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Search results 6001 to 6100 out of 30763 for seed protein

Category restricted to ProteinDomain (x)

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Categories

Category: ProteinDomain
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Type Details Score
Protein Domain
IPR024912
Name: Protein translocase subunit SecD, archaeal
Type: Family
Description: Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them tothe translocase component [ ]. From there, the mature proteins are either targeted to the outermembrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integralmembrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers"in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membraneprotein ATPase SecA for secretion [ ]. Together with SecY and SecG, SecE forms a multimericchannel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of theEscherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide,denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDFof B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps [].Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conservedregions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembranedomains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters [].This family consists of various archaeal SecD proteins. They show a high degree of structural and functional similarity to their bacterial homologues, despite the different composition of their translocation machineries [ ].
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Protein Domain
IPR024919
Name: ECF transporter transmembrane protein EcfT
Type: Family
Description: Energy-coupling factor (ECF) transporters consist of a substrate-specific component (known as the S component), and an energy-coupling module [ ]. The substrate-binding component is a small integral membrane protein which captures specific substrates and forms an active transporter in the presence of the energy-coupling AT module. The energy coupling module is composed of an ATPase typical of the ATP binding cassette (ABC) superfamily (A component) and a characteristic transmembrane protein (T component). Unlike the ABC transporters, an energy coupling module can be shared between multiple different substrate-binding components.This entry represents the transmembrane component from a number of ECF transporters. The function of this component is not known, but it contains two conserved motifs (I and II) that are important for transporter function [ ]. Motif I is essential for intramolecular signaling while motifs I and II together are essential for subunit assembly of modular ECF transporters
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Protein Domain
IPR009337
Name: Protein of unknown function DUF995
Type: Family
Description: This is a family of uncharacterised Proteobacteria proteins.
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Protein Domain
IPR009338
Name: Protein of unknown function Orf51
Type: Family
Description: This entry is represents a family of predicted proteins found in bacteriophages and prophages.
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Protein Domain
IPR010323
Name: Protein of unknown function DUF924
Type: Family
Description: This entry consists of several hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR009339
Name: Protein of unknown function DUF998
Type: Family
Description: This is a family of proteins with no known function.
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Protein Domain
IPR010328
Name: Protein of unknown function DUF928
Type: Family
Description: This is a family of uncharacterised bacterial proteins.
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Protein Domain
IPR009333
Name: Protein of unknown function DUF992
Type: Family
Description: This entry consists of several hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR009334
Name: Protein of unknown function DUF993
Type: Family
Description: This entry consists of several hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR024979
Name: Protein of unknown function DUF3884
Type: Family
Description: This family of proteins is functionally uncharacterised. Several of them are annotated as Tagatose 1,6-diphosphate aldolase, but there appears to be no direct evidence to support this. Proteins in this family are typically between 61 and 106 amino acids in length and have two completely conserved residues (Y and F) that may be functionally important.
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Protein Domain
IPR010321
Name: Protein of unknown function DUF922
Type: Family
Description: This entry consists of several hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR036950
Name: Penicillin binding protein transglycosylase domain
Type: Homologous_superfamily
Description: Penicillin-binding proteins, such as Escherichia coli PBP1b, are bifunctional transglycosylases that consist of a transmembrane helix, a transglycosylase domain and a transpeptidase domain [ ]. The transglycosylase domain catalyses the polymerisation of murein glycan chains []. This domain is also found on its own in monofunctional peptidoglycan transglycosylases [].
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Protein Domain
IPR009340
Name: Protein of unknown function DUF999
Type: Family
Description: This is a family of conserved Schizosaccharomyces proteins with unknown function.
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Protein Domain
IPR009343
Name: Protein of unknown function DUF1002
Type: Family
Description: This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
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Protein Domain
IPR024968
Name: Surface layer protein A domain
Type: Domain
Description: This short domain is found in Lactobacillus S-layer proteins [ ] and in a variety of bacterial cell surface proteins. The domain is about 60 residues in length (although previously defined as 2 copies of this domain). It usually occurs in tandem pairs. It may be distantly related to the SH3 domain.
