF1834). This family of proteins are functionally uncharacterized. One member is the Gp37 protein from the FluMu prophage.¡€0€ª€0€ €CDD¡€ €Äh¢€0€0€ €tpfam08874, DUF1835, Domain of unknown function (DUF1835). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Äi¢€0€0€ €‚4pfam08875, DUF1833, Domain of unknown function (DUF1833). This family of proteins are functionally uncharacterized and are predicted to adopt an all-beta fold. They are often found in gene neighborhoods containing genes for an NlpC peptidase and a Ubiquitin domain predicted to be involved in tail assembly.¡€0€ª€0€ €CDD¡€ €]C¢€0€0€ €tpfam08876, DUF1836, Domain of unknown function (DUF1836). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Äj¢€0€0€ €ƒpfam08877, MepB, MepB protein. MepB is a functionally uncharacterized protein in the mepRAB gene cluster of Staphylococcus aureus.¡€0€ª€0€ €CDD¡€ €Äk¢€0€0€ €tpfam08878, DUF1837, Domain of unknown function (DUF1837). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Äl¢€0€0€ €ùpfam08879, WRC, WRC. The WRC domain, named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localization signal and a zinc-finger motif (C3H). It is suggested that the WRC domain functions in DNA binding.¡€0€ª€0€ €CDD¡€ €Äm¢€0€0€ €‚2pfam08880, QLQ, QLQ. The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions.¡€0€ª€0€ €CDD¡€ €Än¢€0€0€ €Ëpfam08881, CVNH, CVNH domain. CyanoVirin-N Homology domains are found in the sugar-binding antiviral protein cyanovirin-N (CVN) as well as filamentous ascomycetes and in the fern Ceratopteris richardii.¡€0€ª€0€ €CDD¡€ €Äo¢€0€0€ €Ìpfam08882, Acetone_carb_G, Acetone carboxylase gamma subunit. Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalyzing the condensation of acetone and CO(2) to form acetoacetate.¡€0€ª€0€ €CDD¡€ €Äp¢€0€0€ €‚6pfam08883, DOPA_dioxygen, Dopa 4,5-dioxygenase family. This family of proteins are related to a DOPA 4,5-dioxygenase that is involved in synthesis of betalain. DOPA-dioxygenase is the key enzyme involved in betalain biosynthesis. It converts 3,4-dihydroxyphenylalanine to betalamic acid, a yellow chromophore.¡€0€ª€0€ €CDD¡€ €Äq¢€0€0€ €‚(pfam08884, Flagellin_D3, Flagellin D3 domain. This domain is found in the central portion bacterial flagellin FliC. The domain contains a structural motif called a beta-folium fold. Although no specific function is assigned to this domain its deletion leads to a reduction in filament stability.¡€0€ª€0€ €CDD¡€ €Är¢€0€0€ €‚pfam08885, GSCFA, GSCFA family. This family of proteins are functionally uncharacterized. They have been named GSCFA after a highly conserved N-terminal motif in the alignment. Distant similarity to the pfam00657 lipases suggests these proteins are likely to be enzymes.¡€0€ª€0€ €CDD¡€ €Äs¢€0€0€ €‚ïpfam08886, GshA, Glutamate-cysteine ligase. This is a rare family of glutamate--cysteine ligases, EC:6.3.2.2, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase. The structure of this family has been solved, and is similar to that of human glutathione synthetase and very different to gamma-glutamylcysteine synthetase from Escherichia coli.¡€0€ª€0€ €CDD¡€ €Ät¢€0€0€ €—pfam08887, GAD-like, GAD-like domain. This domain is functionally uncharacterized, but it appears to be distantly related to the GAD domain pfam02938.¡€0€ª€0€ €CDD¡€ €Äu¢€0€0€ €‚;pfam08888, HopJ, HopJ type III effector protein. Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system. The proteins in this family are called HopJ after the original member HopPmaJ.¡€0€ª€0€ €CDD¡€ €Äv¢€0€0€ €‚!pfam08889, WbqC, WbqC-like protein family. This family of proteins are functionally uncharacterized. However it is found in an O-antigen gene cluster in E. coli and other bacteria suggesting a role in O-antigen production. Feng et al. suggest that wbnG may code for a glycine transferase.¡€0€ª€0€ €CDD¡€ €Äw¢€0€0€ €×pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC. This is a family of phage tail assembly chaperone proteins, TACs, from Gram-positive bacteriophages, in particular PBSX from Firmicutes.¡€0€ª€0€ €CDD¡€ €Äx¢€0€0€ €’pfam08891, YfcL, YfcL protein. This family of proteins are functionally uncharacterized. THey are related to the short YfcL protein from E. coli.¡€0€ª€0€ €CDD¡€ €Äy¢€0€0€ €ïpfam08892, YqcI_YcgG, YqcI/YcgG family. This family of proteins are functionally uncharacterized. The family include YqcI and YcgG from B. subtilis. The alignment contains a conserved FPC motif at the N-terminus and CPF at the C-terminus.¡€0€ª€0€ €CDD¡€ €Äz¢€0€0€ €tpfam08893, DUF1839, Domain of unknown function (DUF1839). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä{¢€0€0€ €upfam08894, DUF1838, Protein of unknown function (DUF1838). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä|¢€0€0€ €tpfam08895, DUF1840, Domain of unknown function (DUF1840). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä}¢€0€0€ €”pfam08896, DUF1842, Domain of unknown function (DUF1842). This domain is found at the N-terminus of proteins that are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä~¢€0€0€ €tpfam08897, DUF1841, Domain of unknown function (DUF1841). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €‚ pfam08898, DUF1843, Domain of unknown function (DUF1843). This domain is found at the C-terminus of a family of proteins that are functionally uncharacterized. The presumed domain is about 60 amino acid residues in length and is found independently in some proteins.¡€0€ª€0€ €CDD¡€ €Ä€¢€0€0€ €tpfam08899, DUF1844, Domain of unknown function (DUF1844). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €tpfam08900, DUF1845, Domain of unknown function (DUF1845). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ä‚¢€0€0€ €¾pfam08901, DUF1847, Protein of unknown function (DUF1847). This family of proteins are functionally uncharacterized. THey contain 4 N-terminal cysteines that may form a zinc binding domain.¡€0€ª€0€ €CDD¡€ €ă¢€0€0€ €õpfam08902, DUF1848, Domain of unknown function (DUF1848). This family of proteins are functionally uncharacterized. The C-terminus contains a cluster of cysteines that are similar to the iron-sulfur cluster found at the N-terminus of pfam04055.¡€0€ª€0€ €CDD¡€ €Ä„¢€0€0€ €ïpfam08903, DUF1846, Domain of unknown function (DUF1846). This family of proteins are functionally uncharacterized. Some members of the family are annotated as ATP-dependent peptidases. However, we can find no support for this annotation.¡€0€ª€0€ €CDD¡€ €Ä…¢€0€0€ €tpfam08904, DUF1849, Domain of unknown function (DUF1849). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ć¢€0€0€ €Þpfam08905, DUF1850, Domain of unknown function (DUF1850). This family of proteins are functionally uncharacterized. Some members of this family appear to be misannotated as RocC an amino acid transporter from B. subtilis.¡€0€ª€0€ €CDD¡€ €ć¢€0€0€ €¡pfam08906, DUF1851, Domain of unknown function (DUF1851). This domain is found at the C-terminus of a variety of proteins that are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ĉ¢€0€0€ €tpfam08907, DUF1853, Domain of unknown function (DUF1853). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ĉ¢€0€0€ €tpfam08908, DUF1852, Domain of unknown function (DUF1852). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ÄŠ¢€0€0€ €ñpfam08909, DUF1854, Domain of unknown function (DUF1854). This potential domain is functionally uncharacterized. It is found at the C-terminus of a number of ATP transporter proteins suggesting this domain may be involved in ligand binding.¡€0€ª€0€ €CDD¡€ €Ä‹¢€0€0€ €ƒpfam08910, Aida_N, Aida N-terminus. This is the N-terminal domain of the axin interactor, dorsalization-associated protein family.¡€0€ª€0€ €CDD¡€ €ÄŒ¢€0€0€ €‚apfam08911, NUP50, NUP50 (Nucleoporin 50 kDa). Nucleoporin 50 kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localization signals from importin-alpha.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €‚ pfam08912, Rho_Binding, Rho Binding. Rho Binding Domain is responsible for the recognition and binding of Rho binding domain-containing proteins (such as ROCK) to Rho, resulting in activation of the GTPase which in turn modulates the phosphorylation of various signalling proteins. This domain is within an amphipathic alpha-helical coiled-coil and interacts with Rho through predominantly hydrophobic interactions.¡€0€ª€0€ €CDD¡€ €ÄŽ¢€0€0€ €‚8pfam08913, VBS, Vinculin Binding Site. Vinculin binding sites are predominantly found in talin and talin-like molecules, enabling binding of vinculin to talin, stabilizing integrin-mediated cell-matrix junctions. Talin, in turn, links integrins to the actin cytoskeleton. The consensus sequence for Vinculin binding sites is LxxAAxxVAxxVxxLIxxA, with a secondary structure prediction of four amphipathic helices. The hydrophobic residues that define the VBS are themselves 'masked' and are buried in the core of a series of helical bundles that make up the talin rod.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €‚apfam08914, Myb_DNA-bind_2, Rap1 Myb domain. The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function of this domain is unclear: it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions.¡€0€ª€0€ €CDD¡€ €]j¢€0€0€ €‚_pfam08915, tRNA-Thr_ED, Archaea-specific editing domain of threonyl-tRNA synthetase. Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €‚pfam08916, Phe_ZIP, Phenylalanine zipper. The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS, SH2-B and Lnk.¡€0€ª€0€ €CDD¡€ €Ä‘¢€0€0€ €‚öpfam08917, ecTbetaR2, Transforming growth factor beta receptor 2 ectodomain. The Transforming growth factor beta receptor 2 ectodomain is a compact fold consisting of nine beta-strands and a single helix stabilized by a network of six intra strand disulphide bonds. The folding topology includes a central five-stranded antiparallel beta-sheet, eight-residues long at its centre, covered by a second layer consisting of two segments of two-stranded antiparallel beta-sheets (beta1-beta4, beta3-beta9).¡€0€ª€0€ €CDD¡€ €Ä’¢€0€0€ €‚ôpfam08918, PhoQ_Sensor, PhoQ Sensor. The PhoQ Sensor is required for the virulence of various Gram-negative bacteria by allowing interaction of PhoPQ with the intracellular membrane, resulting in remodelling of the bacterial cell surface and subsequent bacterial resistance to host antimicrobial peptides. The domain contains a major flat acidic surface, which binds to at least 3 calcium ions, neutralising the domain's negative charge and allowing interaction with the negatively charged membrane.¡€0€ª€0€ €CDD¡€ €Ä“¢€0€0€ €‚dpfam08919, F_actin_bind, F-actin binding. The F-actin binding domain forms a compact bundle of four antiparallel alpha-helices, which are arranged in a left-handed topology. Binding of F-actin to the F-actin binding domain may result in cytoplasmic retention and subcellular distribution of the protein, as well as possible inhibition of protein function.¡€0€ª€0€ €CDD¡€ €Ä”¢€0€0€ €‚Gpfam08920, SF3b1, Splicing factor 3B subunit 1. This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly.¡€0€ª€0€ €CDD¡€ €Ä•¢€0€0€ €|pfam08921, DUF1904, Domain of unknown function (DUF1904). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä–¢€0€0€ €|pfam08922, DUF1905, Domain of unknown function (DUF1905). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä—¢€0€0€ €‚spfam08923, MAPKK1_Int, Mitogen-activated protein kinase kinase 1 interacting. Mitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer.¡€0€ª€0€ €CDD¡€ €Ę¢€0€0€ €Œpfam08924, DUF1906, Domain of unknown function (DUF1906). This domain is found in a set of uncharacterized hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä™¢€0€0€ €‚)pfam08925, DUF1907, Domain of Unknown Function (DUF1907). The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an HxHxxxxxxxxxH motif that coordinates a zinc ion, and an acetate anion at a site that likely supports the enzymatic activity of an ester hydrolase.¡€0€ª€0€ €CDD¡€ €Äš¢€0€0€ €ˆpfam08926, DUF1908, Domain of unknown function (DUF1908). This domain is found in a set of hypothetical/structural eukaryotic proteins.¡€0€ª€0€ €CDD¡€ €Ä›¢€0€0€ €|pfam08928, DUF1910, Domain of unknown function (DUF1910). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Äœ¢€0€0€ €|pfam08929, DUF1911, Domain of unknown function (DUF1911). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €Œpfam08930, DUF1912, Domain of unknown function (DUF1912). This domain has no known function. It is found in various Streptococcal proteins.¡€0€ª€0€ €CDD¡€ €]y¢€0€0€ €‚tpfam08931, Caudo_bapla_RBP, Receptor-binding protein of phage tail base-plate Siphoviridae, head. Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein species, shoulders, neck, and head, that form the phage tail base-plate. In the overall structure this head domain exists as six trimers, and is necessary for specific recognition of the receptors at the host cell surface. Siphoviridae are the P2-like Caudovirales of Lactococcus. This family now includes DUF1914. Family Baseplate, pfam16774, is the ORF15 or shoulder component of the base-plate complex.¡€0€ª€0€ €CDD¡€ €]z¢€0€0€ € pfam08933, DUF1864, Domain of unknown function (DUF1864). This domain has no known function. It is found in various hypothetical and conserved domain proteins.¡€0€ª€0€ €CDD¡€ €ä‹¢€0€0€ €‚®pfam08934, Rb_C, Rb C-terminal domain. The Rb C-terminal domain is required for high-affinity binding to E2F-DP complexes and for maximal repression of E2F-responsive promoters, thereby acting as a growth suppressor by blocking the G1-S transition of the cell cycle. This domain has a strand-loop-helix structure, which directly interacts with both E2F1 and DP1, followed by a tail segment that lacks regular secondary structure.¡€0€ª€0€ €CDD¡€ €Äž¢€0€0€ €‚êpfam08935, VP4_2, Viral protein VP4 subunit. This domain is predominantly found in viral proteins from the family Picornaviridae. It is VP4 of the viral polyprotein which, in poliovirus, is part of the capsid that consists of 60 copies each of four proteins VP1, VP2, VP3, and VP4 arranged on an icosahedral lattice. VP4 is on the inside and differs from the others in being small, myristoylated and having an extended structure. Productive infection involves the externalisation of the VP4, which is cleaved from the rest, along with the N-terminus of VP1. There thus seem to be three stages of the virus, ie a multi-step process for cell entry involving RNA translocation through a membrane channel formed by the externalised N termini of VP1.¡€0€ª€0€ €CDD¡€ €]|¢€0€0€ €‚êpfam08936, CsoSCA, Carboxysome Shell Carbonic Anhydrase. Carboxysome Shell Carbonic Anhydrase is a bacterial carbonic anhydrase localized in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains, these being: (1) an N-terminal domain composed primarily of four alpha-helices; (2) a catalytic domain containing a tightly bound zinc ion and (3) a C-terminal domain with weak structural similarity to the catalytic domain.¡€0€ª€0€ €CDD¡€ €ÄŸ¢€0€0€ €‚·pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863). This domain adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein. This domain is similar to the TIR domain.¡€0€ª€0€ €CDD¡€ €Ä ¢€0€0€ €¢pfam08938, HBS1_N, HBS1 N-terminus. This domain is found at the N-terminus of HBS1 proteins. It interacts with the ribosomal protein rpS3 at the mRNA entry site.¡€0€ª€0€ €CDD¡€ €Ä¡¢€0€0€ €¤pfam08939, DUF1917, Domain of unknown function (DUF1917). This domain is found in various hypothetical and basophilic leukaemia proteins. It has no known function.¡€0€ª€0€ €CDD¡€ €Ä¢¢€0€0€ €pfam08940, DUF1918, Domain of unknown function (DUF1918). This domain, found in various hypothetical bacterial proteins, has no known function.¡€0€ª€0€ €CDD¡€ €Ä£¢€0€0€ €mpfam08941, USP8_interact, USP8 interacting. This domain interacts with the UBP deubiquitinating enzyme USP8.¡€0€ª€0€ €CDD¡€ €Ĥ¢€0€0€ €¢pfam08942, DUF1919, Domain of unknown function (DUF1919). This domain has no known function. It is found in various hypothetical and putative bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä¥¢€0€0€ €‚pfam08943, CsiD, CsiD. This family consists of various bacterial proteins pertaining to the non-haem Fe(II)-dependent oxygenase family. Exact function is unknown, but a putative role includes involvement in the control of utilisation of gamma-aminobutyric acid.¡€0€ª€0€ €CDD¡€ €Ħ¢€0€0€ €‚gpfam08944, p47_phox_C, NADPH oxidase subunit p47Phox, C terminal domain. The C terminal domain of the phagocyte NADPH oxidase subunit p47Phox contains conserved PxxP motifs that allow binding to SH3 domains, with subsequent activation of the NADPH oxidase, and generation of superoxide, which plays a crucial role in host defense against microbial infection.¡€0€ª€0€ €CDD¡€ €ħ¢€0€0€ €ýpfam08945, Bclx_interact, Bcl-x interacting, BH3 domain. This domain is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11. This domain is also known as the BH3 domain between residues 146 and 161.¡€0€ª€0€ €CDD¡€ €Ĩ¢€0€0€ €‚Œpfam08946, Osmo_CC, Osmosensory transporter coiled coil. The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function.¡€0€ª€0€ €CDD¡€ €Ä©¢€0€0€ €‚®pfam08947, BPS, BPS (Between PH and SH2). The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor.¡€0€ª€0€ €CDD¡€ €Ī¢€0€0€ €ªpfam08948, DUF1859, Domain of unknown function (DUF1859). This domain has no known function. It is predominantly found in the N-terminus of bacteriophage spike proteins.¡€0€ª€0€ €CDD¡€ €]‰¢€0€0€ €ªpfam08949, DUF1860, Domain of unknown function (DUF1860). This domain has no known function. It is predominantly found in the C-terminus of bacteriophage spike proteins.¡€0€ª€0€ €CDD¡€ €Ä«¢€0€0€ € pfam08950, DUF1861, Protein of unknown function (DUF1861). This hypothetical protein, found in bacteria and in the eukaryote Leishmania, has no known function.¡€0€ª€0€ €CDD¡€ €Ĭ¢€0€0€ €‚Òpfam08951, EntA_Immun, Enterocin A Immunity. Gram-positive lactobacilli produce bacteriocins to kill closely-related competitor species. To protect themselves from the bacteriocidal activity of this molecule they co-express an immunity protein (for discussion of this operon see Bacteriocin_IIc pfam10439). The immunity protein structure is a soluble, cytoplasmic, antiparallel four alpha-helical globular bundle with a fifth, more flexible and more divergent C-terminal helical hair-pin. The C-terminal hair-pin recognizes the C-terminus of the producer bacteriocin and this interaction is sufficient to dis-orient the bacteriocin within the membrane and close up the permeabilising pore that on its own the bacteriocin creates. These immunity proteins interact in the same way with other bacteriocins, family Bacteriocin_II, pfam01721. Since many enterococci can produce more than one bacteriocin it seems likely that the whole operon can be carried on transferable plasmids.¡€0€ª€0€ €CDD¡€ €Ä­¢€0€0€ €upfam08952, DUF1866, Domain of unknown function (DUF1866). This domain, found in Synaptojanin, has no known function.¡€0€ª€0€ €CDD¡€ €]¢€0€0€ €Œpfam08953, DUF1899, Domain of unknown function (DUF1899). This set of domains is found in various eukaryotic proteins. Function is unknown.¡€0€ª€0€ €CDD¡€ €Ä®¢€0€0€ €õpfam08954, Trimer_CC, Trimerisation motif. This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It appears to have the function of stabilizing the topology of short coiled-coils in proteins.¡€0€ª€0€ €CDD¡€ €]¢€0€0€ €Øpfam08955, BofC_C, BofC C-terminal domain. The C-terminal domain of the bacterial protein 'bypass of forespore C' contains a three-stranded beta-sheet and three alpha-helices. Its exact function is, as yet, unknown.¡€0€ª€0€ €CDD¡€ €į¢€0€0€ €|pfam08956, DUF1869, Domain of unknown function (DUF1869). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä°¢€0€0€ €™pfam08958, DUF1871, Domain of unknown function (DUF1871). This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus.¡€0€ª€0€ €CDD¡€ €]’¢€0€0€ €†pfam08960, DUF1874, Domain of unknown function (DUF1874). This domain is found in a set of hypothetical viral and bacterial proteins.¡€0€ª€0€ €CDD¡€ €ı¢€0€0€ €‚¡pfam08961, NRBF2, Nuclear receptor-binding factor 2, autophagy regulator. NRBF2 plays an essential role in autophagy, the cellular pathway that degrades long-lived proteins and other cytoplasmic contents through lysosomes. NRBF2 binds Atg14L - a Beclin-binding protein - directly via the MIT domain and enhances Atg14L-linked Vps34 kinase (a class III phosphatidylinositol-3 kinase) activity and autophagy induction.¡€0€ª€0€ €CDD¡€ €IJ¢€0€0€ €|pfam08962, DUF1876, Domain of unknown function (DUF1876). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €ij¢€0€0€ €}pfam08963, DUF1878, Protein of unknown function (DUF1878). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä´¢€0€0€ €þpfam08964, Crystall_3, Beta/Gamma crystallin. This family of beta/gamma crystallins includes the N-terminal domain of Dictyostelium discoideum Calcium-dependent cell adhesion molecule 1, which mediates cell-cell adhesion through homophilic interactions.¡€0€ª€0€ €CDD¡€ €ĵ¢€0€0€ €Ãpfam08965, DUF1870, Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins. It contains a helix-turn-helix domain so may be a DNA-binding protein.¡€0€ª€0€ €CDD¡€ €]˜¢€0€0€ €|pfam08966, DUF1882, Domain of unknown function (DUF1882). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ķ¢€0€0€ €³pfam08967, DUF1884, Domain of unknown function (DUF1884). This domain is found in a set of hypothetical bacterial proteins. It shows similarity to the N-terminus of ATP-synthase.¡€0€ª€0€ €CDD¡€ €]š¢€0€0€ €pfam08968, DUF1885, Domain of unknown function (DUF1885). This domain is found in a set of hypothetical proteins produced by bacteria of the Bacillus genus.¡€0€ª€0€ €CDD¡€ €Ä·¢€0€0€ €Ópfam08969, USP8_dimer, USP8 dimerisation domain. This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It forms a five helical bundle that dimerizes.¡€0€ª€0€ €CDD¡€ €ĸ¢€0€0€ €‚fpfam08970, Sda, Sporulation inhibitor A. Members of this protein family contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilized by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A).¡€0€ª€0€ €CDD¡€ €Ĺ¢€0€0€ €‚-pfam08971, GlgS, Glycogen synthesis protein. Members of this family are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them.¡€0€ª€0€ €CDD¡€ €]ž¢€0€0€ €Üpfam08972, DUF1902, Domain of unknown function (DUF1902). Members of this family of prokaryotic proteins adopt a fold consisting of one alpha-helix and four beta-strands. Their function has not, as yet, been elucidated.¡€0€ª€0€ €CDD¡€ €ĺ¢€0€0€ €‚mpfam08973, TM1506, Domain of unknown function (DUF1893). A member of the deaminase fold that binds an unknown ligand in the crystal structure. The protein is ADP-ribosylated at a conserved aspartate. Contextual analysis suggests that the domain is likely to bind NAD or ADP ribose either to sense redox states or to function as a regulatory ADP ribosyltransferase.¡€0€ª€0€ €CDD¡€ €Ä»¢€0€0€ €|pfam08974, DUF1877, Domain of unknown function (DUF1877). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €ļ¢€0€0€ €‚%pfam08975, 2H-phosphodiest, Domain of unknown function (DUF1868). This group of 2H-phosphodiesterases comprises a single family typified by the protein mlr3352 from M.loti. Members are also present in various alpha-proteobacteria, Synechocystis, Streptococcus and Chilo iridescent virus. The presence of a member of this predominantly bacterial group in a large eukaryotic DNA virus represents a potential case of horizontal transfer from a bacterial source into a virus. Several proteins of bacterial origin have been noticed in the insect viruses (L.M.Iyer, E.V.Koonin and L.Aravind, unpublished observations and these appear to have been acquired from endo-symbiotic or parasitic bacteria that share the same host cells with the viruses. Presence of 2H proteins in the proteomes of large DNA viruses (e.g. T4 57B protein and the Fowl-pox virus FPV025) may point to some role for these proteins in regulating the viral tRNA metabolism. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family.¡€0€ª€0€ €CDD¡€ €]¢¢€0€0€ €bpfam08976, EF-hand_11, EF-hand domain. This domain is found predominantly in DJ binding proteins.¡€0€ª€0€ €CDD¡€ €Ľ¢€0€0€ €‚ pfam08977, BOFC_N, Bypass of Forespore C, N terminal. The N-terminal domain of 'bypass of forespore C' is composed of a four-stranded beta-sheet covered by an alpha-helix. The beta-sheet has a beta2-beta1-beta4-beta3 topology, where strands beta1 and beta2 and strands beta3 and beta4 are connected by beta-turns, whereas strands beta2 and beta3 are joined by an alpha-helix that runs across one face of the beta-sheet. This domain is similar to the third immunoglobulin G-binding domain of protein G from Streptococcus, the latter belonging to a large and diverse group of cell surface-associated proteins that bind to immunoglobulins. It has been hypothesized that this domain may be a mediator of protein-protein interactions involved in proteolytic events at the cell surface.¡€0€ª€0€ €CDD¡€ €]¤¢€0€0€ €„pfam08978, Reoviridae_Vp9, Reoviridae VP9. This domain is found in various VP9 viral outer-coat proteins. It has no known function.¡€0€ª€0€ €CDD¡€ €Ë(¢€0€0€ €‚Upfam08979, DUF1894, Domain of unknown function (DUF1894). Members of this family have an important role in methanogenesis. They assume an alpha-beta globular structure consisting of six beta-strands and three alpha-helices forming the secondary structural topological arrangement of alpha1-beta1-alpha2-beta2-beta3-beta4-beta5-beta6-alpha3.¡€0€ª€0€ €CDD¡€ €ľ¢€0€0€ €|pfam08980, DUF1883, Domain of unknown function (DUF1883). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä¿¢€0€0€ € pfam08982, DUF1857, Domain of unknown function (DUF1857). This domain has no known function. It is found in various hypothetical bacterial and fungal proteins.¡€0€ª€0€ €CDD¡€ €ÄÀ¢€0€0€ €¥pfam08983, DUF1856, Domain of unknown function (DUF1856). This domain has no known function. It is found in the C-terminal segment of various vasopressin receptors.¡€0€ª€0€ €CDD¡€ €ÄÁ¢€0€0€ €•pfam08984, DUF1858, Domain of unknown function (DUF1858). This domain has no known function. It is found in various hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä¢€0€0€ €œpfam08985, DP-EP, DP-EP family. The DP-EP family of proteins, formerly known as DUF1888 have been shown to catalyze a cleavage of an internal peptide bond.¡€0€ª€0€ €CDD¡€ €Äâ€0€0€ €|pfam08986, DUF1889, Domain of unknown function (DUF1889). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €ÄÄ¢€0€0€ €‚Tpfam08987, DUF1892, Protein of unknown function (DUF1892). Members of this family, that are synthesized by Saccharomycetes, adopt a structure consisting of a four-stranded beta-sheet, with strand order beta2-beta1-beta4-beta3, and two alpha-helices, with an overall topology of beta-beta-alpha-beta-beta-alpha. They have no known function.¡€0€ª€0€ €CDD¡€ €ÄÅ¢€0€0€ €‚ìpfam08988, T3SS_needle_E, Type III secretion system, cytoplasmic E component of needle. T3SS_needle_E is a family of proteins from the operon that builds and controls the needle of the injection system of type III secretion. The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The family is cytoplasmic and may help to stabilize and prevent early polymerization of the needle-protein F.¡€0€ª€0€ €CDD¡€ €]­¢€0€0€ €|pfam08989, DUF1896, Domain of unknown function (DUF1896). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €]®¢€0€0€ €‚bpfam08990, Docking, Erythronolide synthase docking. The N terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerize to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function.¡€0€ª€0€ €CDD¡€ €ÄÆ¢€0€0€ €‚pfam08991, MTCP1, Mature-T-Cell Proliferation I type. Members of this family adopt a coiled coil structure, with two antiparallel alpha-helices that are tightly strapped together by two disulfide bridges at each end. The protein sequence shows a cysteine motif, required for the stabilisation of the coiled-coil-like structure. Additional inter-helix hydrophobic contacts impart stability to this scaffold. The precise function of this eukaryotic domain is, as yet, unknown. MTCP1 is found in mitochondria. Mature-T-Cell Proliferation) is the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype.¡€0€ª€0€ €CDD¡€ €ÄÇ¢€0€0€ €‚“pfam08992, QH-AmDH_gamma, Quinohemoprotein amine dehydrogenase, gamma subunit. Members of this family contain a cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone, which is required for catalysis of the oxidative deamination of a wide range of aliphatic and aromatic amines. The domain assumes a globular secondary structure, with two short alpha-helices having many turns and bends.¡€0€ª€0€ €CDD¡€ €ÄÈ¢€0€0€ €‚žpfam08993, T4_Gp59_N, T4 gene Gp59 loader of gp41 DNA helicase. Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the N-terminal domain that consists of six alpha-helices linked by loop segments and short turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. This domain has structural similarity to members of the high-mobility-group (HMG) family of DNA minor groove binding proteins including rat HMG1A and lymphoid enhancer-binding factor, and is required for binding of the helicase to the DNA minor groove.¡€0€ª€0€ €CDD¡€ €]²¢€0€0€ €‚ôpfam08994, T4_Gp59_C, T4 gene Gp59 loader of gp41 DNA helicase C-term. Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the C-terminal domain that consists of seven alpha-helices with short intervening loops and turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. The hydrophobic region on the 'bottom' surface of the domain near the C-terminal helix binds the leading strand DNA, whilst the hydrophobic region on the 'top' surface of the domain lies between the two arms of the fork DNA, allowing for T4 gene 41 helicase binding and assembly into a hexameric complex around the lagging strand.¡€0€ª€0€ €CDD¡€ €]³¢€0€0€ €‚npfam08995, NIP_1, Necrosis inducing protein-1. Necrosis inducing protein-1, a fungal avirulence protein produced by plants, consists of two parts containing beta-sheets of two and three anti-parallel strands, respectively. Five intramolecular disulfide bonds, stabilize these parts and their position with respect to each other, providing a high level of stability.¡€0€ª€0€ €CDD¡€ €Ë9¢€0€0€ €‚lpfam08996, zf-DNA_Pol, DNA Polymerase alpha zinc finger. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain.¡€0€ª€0€ €CDD¡€ €ÄÉ¢€0€0€ €‚‰pfam08997, UCR_6-4kD, Ubiquinol-cytochrome C reductase complex, 6.4kD protein. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is an essential component of the mitochondrial cellular respiratory chain. This family represents the 6.4kD protein, which may be closely linked to the iron-sulphur protein in the complex and function as an iron-sulphur protein binding factor.¡€0€ª€0€ €CDD¡€ €ÄÊ¢€0€0€ €‚dpfam08998, Epsilon_antitox, Bacterial epsilon antitoxin. The epsilon antitoxin, produced by various prokaryotes, forms part of a postsegregational killing system which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly interacts with the zeta toxin, inactivating it.¡€0€ª€0€ €CDD¡€ €ÄË¢€0€0€ €‚þpfam08999, SP_C-Propep, Surfactant protein C, N terminal propeptide. The N-terminal propeptide of surfactant protein C adopts an alpha-helical structure, with turn and extended regions. It's main function is the stabilisation of metastable surfactant protein C (SP-C), since the latter can irreversibly transform from its native alpha-helical structure to beta-sheet aggregates and form amyloid-like fibrils. The correct intracellular trafficking of proSP-C has also been reported to depend on the propeptide.¡€0€ª€0€ €CDD¡€ €]·¢€0€0€ €‚pfam09000, Cytotoxic, Cytotoxic. The cytotoxic domain confers cytotoxic activity to proteins, enabling the formation of nucleolytic breaks in 16S ribosomal RNA. The structure of the domain reveals a highly twisted central beta-sheet elaborated with a short N-terminal alpha-helix.¡€0€ª€0€ €CDD¡€ €ÄÌ¢€0€0€ €{pfam09001, DUF1890, Domain of unknown function (DUF1890). This domain is found in a set of hypothetical archaeal proteins.¡€0€ª€0€ €CDD¡€ €ÄÍ¢€0€0€ €|pfam09002, DUF1887, Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins.¡€0€ª€0€ €CDD¡€ €Ä΢€0€0€ €‚Lpfam09003, Phage_integ_N, Bacteriophage lambda integrase, N-terminal domain. The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage.¡€0€ª€0€ €CDD¡€ €ÄÏ¢€0€0€ €}pfam09004, DUF1891, Domain of unknown function (DUF1891). This domain is found in a set of hypothetical eukaryotic proteins.¡€0€ª€0€ €CDD¡€ €ËB¢€0€0€ €Âpfam09005, DUF1897, Domain of unknown function (DUF1897). This domain is found in Psi proteins produced by Drosophila, and in various eukaryotic hypothetical proteins. It has no known function.¡€0€ª€0€ €CDD¡€ €ÄТ€0€0€ €èpfam09006, Surfac_D-trimer, Lung surfactant protein D coiled-coil trimerisation. This domain, predominantly found in lung surfactant protein D, forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein.¡€0€ª€0€ €CDD¡€ €]½¢€0€0€ €‚^pfam09007, EBP50_C, EBP50, C-terminal. This C terminal domain allows interaction of EBP50 with FERM (four-point one ERM) domains, resulting in the activation of Ezrin-radixin-moesin (ERM), with subsequent cytoskeletal modulation and cellular growth control. It includes a disordered section between two reasonably well conserved hydrophobic regions.¡€0€ª€0€ €CDD¡€ €ÄÑ¢€0€0€ €‚Àpfam09008, Head_binding, Head binding. The head binding domain found in the Phage P22 tailspike protein contains two regular beta-sheets, A and B, oriented nearly perpendicular to each other and composed of five and three strands respectively. The topology of the strands is exclusively antiparallel. The tailspike protein trimerizes through this domain, and the direction of the strands with respect to the molecular triad is almost parallel for beta-sheet A, whereas beta-sheet B is perpendicular to the triad, forming a dome-like structure. This domain is dispensable for thermostability and SDS resistance of the intact protein, and its deletion has only minor effects on tailspike folding kinetics.¡€0€ª€0€ €CDD¡€ €ÄÒ¢€0€0€ €‚#pfam09009, Exotox-A_cataly, Exotoxin A catalytic. Members of this family, which are found in prokaryotic exotoxin A, catalyze the transfer of ADP ribose from nicotinamide adenine dinucleotide (NAD) to elongation factor-2 in eukaryotic cells, with subsequent inhibition of protein synthesis.¡€0€ª€0€ €CDD¡€ €ÄÓ¢€0€0€ €‚ pfam09010, AsiA, Anti-Sigma Factor A. Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements.¡€0€ª€0€ €CDD¡€ €]Á¢€0€0€ €‚Æpfam09011, HMG_box_2, HMG-box domain. This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.¡€0€ª€0€ €CDD¡€ €]¢€0€0€ €Õpfam09012, FeoC, FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor.¡€0€ª€0€ €CDD¡€ €ÄÔ¢€0€0€ €‚¾pfam09013, YopH_N, YopH, N-terminal. The N-terminal domain of YopH is a compact structure composed of four alpha-helices and two beta-hairpins. Helices alpha-1 and alpha-3 are parallel to each other and antiparallel to helices alpha-2 and alpha-4. This domain targets YopH for secretion from the bacterium and translocation into eukaryotic cells, and has phosphotyrosyl peptide-binding activity, allowing for recognition of p130Cas and paxillin.¡€0€ª€0€ €CDD¡€ €]Ä¢€0€0€ €‚~pfam09014, Sushi_2, Beta-2-glycoprotein-1 fifth domain. The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies.¡€0€ª€0€ €CDD¡€ €ÄÕ¢€0€0€ €‚÷pfam09015, NgoMIV_restric, NgoMIV restriction enzyme. Members of this family are prokaryotic DNA restriction enzymes, exhibiting an alpha/beta structure, with a central region comprising a mixed six-stranded beta-sheet with alpha-helices on each side. A long 'arm' protrudes out of the core of the domain between strands beta2 and beta3 and is mainly involved in the tetramerisation interface of the protein. These restriction enzymes recognize the double-stranded sequence GCCGGC and cleave after G-1.¡€0€ª€0€ €CDD¡€ €]Æ¢€0€0€ €‚²pfam09016, Pas_Saposin, Pas factor saposin fold. Members of this family adopt a compact structure comprising five alpha helices. Charged and polar residues are exposed mostly on the surface, while most of the hydrophobic residues are buried inside the hydrophobic core of the helical bundle. The precise function of this domain is unknown, but it is has been shown to induce secretion of periplasmic proteins, especially collagenase.¡€0€ª€0€ €CDD¡€ €ÄÖ¢€0€0€ €‚•pfam09017, Transglut_prok, Microbial transglutaminase. Microbial transglutaminase (MTG) catalyzes an acyl transfer reaction by means of a Cys-Asp diad mechanism, in which the gamma-carboxyamide groups of peptide-bound glutamine residues act as the acyl donors. The MTG molecule forms a single, compact domain belonging to the alpha+beta folding class, containing 11 alpha-helices and 8 beta-strands. The alpha-helices and the beta-strands are concentrated mainly at the amino and carboxyl ends of the polypeptide, respectively. These secondary structures are arranged so that a beta-sheet is surrounded by alpha-helices, which are clustered into three regions.¡€0€ª€0€ €CDD¡€ €ËO¢€0€0€ €‚Ypfam09018, Phage_Capsid_P3, P3 major capsid protein. The P3 major capsid protein adopts a 'double-barrel' structure comprising two eight-stranded viral beta-barrels or jelly rolls, each of which contains a 12-residue alpha-helix. This protein then trimerizes through a 'trimerisation loop' sequence, and is incorporated within the viral capsid.¡€0€ª€0€ €CDD¡€ €Ä×¢€0€0€ €‚'pfam09019, EcoRII-C, EcoRII C terminal. The C-terminal catalytic domain of the Restriction Endonuclease EcoRII has a restriction endonuclease-like fold with a central five-stranded mixed beta-sheet surrounded on both sides by alpha-helices. It cleaves DNA specifically at single 5' CCWGG sites.¡€0€ª€0€ €CDD¡€ €]É¢€0€0€ €—pfam09020, YopE_N, YopE, N terminal. The N terminal YopE domain targets YopE for secretion from the bacterium and translocation into eukaryotic cells.¡€0€ª€0€ €CDD¡€ €]Ê¢€0€0€ €‚£pfam09021, HutP, HutP. The HutP protein family regulates the expression of Bacillus 'hut' structural genes by an anti-termination complex, which recognizes three UAG triplet units, separated by four non-conserved nucleotides on the RNA terminator region. L-histidine and Mg2+ ions are also required. These proteins exhibit the structural elements of alpha/beta proteins, arranged in the order: alpha-alpha-beta-alpha-alpha-beta-beta-beta in the primary structure, and the four antiparallel beta-strands form a beta-sheet in the order beta1-beta2-beta3-beta4, with two alpha-helices each on the front (alpha1 and alpha2) and at the back (alpha3 and alpha4) of the beta-sheet.¡€0€ª€0€ €CDD¡€ €ÄØ¢€0€0€ €‚£pfam09022, Staphostatin_A, Staphostatin A. The staphostatin A polypeptide chain folds into a slightly deformed, eight-stranded beta-barrel, with strands beta-4 through beta-8 forming an antiparallel sheet while the N-terminus forms a a psi-loop motif. Members of this family constitute a class of cysteine protease inhibitors distinct in the fold and the mechanism of action from any known inhibitors of these enzymes.¡€0€ª€0€ €CDD¡€ €]Ì¢€0€0€ €‚gpfam09023, Staphostatin_B, Staphostatin B. Staphostatin B inhibits the cysteine protease Staphopain B, produced by Staphylococcus aureus, by blocking the active site of the enzyme. The domain adopts an eight-stranded mixed beta-barrel structure, with a deviation from the up-down topology of canonical beta-barrels in the amino-terminal part of the molecule.¡€0€ª€0€ €CDD¡€ €]Í¢€0€0€ €‚spfam09025, T3SS_needle_reg, YopR, type III needle-polymerization regulator. The YopR core domain, predominantly found in the Gammaproteobacteria virulence factor YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle. Little is known about this domain, though it may contribute to the virulence of the protein YopR. YopR controls the selective access of early (YscF, YscI and YscP) substrates to the type III secretion machines of yersiniae and other Gammaproteobacteriae. YopR is a mobile regulatory component thought to function as a checkpoints probing the completion of discrete intermediary stages in the assembly of the type III injection pathway. The location of secreted YopR (into the medium) is directly controlling the secretion of YscF, the polymerized needle protein pfam09392, thereby impacting the assembly of type III machines.¡€0€ª€0€ €CDD¡€ €]΢€0€0€ €‚]pfam09026, CENP-B_dimeris, Centromere protein B dimerisation domain. The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerize to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation.¡€0€ª€0€ €CDD¡€ €]Ï¢€0€0€ €Ýpfam09027, GTPase_binding, GTPase binding. The GTPase binding domain binds to the G protein Cdc42, inhibiting both its intrinsic and stimulated GTPase activity. The domain is largely unstructured in the absence of Cdc42.¡€0€ª€0€ €CDD¡€ €ÄÙ¢€0€0€ €‚pfam09028, Mac-1, Mac 1. The bacterial protein Mac 1 adopts an alpha/beta fold, with 14 beta strands and 9 alpha helices. The N-terminal domain is made up predominantly of alpha helices, whereas the C-terminal domain consists predominantly of beta sheets. Mac 1 blocks polymorphonuclear opsonophagocytosis, inhibits the production of reactive oxygen species and contains IgG endopeptidase activity.¡€0€ª€0€ €CDD¡€ €]Ñ¢€0€0€ €‚Ïpfam09029, Preseq_ALAS, 5-aminolevulinate synthase presequence. The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import.¡€0€ª€0€ €CDD¡€ €ÄÚ¢€0€0€ €‚¼pfam09030, Creb_binding, Creb binding. The Creb binding domain assumes a structure comprising of three alpha-helices which pack in a bundle, exposing a hydrophobic groove between alpha-1 and alpha-3 within which complimentary domains found in the protein 'activator for thyroid hormone and retinoid receptors' (ACTR) can dock. Docking of these domains is required for the recruitment of RNA polymerase II and the basal transcription machinery.¡€0€ª€0€ €CDD¡€ €ÄÛ¢€0€0€ €‚Üpfam09032, Siah-Interact_N, Siah interacting protein, N terminal. The N terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilized by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesized that SIP can dimerize through this N terminal domain.¡€0€ª€0€ €CDD¡€ €ÄÜ¢€0€0€ €‚Àpfam09033, DFF-C, DNA Fragmentation factor 45kDa, C terminal domain. The C terminal domain of DNA Fragmentation factor 45kDa (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFF40 by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFF40, the C-terminal region of DFF45 is also important for the DFF40-specific folding chaperone activity, as demonstrated by the ability of DFF45 to refold DFF40.¡€0€ª€0€ €CDD¡€ €ÄÝ¢€0€0€ €‚“pfam09034, TRADD_N, TRADD, N-terminal domain. The N terminal domain of 'tumor necrosis factor receptor type 1 associated death domain protein' (TRADD) folds into an alpha-beta sandwich with a four-stranded beta sheet and six alpha helices, each forming one layer of the structure. The domain allows docking of TRADD onto 'tumor necrosis factor receptor-associated factor' (TRAF): the binding is at the beta-sandwich domain, away from the coiled-coil domain. Binding ensures the recruitment of cIAPs to the signaling complex, which may be important for direct caspase-8 inhibition and the immediate suppression of apoptosis at the apical point of the cascade.¡€0€ª€0€ €CDD¡€ €ÄÞ¢€0€0€ €‚­pfam09035, Tn916-Xis, Excisionase from transposon Tn916. The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilizing distorted DNA structures.¡€0€ª€0€ €CDD¡€ €]×¢€0€0€ €‚Ûpfam09036, Bcr-Abl_Oligo, Bcr-Abl oncoprotein oligomerization domain. The Bcr-Abl oncoprotein oligomerization domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerization domain is essential for the oncogenicity of the Bcr-Abl protein.¡€0€ª€0€ €CDD¡€ €Äߢ€0€0€ €‚pfam09180, ProRS-C_1, Prolyl-tRNA synthetase, C-terminal. Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif.¡€0€ª€0€ €CDD¡€ €Å9¢€0€0€ €‚>pfam09181, ProRS-C_2, Prolyl-tRNA synthetase, C-terminal. Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif.¡€0€ª€0€ €CDD¡€ €^R¢€0€0€ €‚òpfam09182, PuR_N, Bacterial purine repressor, N-terminal. The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA.¡€0€ª€0€ €CDD¡€ €Å:¢€0€0€ €»pfam09183, DUF1947, Domain of unknown function (DUF1947). Members of this family are found in a set of hypothetical Archaeal proteins. Their exact function has not, as yet, been defined.¡€0€ª€0€ €CDD¡€ €Å;¢€0€0€ €‚pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes.¡€0€ª€0€ €CDD¡€ €Å<¢€0€0€ €‚pfam09185, DUF1948, Domain of unknown function (DUF1948). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined.¡€0€ª€0€ €CDD¡€ €^V¢€0€0€ €úpfam09186, DUF1949, Domain of unknown function (DUF1949). Members of this family pertain to a set of functionally uncharacterized hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement.¡€0€ª€0€ €CDD¡€ €Å=¢€0€0€ €£pfam09187, DUF1950, Domain of unknown function(DUF1950). Members of this family pertain to a set of functionally uncharacterized hypothetical eukaryotic proteins.¡€0€ª€0€ €CDD¡€ €^X¢€0€0€ €Þpfam09188, DUF1951, Domain of unknown function (DUF1951). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with a buried central helix. Their function has not, as yet, been determined.¡€0€ª€0€ €CDD¡€ €^Y¢€0€0€ €¼pfam09189, DUF1952, Domain of unknown function (DUF1952). Members of this family are found in various Thermus thermophilus proteins. Their exact function has not, as yet, been determined.¡€0€ª€0€ €CDD¡€ €^Z¢€0€0€ €Ypfam09190, DALR_2, DALR domain. This DALR domain is found in cysteinyl-tRNA-synthetases.¡€0€ª€0€ €CDD¡€ €^[¢€0€0€ €‚Ppfam09191, CD4-extracel, CD4, extracellular. Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens.¡€0€ª€0€ €CDD¡€ €Å>¢€0€0€ €‚Gpfam09192, Act-Frag_cataly, Actin-fragmin kinase, catalytic. Members of this family assume a secondary structure consisting of eight beta strands and 11 alpha-helices, organised in two lobes. They are predominantly found in actin-fragmin kinase, where they act as a catalytic domain that mediates the phosphorylation of actin.¡€0€ª€0€ €CDD¡€ €Å?