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Protein Domain
IPR012965
Name: Meiotically up-regulated protein Msb1/Mug8 domain
Type: Domain
Description: This domain of unknown function is found in fungal proteins, including Mug8 from Schizosaccharomyces pombe which may have a role in meiosis and septation [ ]. Saccharomyces cerevisiae homologue MSB1() may be involved in positive regulation of 1,3-beta-glucan synthesis and the Pkc1p-MAPK pathway [ ].
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Protein Domain
IPR012964
Name: Protein of unknown function DUF1702
Type: Family
Description: This family of proteins contains many bacterial proteins that are encoded by the unbL gene. The function of these proteins is unknown.
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Protein Domain
IPR012963
Name: Protein of unknown function DUF1700
Type: Family
Description: This family contains many hypothetical bacterial proteins and two putative membrane proteins ( and ).
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Protein Domain
IPR009319
Name: Lactococcus phage , Structural protein
Type: Family
Description: This entry represents Structural protein from Lactococcus phage and similar proteins from tailed bacteriophages and bacterial prophages.
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Protein Domain
IPR036931
Name: Polyomavirus capsid protein VP1 superfamily
Type: Homologous_superfamily
Description: This entry represents the major capsid protein VP1 (viral protein 1) from Polyomaviruses, such as Murine polyomavirus (strain P16 small-plaque) (MPyV) [ ]. Polyomaviruses are dsDNA viruses with no RNA stage in their life cycle. The virus capsid is composed of 72 icosahedral units, each of which is composed of five copies of VP1. The virus attaches to the cell surface by recognition of oligosaccharides terminating in alpha(2,3)-linked sialic acid. The capsid protein VP1 forms a pentamer. The complete capsid is composed of 72 VP1 pentamers, with a minor capsid protein, VP2 or VP3, inserted into the centre of each pentamer like a hairpin. This structure restricts the exposure of internal proteins during viral entry. Polyomavirus coat assembly is rigorously controlled by chaperone-mediated assembly. During viral infection, the heat shock chaperone hsc70 binds VP1 and co-localises it in the nucleus, thereby regulating capsid assembly [].
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Protein Domain
IPR009325
Name: Protein of unknown function DUF983
Type: Family
Description: This family consists of several bacterial proteins of unknown function.
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Protein Domain
IPR009326
Name: Protein of unknown function DUF984
Type: Family
Description: This is a family of bacterial proteins with unknown function. This entry includes the uncharacterised protein YhfF from Bacillus subtilis.
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Protein Domain
IPR009328
Name: Protein of unknown function DUF986
Type: Family
Description: This family consists of several bacterial putative membrane proteins of unknown function.
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Protein Domain
IPR009329
Name: Protein of unknown function DUF987
Type: Family
Description: This is a family of bacterial proteins that are related to the hypothetical protein YeeT.
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Protein Domain
IPR010318
Name: Protein of unknown function DUF917
Type: Family
Description: This family consists of hypothetical bacterial, archaeal and eukaryotic proteins of unknown function.
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Protein Domain
IPR009321
Name: Protein of unknown function DUF973
Type: Family
Description: This family consists of proteins of unknown function.
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Protein Domain
IPR009323
Name: Protein of unknown function DUF979
Type: Family
Description: This family consists of several putative bacterial membrane proteins. The function of this family is unclear.
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Protein Domain
IPR009324
Name: Protein of unknown function DUF981
Type: Family
Description: This is a family of uncharacterised proteins found in bacteria and archaea.
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Protein Domain
IPR009372
Name: Poxvirus virion membrane protein A14.5
Type: Family
Description: This is a family of Poxvirus proteins. It includes virion membrane protein A14.5 from Vaccinia virus, which has been shown to enhance virulence in mice [ ].
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Protein Domain
IPR009376
Name: Protein of unknown function DUF1031
Type: Family
Description: This family of uncharacterised proteins is found mostly in Lactococcus species and their bacteriophages.
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Protein Domain
IPR046318
Name: Protein of unknown function DUF5344
Type: Family
Description: This is a bacterial family of unknown function which includes YxiC and YwqI proteins from Bacillus subtilis. Family members are predicted to belong to Type VII secretion (T7S) system. There is a conserved YxxxD/E sequence. It is a general secretion signal that is present in all known mycobacterial T7S substrates or substrate complexes [ ].
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Protein Domain
IPR046314
Name: Protein of unknown function DUF6466
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Bacteria. Proteins in this family are approximately 190 amino acids in length. They contain the conserved motifs QQQQ, SxxLT and KPW. Members in this family are probably cell surface proteins, some of them are likely elastin binding proteins.
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Protein Domain
IPR046313
Name: Protein of unknown function DUF6465
Type: Family
Description: This family of proteins is functionally uncharacterised, predominantly found in bacteria. Proteins in this family have a highly charged N terminus.
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Protein Domain
IPR046311
Name: Protein of unknown function DUF6426
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001396) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the aldgamycin J biosynthetic gene cluster from Streptomyces sp. A1(2016) [ ].
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Protein Domain
IPR046310
Name: Protein of unknown function DUF6425
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001281) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ustilagic acid biosynthetic gene cluster from Ustilago maydis 521 [ ]. This family appears to be predominantly found in fungi.
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Protein Domain
IPR009380
Name: Protein of unknown function DUF1036
Type: Family
Description: This entry consists of several hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR010360
Name: Protein of unknown function DUF956
Type: Family
Description: This is a family of bacterial sequences with undetermined function.
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Protein Domain
IPR010365
Name: Protein of unknown function DUF961
Type: Family
Description: This entry consists of several hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR036988
Name: Picornavirus coat protein VP4 superfamily
Type: Homologous_superfamily
Description: Picornaviruses are single-stranded RNA viruses. Processing of the viral polyprotein by picornains 3C and 2A generates capsid proteins VP0, VP1 and VP3, but VP0 undergoes an autolytic cleavage during virion assembly to generate capsid proteins VP2 and VP4 [ ]. The autolytic cleavage was originally thought to be the action of a serine-type peptidase, but from analogy with the similar autoproteolytic cleavages that are known for capsid proteins from nodaviruses (MEROPS peptidase family N1), tetraviruses (MEROPS peptidase family N2), picobirnaviruses (MEROPS peptidase family N5) and reoviruses (MEROPS peptidase family N7), it is more likely that VP0 is an asparagine-type peptidase; autocatalytic cleavage being promoted by cyclization of a conserved asparagine. .
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Protein Domain
IPR009383
Name: Protein of unknown function DUF1040
Type: Family
Description: This family consists of several bacterial YihD proteins of unknown function [ ].
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Protein Domain
IPR046309
Name: Protein of unknown function DUF6424
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000379) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the glycinocin A biosynthetic gene cluster from streptomyces viridochromogenes [ ].
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Protein Domain
IPR046308
Name: Protein of unknown function DUF6423
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp. [ ].
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Protein Domain
IPR046307
Name: Protein of unknown function DUF6422
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the lavendiol biosynthetic gene cluster from Streptomyces lavendulae [ ].