¢€0€0€ €‚|pfam09193, CholecysA-Rec_N, Cholecystokinin A receptor, N-terminal. Members of this family are found in the extracellular region of the cholecystokinin A receptor, where they adopt a tertiary structure consisting of a few helical turns and a disulphide-crosslinked loop. They are required for interaction of the cholecystokinin A receptor with it's corresponding hormonal ligand.¡€0€ª€0€ €CDD¡€ €Å@¢€0€0€ €‚Upfam09194, Endonuc-BsobI, Restriction endonuclease BsobI. Members of this family of prokaryotic restriction endonucleases recognize the double-stranded sequence CYCGRG (where Y = T/C, and R = A/G) and cleave after C-1. They catalyze the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.¡€0€ª€0€ €CDD¡€ €ÅA¢€0€0€ €‚ópfam09195, Endonuc-BglII, Restriction endonuclease BglII. Members of this family are predominantly found in prokaryotic restriction endonuclease BglII, and adopt a structure consisting of an alpha/beta core containing a six-stranded beta-sheet surrounded by five alpha-helices, two of which are involved in homodimerisation of the endonuclease. They recognize the double-stranded DNA sequence AGATCT and cleave after A-1, resulting in specific double-stranded fragments with terminal 5'-phosphates.¡€0€ª€0€ €CDD¡€ €ÅB¢€0€0€ €Ðpfam09196, DUF1953, Domain of unknown function (DUF1953). This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined.¡€0€ª€0€ €CDD¡€ €^a¢€0€0€ €‚Lpfam09197, Rap1-DNA-bind, Rap1, DNA-binding. Members of this family, which are predominantly found in the yeast protein rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACACC region in the 3' region of the DNA-binding site.¡€0€ª€0€ €CDD¡€ €ÅC¢€0€0€ €ûpfam09198, T4-Gluco-transf, Bacteriophage T4 beta-glucosyltransferase. Members of this family are DNA-modifying enzymes encoded by bacteriophage T4 that transfer glucose from uridine diphosphoglucose to 5-hydroxymethyl cytosine bases of phage T4 DNA.¡€0€ª€0€ €CDD¡€ €¦¢€0€0€ €‚øpfam09199, SSL_OB, Staphylococcal superantigen-like OB-fold domain. This OB-fold domain folds into a five-stranded beta-barrel. Members of this family are found in various staphylococcal toxins described as staphylococcal superantigen-like (SSL) proteins that are related to the staphylococcal enterotoxins (SEs) or superantigens. These SSL proteins of which 11 have so far been characterized have a typical SE tertiary structure consisting of a distinct oligonucleotide/oligosaccharide binding (OB-fold), this domain, linked to a beta-grasp domain, family Stap_Strp_tox_C, pfam02876. SSLs do not bind to T-cell receptors or major histocompatibility complex class II molecules and do not stimulate T cells. SSLs target components of innate immunity, such as complement, Fc receptors, and myeloid cells 2,3,4,5,6,7,8]. SSL protein 7 (SSL7) is the best characterized of the SSLs and binds complement factor C5 and IgA with high affinity and inhibits the end stage of complement activation and IgA binding to FcalphaR.¡€0€ª€0€ €CDD¡€ €^c¢€0€0€ €‚?pfam09200, Monellin, Monellin. Monellin, a protein produced by the West African plant Dioscoreophyllum cumminsii, is approximately 70,000 times sweeter than sucrose on a molar basis. The protein adopts an alpha-beta structure, with a cystatin-like fold, where each helix packs against a coiled antiparallel beta-sheet.¡€0€ª€0€ €CDD¡€ €ÅD¢€0€0€ €‚1pfam09201, SRX, SRX, signal recognition particle receptor alpha subunit. Members of this family, which are predominantly found in eukaryotic signal recognition particle receptor alpha, consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta). Structurally the alpha subunit is SNARE-like.¡€0€ª€0€ €CDD¡€ €ÅE¢€0€0€ €‚]pfam09202, Rio2_N, Rio2, N-terminal. Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains.¡€0€ª€0€ €CDD¡€ €ÅF¢€0€0€ €‚‘pfam09203, MspA, MspA. MspA is a membrane porin produced by Mycobacteria, allowing hydrophilic nutrients to enter the bacterium. The protein forms a tightly interconnected octamer with eightfold rotation symmetry that resembles a goblet and contains a central channel. Each subunit fold contains a beta-sandwich of Ig-like topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel.¡€0€ª€0€ €CDD¡€ €ÅG¢€0€0€ €‚âpfam09204, Colicin_immun, Bacterial self-protective colicin-like immunity. Colicin D, which is synthesized by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg isoacceptors, thereby inactivating prokaryotic protein synthesis and leading to cell death. This family also contains immunity proteins to klebicins and microcins. Many bacteria produce proteins that destroy their competitors. Colicin D is one such. The immunity proteins are expressed on the same operon as their cognate bacteriocins and protect the expressing bacterium from the effects of its own bacteriocin.¡€0€ª€0€ €CDD¡€ €^h¢€0€0€ €Üpfam09205, DUF1955, Domain of unknown function (DUF1955). Members of this family are found in hypothetical proteins synthesized by the Archaeal organism Sulfolobus. Their exact function has not, as yet, been determined.¡€0€ª€0€ €CDD¡€ €ÅH¢€0€0€ €‚Êpfam09206, ArabFuran-catal, Alpha-L-arabinofuranosidase B, catalytic. Members of this family, which are present in fungal alpha-L-arabinofuranosidase B, adopt a beta-sandwich fold similar to that of Concanavalin A-like lectins/glucanase. The beta-sandwich fold consists of two anti-parallel beta-sheets with seven and and six strands, respectively. In addition, there are four helices outside of the beta-strands. The beta-sandwich strands are closely packed and curved with a jelly roll topology, creating a small catalytic pocket. The domain catalyzes the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan.¡€0€ª€0€ €CDD¡€ €ÅI¢€0€0€ €Ôpfam09207, Yeast-kill-tox, Yeast killer toxin. Members of this family, which are produced by Williopsis fungi, adopt a secondary structure consisting of eight strands in two beta sheets, in a Greek-key topology.¡€0€ª€0€ €CDD¡€ €ÅJ¢€0€0€ €‚pfam09208, Endonuc-MspI, Restriction endonuclease MspI. Members of this family of prokaryotic restriction endonucleases recognize the palindromic tetranucleotide sequence 5'-CCGG and cleave between the first and second nucleotides, leaving 2 base 5' overhangs. They fold into an alpha/beta architecture, with a five-stranded mixed beta-sheet sandwiched on both sides by alpha-helices.¡€0€ª€0€ €CDD¡€ €^k¢€0€0€ €Ípfam09209, DUF1956, Domain of unknown function (DUF1956). Members of this family are found in various prokaryotic transcriptional regulator proteins. Their exact function has not, as yet, been identified.¡€0€ª€0€ €CDD¡€ €ÅK¢€0€0€ €®pfam09210, DUF1957, Domain of unknown function (DUF1957). This domain is found in a set of hypothetical bacterial proteins. Its exact function has not, as yet, been defined.¡€0€ª€0€ €CDD¡€ €ÅL¢€0€0€ €¥pfam09211, DUF1958, Domain of unknown function (DUF1958). Members of this functionally uncharacterized family are found in prokaryotic penicillin-binding protein 4.¡€0€ª€0€ €CDD¡€ €ÅM¢€0€0€ €‚‰pfam09212, CBM27, Carbohydrate binding module 27. Members of this family are carbohydrate binding modules that bind to beta-1, 4-manno-oligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. They adopt a beta sandwich structure comprising 13 beta strands with a single, small alpha-helix and a single metal atom.¡€0€ª€0€ €CDD¡€ €Ì¢€0€0€ €‚pfam09213, M3, M3. Members of this family of viral chemokine binding proteins adopt a structure consisting of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds. They bind with the CC-chemokine MCP-1, acting as cytokine decoy receptors.¡€0€ª€0€ €CDD¡€ €Ì¢€0€0€ €‚3pfam09214, Prd1-P2, Bacteriophage Prd1, adsorption protein P2. Members of this family form a set of bacteriophage adsorption proteins, composed mainly of beta-strands whose complicated topology forms an elongated seahorse-shaped molecule with a distinct head, containing a pseudo-beta propeller structure with approximate 6-fold symmetry, and tail. They are required for the attachment of the phage to the host conjugative DNA transfer complex. This is a poorly understood large transmembrane complex of unknown architecture, with at least 11 different proteins.¡€0€ª€0€ €CDD¡€ €^o¢€0€0€ €‚pfam09215, Phage-Gp8, Bacteriophage T4, Gp8. Members of this family of viral baseplate structural proteins adopt a structure consisting of a three-layer beta-sandwich with two finger-like loops containing an alpha-helix at the opposite sides of the sandwich. The two peripheral, five-stranded, antiparallel beta-sheets are stacked against the middle, four-stranded, antiparallel beta-sheet. Attachment of this family of proteins to the baseplate during assembly creates a binding site for subsequent attachment of Gp6.¡€0€ª€0€ €CDD¡€ €^p¢€0€0€ €‚ pfam09216, Pfg27, Pfg27. Members of this family are essential for gametocytogenesis in Plasmodium falciparum. They contain a fold composed of two pseudo dyad-related repeats of the helix-turn-helix motif, serving as a platform for RNA and Src homology-3 (SH3) binding.¡€0€ª€0€ €CDD¡€ €^q¢€0€0€ €‚åpfam09217, EcoRII-N, Restriction endonuclease EcoRII, N-terminal. The N-terminal effector-binding domain of the Restriction Endonuclease EcoRII has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not.¡€0€ª€0€ €CDD¡€ €^r¢€0€0€ €¹pfam09218, DUF1959, Domain of unknown function (DUF1959). This domain is found in a set of uncharacterized Archaeal hypothetical proteins. Its function has not, as yet, been described.¡€0€ª€0€ €CDD¡€ €ÅN¢€0€0€ €—pfam09220, LA-virus_coat, L-A virus, major coat protein. Members of this family form the major coat protein of the Saccharomyces cerevisiae L-A virus.¡€0€ª€0€ €CDD¡€ €^t¢€0€0€ €‚…pfam09221, Bacteriocin_IId, Bacteriocin class IId cyclical uberolysin-like. Members of this family are membrane-interacting peptides, produced by Firmicutes that display a broad anti-microbial spectrum against Gram-positive and Gram-negative bacteria. They adopt a helical structure, with four or five alpha helices forming a Saposin-like fold. The structure has been found to be cyclical. It should be pointed out that one reference implies that both circularin A and gassericin A are class V or IIc-type bacteriocins; however we find that these two proteins fall into different Pfam families families, this one and BacteriocIIc_cy, pfam12173.¡€0€ª€0€ €CDD¡€ €ÅO¢€0€0€ €‚˜pfam09222, Fim-adh_lectin, Fimbrial adhesin F17-AG, lectin domain. Members of this family are carbohydrate-specific lectin domains found in bacterial fimbrial adhesins. They adopt a compact, elongated structure consisting of a beta-sandwich with two major sheets: one consisting of five long strands in mixed orientations, and a front sheet with four antiparallel strands, forming an immunoglobin-like fold.¡€0€ª€0€ €CDD¡€ €ÅP¢€0€0€ €‚Ypfam09223, ZinT, ZinT (YodA) periplasmic lipocalin-like zinc-recruitment. ZinT plays a critical role in recruiting periplasmic zinc to the bacterial zinc-uptake complex ZnuABC, consisting of families pfam01297,pfam00950, pfam00005, regulated by the transcription-regulator FUR, pfam01475. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), pfam01297. Members of this family of prokaryotic domains were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium, and ensure its subsequent elimination.¡€0€ª€0€ €CDD¡€ €ÅQ¢€0€0€ €¿pfam09224, DUF1961, Domain of unknown function (DUF1961). Members of this family are found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been determined.