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Protein Domain
IPR046306
Name: Protein of unknown function DUF6421
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000877) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the polyoxin A biosynthetic gene cluster from Streptomyces cacaoi subsp. asoensis [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR009389
Name: Protein of unknown function DUF1045
Type: Family
Description: This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
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Protein Domain
IPR022363
Name: Bacteriophage TP901-1, major tail protein
Type: Family
Description: Two major structural proteins from the lactococcal temperate bacteriophage TP901-1 have been sequenced: the Major Head Protein (MHP) and the Major Tail Protein (MTP) [ ]. Homologues of the major tail protein have since been found in Staphylococcus, Streptococcus and Lactobacillus phages. The sequences are fairly short, typically ~150-200 amino acid residues in length, and are well conserved. This family of proteins (designated here phage MTP 2) has its own distinct sequence signature that distinguishes it from the MTP 1 family (see MTP1FAMILY ). Sequences belonging to the MTP 2 family are longer than those belonging to the MTP 1 family, and are well conserved across a range of species. This entry represents the lactococcal proteins from the MTP2 family.
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Protein Domain
IPR011855
Name: Phage major tail protein TP901-1
Type: Family
Description: This entry describes the major tail protein (MTP) of the Siphoviridae and MTP genes in prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [ ], including ORFg9 (RCAP_rcc01691) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ]. The tail tube protein gp17.1* from bacteriophage SPP1 forms a sixfold helical, rigid tail tube which ejects of the phage DNA into the host when it binds to the entry receptor on the host cell surface, triggering structural rearrangements of the tail tube [].
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Protein Domain
IPR046305
Name: Protein of unknown function DUF6420
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis [ ].
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Protein Domain
IPR046304
Name: Protein of unknown function DUF6419
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000299) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the alterochromide A biosynthetic gene cluster from Pseudoalteromonas piscicida JCM 20779 [ ].
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Protein Domain
IPR046301
Name: Protein of unknown function DUF6416
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001300) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the anthracimycin biosynthetic gene cluster from Streptomyces sp. CNH365 [ ].
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Protein Domain
IPR046300
Name: Protein of unknown function DUF6415
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR010373
Name: Protein of unknown function DUF968
Type: Family
Description: This is a family of uncharacterised prophage proteins that are also found in bacteria. They have been predicted to have the His-Me finger nuclease domain and may act as a recombinase that participates in DNA repair and replication [ ].
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Protein Domain
IPR010374
Name: Protein of unknown function DUF969
Type: Family
Description: This is a family of uncharacterised bacterial membrane proteins.
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Protein Domain
IPR023976
Name: Conserved hypothetical protein CHP04031, Htur1727
Type: Family
Description: Members of this protein family show homology to the putative PaaH (or PaaB) subunit of the phenylacetate-CoA oxygenase complex. However, all members are found in the Halobacteriales in the vicinity of a radical SAM protein homologous to the PqqE protein of pyroquinoline quinone (PQQ) biosynthesis. Members are well-conserved to about residue 75, but then become low-complexity and hypervariable.
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Protein Domain
IPR024992
Name: Protein of unknown function DUF3891
Type: Family
Description: This family consists of proteins that have not yet been functionally uncharacterised.
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Protein Domain
IPR024995
Name: Protein of unknown function DUF3895
Type: Family
Description: This family of bacterial proteins is functionally uncharacterised. There are two completely conserved residues (Y and L) that may be functionally important.
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Protein Domain
IPR024993
Name: Protein of unknown function DUF3894
Type: Family
Description: This family of bacterial proteins is functionally uncharacterised. They contain two conserved sequence motifs: FNIC and MALLNLT.
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Protein Domain
IPR024994
Name: Protein of unknown function DUF3896
Type: Family
Description: This family of bacterial proteins is functionally uncharacterised.
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Protein Domain
IPR024999
Name: Protein of unknown function DUF3905
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
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Protein Domain
IPR024997
Name: Protein of unknown function DUF3892
Type: Family
Description: DUF3892 is related to the truncated RNaseH fold-containing ribosome hibernation factors. Predicted to function as a possible conflict effector domain at the ribosome, based on comparable genome contextual associations with DUF2188, including repeated association with nucleotide-activated effector conflict systems [ ].
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Protein Domain
IPR024998
Name: Protein of unknown function DUF3906
Type: Family
Description: This family of bacterial proteins is functionally uncharacterised. Family members are approximately 70 amino acids in length. There is a conserved EKK sequence motif.