¡€0€ª€0€ €CDD¡€ €ÅR¢€0€0€ €‚8pfam09225, Endonuc-PvuII, Restriction endonuclease PvuII. Members of this family are predominantly found in prokaryotic restriction endonuclease PvuII. They recognize the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3, resulting in specific double-stranded fragments with terminal 5'-phosphates.¡€0€ª€0€ €CDD¡€ €^x¢€0€0€ €‚@pfam09226, Endonuc-HincII, Restriction endonuclease HincII. Members of this family of prokaryotic restriction endonucleases recognize the double-stranded sequence 5'-GTYRAC-3' and cleave after Y-3. They catalyze the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.¡€0€ª€0€ €CDD¡€ €ÅS¢€0€0€ €…pfam09227, DUF1962, Domain of unknown function (DUF1962). Members of this family of fungal domains are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €^z¢€0€0€ €‚œpfam09228, Prok-TraM, Prokaryotic Transcriptional repressor TraM. Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a 'globular head' and an 'elongated tail', and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation.¡€0€ª€0€ €CDD¡€ €ÅT¢€0€0€ €‚âpfam09229, Aha1_N, Activator of Hsp90 ATPase, N-terminal. Members of this family, which are predominantly found in the protein 'Activator of Hsp90 ATPase' adopt a secondary structure consisting of an N-terminal alpha-helix leading into a four-stranded meandering antiparallel beta-sheet, followed by a C-terminal alpha-helix. The two helices are packed together, with the beta-sheet curving around them. They bind to the molecular chaperone HSP82 and stimulate its ATPase activity.¡€0€ª€0€ €CDD¡€ €ÅU¢€0€0€ €±pfam09230, DFF40, DNA fragmentation factor 40 kDa. Members of this family of eukaryotic apoptotic proteins induce DNA fragmentation and chromatin condensation during apoptosis.¡€0€ª€0€ €CDD¡€ €ÅV¢€0€0€ €‚ pfam09231, RDV-p3, Rice dwarf virus p3. Members of this family are core structural proteins found in the double-stranded RNA virus Phytoreovirus. They are large proteins without apparent domain division, with a number of all-alpha regions and one all beta domain near the C-terminal end.¡€0€ª€0€ €CDD¡€ €^~¢€0€0€ €‚¡pfam09232, Caenor_Her-1, Caenorhabditis elegans Her-1. Her-1 adopts an all-helical structure with two subdomains: residues 19-80 comprise a left-handed three-helix bundle with an overhand connection between the second and third helices, whilst residues 81-164 comprise a left-handed anti-parallel four-helix bundle in which the first helix consists of four consecutive turns of 3-10-helix. Fourteen Cys are conserved in all known HER-1 sequences and form seven disulfide bonds. The protein dictates male development in Caenorhabditis elegans, probably by playing a direct role in cell signaling during C. elegans sex determination. It also inhibits the function of tra-2a.¡€0€ª€0€ €CDD¡€ €^¢€0€0€ €‚>pfam09233, Endonuc-EcoRV, Restriction endonuclease EcoRV. Members of this family of prokaryotic restriction endonucleases recognize the double-stranded sequence 5'-GATATC-3' and cleave after T-3. They catalyze the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.¡€0€ª€0€ €CDD¡€ €ÅW¢€0€0€ €°pfam09234, DUF1963, Domain of unknown function (DUF1963). This domain is found in a set of hypothetical bacterial proteins. Its exact function has not, as yet, been described.¡€0€ª€0€ €CDD¡€ €ÅX¢€0€0€ €‚ pfam09235, Ste50p-SAM, Ste50p, sterile alpha motif. The fungal Ste50p SAM domain consists of five helices, which form a compact, globular fold. It is required for mediation of homodimerisation and heterodimerisation (and in some cases oligomerization) of the protein.¡€0€ª€0€ €CDD¡€ €Ì¢€0€0€ €‚®pfam09236, AHSP, Alpha-haemoglobin stabilizing protein. Alpha-haemoglobin stabilizing protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle.¡€0€ª€0€ €CDD¡€ €ÅY¢€0€0€ €‚“pfam09237, GAGA, GAGA factor. Members of this family bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognizes the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognizes the A in the fourth position of the consensus sequence.¡€0€ª€0€ €CDD¡€ €J¢€0€0€ €‚Ápfam09238, IL4Ra_N, Interleukin-4 receptor alpha chain, N-terminal. Members of this family are related in overall topology to fibronectin type III modules and fold into a sandwich comprising seven antiparallel beta sheets arranged in a three-strand and a four-strand beta-pleated sheet. They are required for binding of interleukin-4 to the receptor alpha chain, which is a crucial event for the generation of a Th2-dominated early immune response.¡€0€ª€0€ €CDD¡€ €ÅZ¢€0€0€ €‚ópfam09239, Topo-VIb_trans, Topoisomerase VI B subunit, transducer. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme.¡€0€ª€0€ €CDD¡€ €Å[¢€0€0€ €‚pfam09240, IL6Ra-bind, Interleukin-6 receptor alpha chain, binding. Members of this family adopt a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, in a Greek-key topology. They are required for binding to the cytokine Interleukin-6.¡€0€ª€0€ €CDD¡€ €Å\¢€0€0€ €‚pfam09241, Herp-Cyclin, Herpesviridae viral cyclin. Members of this family of viral cyclins adopt a helical structure consisting of five alpha-helices, with one helix surrounded by the others. They specifically activate CDK6 of host cells to a very high degree.¡€0€ª€0€ €CDD¡€ €^†¢€0€0€ €‚pfam09242, FCSD-flav_bind, Flavocytochrome c sulphide dehydrogenase, flavin-binding. Members of this family adopt a structure consisting of a beta(3,4)-alpha(3) core, and an alpha+beta sandwich. They are required for binding to flavin, and subsequent electron transfer.¡€0€ª€0€ €CDD¡€ €Å]¢€0€0€ €‚upfam09243, Rsm22, Mitochondrial small ribosomal subunit Rsm22. Rsm22 has been identified as a mitochondrial small ribosomal subunit and is a methyltransferase. In Schizosaccharomyces pombe, Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria.¡€0€ª€0€ €CDD¡€ €^ˆ¢€0€0€ €‚pfam09244, DUF1964, Domain of unknown function (DUF1964). Members of this family of bacterial domains adopt a beta-sandwich fold, with Greek-key topology. They are C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain, and are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Å^¢€0€0€ €‚˜pfam09245, MA-Mit, Mycoplasma arthritidis-derived mitogen. Mycoplasma arthritidis-derived mitogen (MA-Mit) adopts a completely alpha-helical structure consisting of ten alpha helices. It is a superantigen that can activate large fractions of T cells bearing particular TCR V-beta elements. Two MA-Mit molecules form an asymmetric dimer and cross-link two MHC antigens to form a dimerized MA-Mit-MHC complex.¡€0€ª€0€ €CDD¡€ €Å_¢€0€0€ €‚Ppfam09246, PHAT, PHAT. The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding.¡€0€ª€0€ €CDD¡€ €’¢€0€0€ €‚2pfam09247, TBP-binding, TATA box-binding protein binding. Members of this family adopt a structure consisting of three alpha helices and a beta-hairpin. They bind to TATA box-binding protein (TBP), inhibiting TBP interaction with the TATA element, thereby resulting in shutting down of gene transcription.¡€0€ª€0€ €CDD¡€ €Å`¢€0€0€ €Òpfam09248, DUF1965, Domain of unknown function (DUF1965). Members of this family of fungal domains adopt a structure that consists of an alpha/beta motif. Their exact function has not, as yet, been determined.¡€0€ª€0€ €CDD¡€ €Åa¢€0€0€ €‚pfam09249, tRNA_NucTransf2, tRNA nucleotidyltransferase, second domain. Members of this family adopt a structure consisting of a five helical bundle core. They are predominantly found in Archaeal tRNA nucleotidyltransferase, following the catalytic nucleotidyltransferase domain.¡€0€ª€0€ €CDD¡€ €Åb¢€0€0€ €‚#pfam09250, Prim-Pol, Bifunctional DNA primase/polymerase, N-terminal. Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.¡€0€ª€0€ €CDD¡€ €Åc¢€0€0€ €‚|pfam09251, PhageP22-tail, Salmonella phage P22 tail-spike. Members of this family of viral domains adopt a structure consisting of a single-stranded right-handed beta-helix, which in turn is made of parallel beta-strands and short turns. They are required for recognition of the 0-antigenic repeating units of the cell surface, and for subsequent infection of the bacterial cell.¡€0€ª€0€ €CDD¡€ €Åd¢€0€0€ €øpfam09252, Feld-I_B, Allergen Fel d I-B chain. Members of this family of cat allergens adopt a helical structure consisting of eight alpha helices, in a Uteroglobin-like fold. They are one of the most important causes of allergic asthma worldwide.¡€0€ª€0€ €CDD¡€ €Åe¢€0€0€ €‚pfam09253, Ole-e-6, Pollen allergen ole e 6. Members of this family consist of two nearly antiparallel alpha-helices, that are connected by a short loop and followed by a long, unstructured C-terminal tail. They are highly allergenic, primarily mediating olive allergy.¡€0€ª€0€ €CDD¡€ €Åf¢€0€0€ €‚½pfam09254, Endonuc-FokI_C, Restriction endonuclease FokI, C terminal. Members of this family are predominantly found in prokaryotic restriction endonuclease FokI, and adopt a structure consisting of an alpha/beta/alpha core containing a five-stranded beta-sheet. They recognize the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand.¡€0€ª€0€ €CDD¡€ €^’¢€0€0€ €‚Fpfam09255, Antig_Caf1, Caf1 Capsule antigen. Members of this family are predominantly found in the F1 capsule antigen Caf1 synthesized by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection.¡€0€ª€0€ €CDD¡€ €^“¢€0€0€ €ñpfam09256, BaffR-Tall_bind, BAFF-R, TALL-1 binding. Members of this family, which are predominantly found in the tumor necrosis factor receptor superfamily member 13c, BAFF-R, are required for binding to tumor necrosis factor ligand TALL-1.¡€0€ª€0€ €CDD¡€ €Åg¢€0€0€ €ëpfam09257, BCMA-Tall_bind, BCMA, TALL-1 binding. Members of this family, which are predominantly found in the tumor necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumor necrosis factor ligand TALL-1.¡€0€ª€0€ €CDD¡€ €Åh¢€0€0€ €‚Âpfam09258, Glyco_transf_64, Glycosyl transferase family 64 domain. Members of this family catalyze the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate.¡€0€ª€0€ €CDD¡€ €Åi¢€0€0€ €‚&pfam09259, Fve, Fungal immunomodulatory protein Fve. Fve is a major fruiting body protein from Flammulina velutipes, a mushroom possessing immunomodulatory activity. It stimulates lymphocyte mitogenesis, suppresses systemic anaphylaxis reactions and oedema, enhances transcription of IL-2, IFN-gamma and TNF-alpha, and haemagglutinates red blood cells. It appears to be a lectin with specificity for complex cell-surface carbohydrates. Fve adopts a tertiary structure consisting of an immunoglobulin-like beta-sandwich, with seven strands arranged in two beta sheets, in a Greek-key topology. It forms a non-covalently linked homodimer containing no Cys, His or Met residues; dimerisation occurs by 3-D domain swapping of the N-terminal helices and is stabilized predominantly by hydrophobic interactions.¡€0€ª€0€ €CDD¡€ €Ì-¢€0€0€ €«pfam09260, DUF1966, Domain of unknown function (DUF1966). This domain is found in various fungal alpha-amylase proteins. Its exact function has not, as yet, been defined.¡€0€ª€0€ €CDD¡€ €Åj¢€0€0€ €ýpfam09261, Alpha-mann_mid, Alpha mannosidase middle domain. Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase.¡€0€ª€0€ €CDD¡€ €Åk¢€0€0€ €‚ópfam09262, PEX-1N, Peroxisome biogenesis factor 1, N-terminal. Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation.¡€0€ª€0€ €CDD¡€ €Ål¢€0€0€ €‚âpfam09263, PEX-2N, Peroxisome biogenesis factor 1, N-terminal. Members of this family adopt a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation.¡€0€ª€0€ €CDD¡€ €Åm¢€0€0€ €‚•pfam09264, Sial-lect-inser, Vibrio cholerae sialidase, lectin insertion. Members of this family are predominantly found in Vibrio cholerae sialidase, and adopt a beta sandwich structure consisting of 12-14 strands arranged in two beta-sheets. They bind to lectins with high affinity helping to target the protein to sialic acid-rich environments, thereby enhancing the catalytic efficiency of the enzyme.¡€0€ª€0€ €CDD¡€ €^›¢€0€0€ €‚pfam09265, Cytokin-bind, Cytokinin dehydrogenase 1, FAD and cytokinin binding. Members of this family adopt an alpha+beta sandwich structure with an antiparallel beta-sheet, in a ferredoxin-like fold. They are predominantly found in plant cytokinin dehydrogenase 1, where they are capable of binding both FAD and cytokinin substrates. The substrate displays a 'plug-into-socket' binding mode that seals the catalytic site and precisely positions the carbon atom undergoing oxidation in close contact with the reactive locus of the flavin.¡€0€ª€0€ €CDD¡€ €Ån¢€0€0€ €‚pfam09266, VirDNA-topo-I_N, Viral DNA topoisomerase I, N-terminal. Members of this family are predominantly found in viral DNA topoisomerase, and assume a beta(2)-alpha-beta-alpha-beta(2) fold, with a left-handed crossover between strands beta2 and beta3.¡€0€ª€0€ €CDD¡€ €^¢€0€0€ €‚ pfam09267, Dict-STAT-coil, Dictyostelium STAT, coiled coil. Members of this family are found in Dictyostelium STAT proteins and adopt a structure consisting of four long alpha-helices, folded into a coiled coil. They are responsible for nuclear export of the protein.¡€0€ª€0€ €CDD¡€ €Åo¢€0€0€ €àpfam09268, Clathrin-link, Clathrin, heavy-chain linker. Members of this family adopt a structure consisting of alpha-alpha superhelix. They are predominantly found in clathrin, where they act as a heavy-chain linker domain.¡€0€ª€0€ €CDD¡€ €Åp¢€0€0€ €‚%pfam09269, DUF1967, Domain of unknown function (DUF1967). Members of this family contain a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. They are predominantly found in the bacterial GTP-binding protein Obg, and are still functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Åq¢€0€0€ €‚mpfam09270, BTD, Beta-trefoil DNA-binding domain. Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR).¡€0€ª€0€ €CDD¡€ €År¢€0€0€ €‚~pfam09271, LAG1-DNAbind, LAG1, DNA binding. Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding. This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins.¡€0€ª€0€ €CDD¡€ €Ås¢€0€0€ €‚bpfam09272, Hepsin-SRCR, Hepsin, SRCR. Members of this family form an extracellular domain of the serine protease hepsin. They are formed primarily by three elements of regular secondary structure: a 12-residue alpha helix, a twisted five-stranded antiparallel beta sheet, and a second, two-stranded, antiparallel sheet. The two beta-sheets lie at roughly right angles to each other, with the helix nestled between the two, adopting an SRCR fold. The exact function of this domain has not been identified, though it probably may serve to orient the protease domain or place it in the vicinity of its substrate.¡€0€ª€0€ €CDD¡€ €Åt¢€0€0€ €‚Hpfam09273, Rubis-subs-bind, Rubisco LSMT substrate-binding. Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex.¡€0€ª€0€ €CDD¡€ €Åu¢€0€0€ €øpfam09274, ParG, ParG. Members of this family of plasmid partition proteins adopt a ribbon-helix-helix fold, with a core of four alpha-helices. They are an essential component of the DNA partition complex of the multidrug resistance plasmid TP228.¡€0€ª€0€ €CDD¡€ €Ì;¢€0€0€ €Üpfam09275, Pertus-S4-tox, Pertussis toxin S4 subunit. Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology.¡€0€ª€0€ €CDD¡€ €^¤¢€0€0€ €Üpfam09276, Pertus-S5-tox, Pertussis toxin S5 subunit. Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology.¡€0€ª€0€ €CDD¡€ €^¥¢€0€0€ €‚-pfam09277, Erythro-docking, Erythronolide synthase, docking. Members of this family of docking domains are found in prokaryotic erythronolide synthase. They adopt a structure consisting of a bundle of four alpha-helices, and mediate homodimerisation of the protein, stabilizing the resulting complex.¡€0€ª€0€ €CDD¡€ €Ì=¢€0€0€ €‚3pfam09278, MerR-DNA-bind, MerR, DNA binding. Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold.¡€0€ª€0€ €CDD¡€ €Åv¢€0€0€ €‚5pfam09279, EF-hand_like, Phosphoinositide-specific phospholipase C, efhand-like. Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme.¡€0€ª€0€ €CDD¡€ €Åw¢€0€0€ €‚ pfam09280, XPC-binding, XPC-binding domain. Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair.¡€0€ª€0€ €CDD¡€ €Åx¢€0€0€ €èpfam09281, Taq-exonuc, Taq polymerase, exonuclease. Members of this family are found in prokaryotic Taq DNA polymerase, where they assume a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase.¡€0€ª€0€ €CDD¡€ €Åy¢€0€0€ €‚>pfam09282, Mago-bind, Mago binding. Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loop via hydrophobic interactions.¡€0€ª€0€ €CDD¡€ €Åz¢€0€0€ €‚pfam09284, RhgB_N, Rhamnogalacturonan lyase B, N-terminal. Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL).¡€0€ª€0€ €CDD¡€ €Å{¢€0€0€ €‚pfam09285, Elong-fact-P_C, Elongation factor P, C-terminal. Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology.¡€0€ª€0€ €CDD¡€ €Å|¢€0€0€ €þpfam09286, Pro-kuma_activ, Pro-kumamolisin, activation domain. Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide.¡€0€ª€0€ €CDD¡€ €Å}¢€0€0€ €ëpfam09287, CEP1-DNA_bind, CEP-1, DNA binding. Members of this family of DNA-binding domains are found the transcription factor CEP-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology.¡€0€ª€0€ €CDD¡€ €îó¢€0€0€ €èpfam09288, UBA_3, Fungal ubiquitin-associated domain. Members of this family of ubiquitin binding domains adopt a structure consisting of a three alpha-helix bundle. They are predominantly found in fungal ubiquitin-protein ligases.¡€0€ª€0€ €CDD¡€ €ÌH¢€0€0€ €¤pfam09289, FOLN, Follistatin/Osteonectin-like EGF domain. Members of this family are predominantly found in osteonectin and follistatin and adopt an EGF-like fold.¡€0€ª€0€ €CDD¡€ €Å~¢€0€0€ €‚pfam09290, AcetDehyd-dimer, Prokaryotic acetaldehyde dehydrogenase, dimerisation. Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerisation of the protein.¡€0€ª€0€ €CDD¡€ €Å¢€0€0€ €‚,pfam09291, DUF1968, Domain of unknown function (DUF1968). Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined.¡€0€ª€0€ €CDD¡€ €Å€¢€0€0€ €Õpfam09292, Neil1-DNA_bind, Endonuclease VIII-like 1, DNA bind. Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding.¡€0€ª€0€ €CDD¡€ €Å¢€0€0€ €‚*pfam09293, RNaseH_C, T4 RNase H, C terminal. Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork.¡€0€ª€0€ €CDD¡€ €^²¢€0€0€ €‚"pfam09294, Interfer-bind, Interferon-alpha/beta receptor, fibronectin type III. Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha.¡€0€ª€0€ €CDD¡€ €Å‚¢€0€0€ €‚pfam09295, ChAPs, ChAPs (Chs5p-Arf1p-binding proteins). ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialized cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they form also interactions with each other.¡€0€ª€0€ €CDD¡€ €^´¢€0€0€ €­pfam09296, NUDIX-like, NADH pyrophosphatase-like rudimentary NUDIX domain. The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP.¡€0€ª€0€ €CDD¡€ €Ń¢€0€0€ €¡pfam09297, zf-NADH-PPase, NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.¡€0€ª€0€ €CDD¡€ €Å„¢€0€0€ €Ípfam09298, FAA_hydrolase_N, Fumarylacetoacetase N-terminal. The N-terminal domain of fumarylacetoacetate hydrolase is functionally uncharacterized, and adopts a structure consisting of an SH3-like barrel.¡€0€ª€0€ €CDD¡€ €Å…¢€0€0€ €Çpfam09299, Mu-transpos_C, Mu transposase, C-terminal. Members of this family are found in various prokaryotic integrases and transposases. They adopt a beta-barrel structure with Greek-key topology.¡€0€ª€0€ €CDD¡€ €ņ¢€0€0€ €…pfam09300, Tecti-min-caps, Tectiviridae, minor capsid. Members of this family form the minor capsid protein of various Tectiviridae.¡€0€ª€0€ €CDD¡€ €^¹¢€0€0€ €‘pfam09301, DUF1970, Domain of unknown function (DUF1970). Members of this family consist of various uncharacterized viral hypothetical proteins.¡€0€ª€0€ €CDD¡€ €^º¢€0€0€ €‚Mpfam09302, XLF, XLF-Cernunnos, XRcc4-like factor, NHEJ component. XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining. This family contains Nej1 (non-homologous end-joining factor), and Lif1, ligase-interacting factor. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining.¡€0€ª€0€ €CDD¡€ €Ň¢€0€0€ €‚ pfam09303, KcnmB2_inactiv, KCNMB2, ball and chain domain. Members of this family are found in the cytoplasmic N-terminus of KCNMB2, the beta-2 subunit of large conductance calcium and voltage-activated potassium channels. They are responsible for the fast inactivation of these channels.¡€0€ª€0€ €CDD¡€ €^¼¢€0€0€ €‚>pfam09304, Cortex-I_coil, Cortexillin I, coiled coil. Members of this family are predominantly found in the actin-bundling protein Cortexillin I from Dictyostelium discoideum. They adopt a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and are a prerequisite for the assembly of Cortexillin I.¡€0€ª€0€ €CDD¡€ €ň¢€0€0€ €ßpfam09305, TACI-CRD2, TACI, cysteine-rich domain. Members of this family are predominantly found in tumor necrosis factor receptor superfamily, member 13b (TACI), and are required for binding to the ligands APRIL and BAFF.¡€0€ª€0€ €CDD¡€ €ʼn¢€0€0€ €–pfam09306, Phage-scaffold, Bacteriophage, scaffolding protein. Members of this family of scaffolding proteins are produced by various bacteriophages.¡€0€ª€0€ €CDD¡€ €^¿¢€0€0€ €‚pfam09307, MHC2-interact, CLIP, MHC2 interacting. Members of this family are found in class II invariant chain-associated peptide (CLIP), and are required for association with class II major histocompatibility complex (MHC) in the MHC class II processing pathway.¡€0€ª€0€ €CDD¡€ €ÅŠ¢€0€0€ €ãpfam09308, LuxQ-periplasm, LuxQ, periplasmic. Members of this family constitute the periplasmic sensor domain of the prokaryotic protein LuxQ, and assume a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds.¡€0€ª€0€ €CDD¡€ €^Á¢€0€0€ €‚pfam09309, FCP1_C, FCP1, C-terminal. The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains.¡€0€ª€0€ €CDD¡€ €Å‹¢€0€0€ €‚Hpfam09310, PD-C2-AF1, POU domain, class 2, associating factor 1. Members of this family are transcriptional coactivators that specifically associate with either OCT1 or OCT2, through recognition of their POU domains. They are essential for the response of B-cells to antigens and required for the formation of germinal centers.¡€0€ª€0€ €CDD¡€ €ÅŒ¢€0€0€ €‚ pfam09311, Rab5-bind, Rabaptin-like protein. Members of this family are predominantly found in Rabaptin and allow for binding to the GTPase Rab5. This interaction is necessary and sufficient for Rab5-dependent recruitment of Rabaptin5 to early endosomal membranes.¡€0€ª€0€ €CDD¡€ €Å¢€0€0€ €‚pfam09312, SurA_N, SurA N-terminal domain. This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.¡€0€ª€0€ €CDD¡€ €ÅŽ¢€0€0€ €¼pfam09313, DUF1971, Domain of unknown function (DUF1971). Members of this family of functionally uncharacterized domains are predominantly found in bacterial Tellurite resistance protein.¡€0€ª€0€ €CDD¡€ €Å¢€0€0€ €Àpfam09314, DUF1972, Domain of unknown function (DUF1972). Members of this family of functionally uncharacterized domains are found in bacterial glycosyltransferases and rhamnosyltransferases.¡€0€ª€0€ €CDD¡€ €^Ç¢€0€0€ €ñpfam09316, Cmyb_C, C-myb, C-terminal. Members of this family are predominantly found in the proto-oncogene c-myb and the viral transforming protein myb. Truncation of the domain results in 'activation' of c-myb and subsequent tumorigenesis.¡€0€ª€0€ €CDD¡€ €Å¢€0€0€ €Èpfam09317, DUF1974, Domain of unknown function (DUF1974). Members of this family of functionally uncharacterized domains are predominantly found in various prokaryotic acyl-coenzyme a dehydrogenases.¡€0€ª€0€ €CDD¡€ €Å‘¢€0€0€ €‚äpfam09318, Glyco_trans_A_1, Glycosyl transferase 1 domain A. Glyco_trans_A_1 is family of found predominantly at the N-terminus of various prokaryotic alpha-glucosyltransferases. According to whether the domain exists as a whole molecule or as a half molecule determines the number of sugar residues that the molecule transfers. Two-domain proteins are processive in that they transfer more than one sugar residue, processively; single domain proteins transfer just one sugar moiety.¡€0€ª€0€ €CDD¡€ €^Ê¢€0€0€ €¨pfam09320, DUF1977, Domain of unknown function (DUF1977). Members of this family of functionally uncharacterized domains are predominantly found in dnaj-like proteins.¡€0€ª€0€ €CDD¡€ €Å’¢€0€0€ €ãpfam09321, DUF1978, Domain of unknown function (DUF1978). Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.¡€0€ª€0€ €CDD¡€ €Å“¢€0€0€ €¶pfam09322, DUF1979, Domain of unknown function (DUF1979). Members of this family of functionally uncharacterized domains are found in various Oryza sativa mutator-like transposases.¡€0€ª€0€ €CDD¡€ €Å”¢€0€0€ €¿pfam09323, DUF1980, Domain of unknown function (DUF1980). Members of this family are found in a set of prokaryotic hypothetical proteins. Their exact function, has not, as yet, been defined.¡€0€ª€0€ €CDD¡€ €Å•¢€0€0€ €ºpfam09324, DUF1981, Domain of unknown function (DUF1981). Members of this family of functionally uncharacterized domains are found in various plant and yeast protein transport proteins.¡€0€ª€0€ €CDD¡€ €Å–¢€0€0€ €“pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin that functions in membrane trafficking. This is the C terminal dimerisation domain.¡€0€ª€0€ €CDD¡€ €Å—¢€0€0€ €ßpfam09326, NADH_dhqG_C, NADH-ubiquinone oxidoreductase subunit G, C-terminal. Members of this family of are found at the C-terminus of NADH dehydrogenases subunit G or NADH-ubiquinone oxidoreductase subunit G. EC:1.6.99.5.¡€0€ª€0€ €CDD¡€ €Ř¢€0€0€ €·pfam09327, DUF1983, Domain of unknown function (DUF1983). Members of this family of functionally uncharacterized domains are found in various bacteriophage host specificity proteins.¡€0€ª€0€ €CDD¡€ €Å™¢€0€0€ €¿pfam09328, Phytochelatin_C, Domain of unknown function (DUF1984). Members of this family of functionally uncharacterized domains are found at the C-terminus of plant phytochelatin synthases.¡€0€ª€0€ €CDD¡€ €Åš¢€0€0€ €vpfam09329, zf-primase, Primase zinc finger. This zinc finger is found in yeast Mcm10 proteins and DnaG-type primases.¡€0€ª€0€ €CDD¡€ €Å›¢€0€0€ €‚Spfam09330, Lact-deh-memb, D-lactate dehydrogenase, membrane binding. Members of this family are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association.¡€0€ª€0€ €CDD¡€ €Åœ¢€0€0€ €»pfam09331, DUF1985, Domain of unknown function (DUF1985). Members of this family of functionally uncharacterized domains are found in a set of Arabidopsis thaliana hypothetical proteins.¡€0€ª€0€ €CDD¡€ €Å¢€0€0€ €©pfam09332, Mcm10, Mcm10 replication factor. Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha.¡€0€ª€0€ €CDD¡€ €Åž¢€0€0€ €Ápfam09333, ATG_C, Autophagy-related protein C terminal domain. ATG2 (also known as Apg2) is a peripheral membrane protein. It functions in both cytoplasm-to-vacuole targeting and in autophagy.¡€0€ª€0€ €CDD¡€ €ÅŸ¢€0€0€ €hpfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family includes methionyl tRNA synthetases.¡€0€ª€0€ €CDD¡€ €^Ø¢€0€0€ €®pfam09335, SNARE_assoc, SNARE associated Golgi protein. This is a family of SNARE associated Golgi proteins. The yeast member of this family localizes with the t-SNARE Tlg2.¡€0€ª€0€ €CDD¡€ €Å ¢€0€0€ €Úpfam09336, Vps4_C, Vps4 C terminal oligomerization domain. This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerization.¡€0€ª€0€ €CDD¡€ €Å¡¢€0€0€ €ÿpfam09337, zf-H2C2, His(2)-Cys(2) zinc finger. This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters. Added to clan to resolve overlaps with PF16721 but neither are classic zf_C2H2 zinc-fingers.¡€0€ª€0€ €CDD¡€ €Å¢¢€0€0€ €‚)pfam09338, Gly_reductase, Glycine/sarcosine/betaine reductase component B subunits. This is a family of glycine reductase, sarcosine reductase and betaine reductases. These enzymes catalyze the following reactions. sarcosine reductase: Acetyl phosphate + methylamine + thioredoxin disulphide = N-methylglycine + phosphate + thioredoxin Acetyl phosphate + NH(3) + thioredoxin disulphide = glycine + phosphate + thioredoxin. betaine reductase: Acetyl phosphate + trimethylamine + thioredoxin disulphide = N,N,N-trimethylglycine + phosphate + thioredoxin.¡€0€ª€0€ €CDD¡€ €Å£¢€0€0€ €4pfam09339, HTH_IclR, IclR helix-turn-helix domain. ¡€0€ª€0€ €CDD¡€ €^Ý¢€0€0€ €‚[pfam09340, NuA4, Histone acetyltransferase subunit NuA4. The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control.¡€0€ª€0€ €CDD¡€ €Ť¢€0€0€ €§pfam09341, Pcc1, Transcription factor Pcc1. Pcc1 is a transcription factor that functions in regulating genes involved in cell cycle progression and polarised growth.¡€0€ª€0€ €CDD¡€ €Å¥¢€0€0€ €‘pfam09342, DUF1986, Domain of unknown function (DUF1986). This domain is found in serine proteases and is predicted to contain disulphide bonds.¡€0€ª€0€ €CDD¡€ €^ࢀ0€0€ €çpfam09343, DUF2460, Conserved hypothetical protein 2217 (DUF2460). This model represents a family of conserved hypothetical proteins. It is usually (but not always) found in apparent phage-derived regions of bacterial chromosomes.¡€0€ª€0€ €CDD¡€ €Ŧ¢€0€0€ €‚8pfam09344, Cas_CT1975, CT1975-like protein. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum.¡€0€ª€0€ €CDD¡€ €ŧ¢€0€0€ €tpfam09345, DUF1987, Domain of unknown function (DUF1987). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ũ¢€0€0€ €‚pfam09346, SMI1_KNR4, SMI1 / KNR4 family (SUKH-1). Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems.¡€0€ª€0€ €CDD¡€ €Å©¢€0€0€ €tpfam09347, DUF1989, Domain of unknown function (DUF1989). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Ū¢€0€0€ €tpfam09348, DUF1990, Domain of unknown function (DUF1990). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Å«¢€0€0€ €‚}pfam09349, OHCU_decarbox, OHCU decarboxylase. The proteins in this family are OHCU decarboxylase - enzymes of the purine catabolism that catalyze the conversion of OHCU into S(+)-allantoin. This is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalyzed by urate oxidase (pfam01014) and step two is catalyzed by HIUases (pfam00576).¡€0€ª€0€ €CDD¡€ €Ŭ¢€0€0€ €tpfam09350, DUF1992, Domain of unknown function (DUF1992). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Å­¢€0€0€ €tpfam09351, DUF1993, Domain of unknown function (DUF1993). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Å®¢€0€0€ €tpfam09353, DUF1995, Domain of unknown function (DUF1995). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ů¢€0€0€ €‚Fpfam09354, HNF_C, HNF3 C-terminal domain. This presumed domain is found in the C-terminal region of Hepatocyte Nuclear Factor 3 alpha and beta chains. Its specific function is uncertain. The N-terminal region of this presumed domain contains an EH1 (engrailed homology 1) motif, that is characterized by the FxIxxIL sequence.¡€0€ª€0€ €CDD¡€ €Å°¢€0€0€ €pfam09355, Phage_Gp19, Phage protein Gp19/Gp15/Gp42. This family of proteins are functionally uncharacterized. They are found in a variety of bacteriophage.¡€0€ª€0€ €CDD¡€ €^좀0€0€ €‚Ùpfam09356, Phage_BR0599, Phage conserved hypothetical protein BR0599. This entry describes a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.¡€0€ª€0€ €CDD¡€ €ű¢€0€0€ €‚pfam09357, RteC, RteC protein. Human colonic Bacteroides species harbor a family of large conjugative transposons, called tetracycline resistance (Tcr) elements. Activities of these elements are enhanced by pregrowth of bacteria in medium containing tetracycline, indicating that at least some Tcr element genes are regulated by tetracycline. An insertional disruption in the rteC gene abolished self-transfer of the Tcr element to Bacteroides recipients, indicating that the gene was essential for self-transfer.¡€0€ª€0€ €CDD¡€ €Ų¢€0€0€ €«pfam09358, E1_UFD, Ubiquitin fold domain. The ubiquitin fold domain is found at the C-terminus of ubiquitin-activating E1 family enzymes. This domain binds to E2 enzymes.¡€0€ª€0€ €CDD¡€ €ų¢€0€0€ €Àpfam09359, VTC, VTC domain. This presumed domain is found in the yeast vacuolar transport chaperone proteins VTC2, VTC3 and VTC4. This domain is also found in a variety of bacterial proteins.¡€0€ª€0€ €CDD¡€ €Å´¢€0€0€ €‚Gpfam09360, zf-CDGSH, Iron-binding zinc finger CDGSH type. The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, pfam10660. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm.¡€0€ª€0€ €CDD¡€ €ŵ¢€0€0€ €‚?pfam09361, Phasin_2, Phasin protein. This entry describes a group of small proteins found associated with inclusions in bacterial cells. Most associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB). These are designated granule-associate proteins or phasins.¡€0€ª€0€ €CDD¡€ €Ŷ¢€0€0€ €tpfam09362, DUF1996, Domain of unknown function (DUF1996). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Å·¢€0€0€ €ìpfam09363, XFP_C, XFP C-terminal domain. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22.¡€0€ª€0€ €CDD¡€ €Ÿ¢€0€0€ €‚/pfam09364, XFP_N, XFP N-terminal domain. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22. This family is distantly related to transketolases e.g. pfam02779.¡€0€ª€0€ €CDD¡€ €^õ¢€0€0€ €‚pfam09365, DUF2461, Conserved hypothetical protein (DUF2461). Members of this family are widely (though sparsely) distributed bacterial proteins, about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown.¡€0€ª€0€ €CDD¡€ €Ź¢€0€0€ €upfam09366, DUF1997, Protein of unknown function (DUF1997). This family of proteins are functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €ź¢€0€0€ €opfam09367, CpeS, CpeS-like protein. This family, that includes CpeS proteins, is functionally uncharacterized.¡€0€ª€0€ €CDD¡€ €Å»¢€0€0€ €Ùpfam09368, Sas10, Sas10 C-terminal domain. Sas10 is an Essential subunit of U3-containing Small Subunit (SSU) processome complex involved in the production of the 18S rRNA and assembly of the small ribosomal subunit.¡€0€ª€0€ €CDD¡€ €ż¢€0€0€ €þpfam09369, DUF1998, Domain of unknown function (DUF1998). This family of proteins are functionally uncharacterized. They are mainly found in helicase proteins so could be RNA binding. This family includes a probable zinc binding motif at its C-terminus.¡€0€ª€0€ €CDD¡€ €Ž¢€0€0€ €¨pfam09370, PEP_hydrolase, Phosphoenolpyruvate hydrolase-like. This domain has a TIM barrel fold related to IGPS and to phosphoenolpyruvate mutase/aldolase/carboxylase.¡€0€ª€0€ €CDD¡€ €ž¢€0€0€ €Ùpfam09371, Tex_N, Tex-like protein N-terminal domain. This presumed domain is found at the N-terminus of Bordetella pertussis tex. This protein defines a novel family of prokaryotic transcriptional accessory factors.¡€0€ª€0€ €CDD¡€ €Å¿¢€0€0€ €‚Upfam09372, PRANC, PRANC domain. This presumed domain is found at the C-terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin - C terminal) domain is also found on its own in some proteins. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role.¡€0€ª€0€ €CDD¡€ €^ý¢€0€0€ €‚Gpfam09373, PMBR, Pseudomurein-binding repeat. Methanothermobacter thermautotrophicus is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.¡€0€ª€0€ €CDD¡€ €Ì›¢€