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Protein Domain
IPR010342
Name: Protein of unknown function DUF938
Type: Family
Description: This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. Chordate members are known as 'methyltransferase-like 26'. The function of this family is unknown.
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Protein Domain
IPR024980
Name: Protein of unknown function DUF3886
Type: Family
Description: This family of proteins is functionally uncharacterised. Proteins in this family are approximately 90 amino acids in length and contain two completely conserved L residues that may be functionally important.
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Protein Domain
IPR022322
Name: Insulin-like growth factor-binding protein 1
Type: Family
Description: Insulin-like growth factors (IGFs)-I and -II are small secreted peptides that stimulate the survival, and promote the proliferation and differentiation, of many cell types [ ]. In biological fluids, these growth factors are usually bound to IGF binding proteins (IGFBPs), which regulate their availability and activity by prolonging their half-life and modulating their receptor interactions. To date, six IGFBP family members have been identified (termed IGFBP1-6) [ ]. They share a conserved gene (intron-exon) organisation and high IGF binding affinity. Structurally, the proteins also share a common domain architecture, possessing a conserved N-terminal IGFBP domain, a highly variable mid-section, and a thyroglobulin type-1 (Tg1) domain in their C-terminal regions. In addition to their role in the regulation of IGF activity, there is evidence for the direct association of IGFBPs with a variety of extracellular and cell surface molecules [ , ], with consequent effects upon important biological processes. These include modulation of bone cell proliferation [ ], and growth arrest of breast and prostate cancer cells [, ]. IGFBP1 (also known as amniotic fluid binding protein (AFBP) and placental protein-12) is involved in the regulation of foetal growth: there is a strong inverse correlation between circulating IGFBP1 levels and foetal size [ ]. It also functions as a survival factor and pro-regeneration factor in the liver [].
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Protein Domain
IPR022326
Name: Insulin-like growth factor-binding protein 6
Type: Family
Description: Insulin-like growth factors (IGFs)-I and -II are small secreted peptides that stimulate the survival, and promote the proliferation and differentiation, of many cell types [ ]. In biological fluids, these growth factors are usually bound to IGF binding proteins (IGFBPs), which regulate their availability and activity by prolonging their half-life and modulating their receptor interactions. To date, six IGFBP family members have been identified (termed IGFBP1-6) [ ]. They share a conserved gene (intron-exon) organisation and high IGF binding affinity. Structurally, the proteins also share a common domain architecture, possessing a conserved N-terminal IGFBP domain, a highly variable mid-section, and a thyroglobulin type-1 (Tg1) domain in their C-terminal regions. In addition to their role in the regulation of IGF activity, there is evidence for the direct association of IGFBPs with a variety of extracellular and cell surface molecules [ , ], with consequent effects upon important biological processes. These include modulation of bone cell proliferation [], and growth arrest of breast and prostate cancer cells [, ]. IGFBP6 is a potent inducer of programmed cell death in lung cancer cells [ ]. The protein may therefore represent a potential target as a cancer therapeutic.
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Protein Domain
IPR022327
Name: Insulin-like growth factor-binding protein 4
Type: Family
Description: Insulin-like growth factors (IGFs)-I and -II are small secreted peptides that stimulate the survival, and promote the proliferation and differentiation, of many cell types [ ]. In biological fluids, these growth factors are usually bound to IGF binding proteins (IGFBPs), which regulate their availability and activity by prolonging their half-life and modulating their receptor interactions. To date, six IGFBP family members have been identified (termed IGFBP1-6) [ ]. They share a conserved gene (intron-exon) organisation and high IGF binding affinity. Structurally, the proteins also share a common domain architecture, possessing a conserved N-terminal IGFBP domain, a highly variable mid-section, and a thyroglobulin type-1 (Tg1) domain in their C-terminal regions. In addition to their role in the regulation of IGF activity, there is evidence for the direct association of IGFBPs with a variety of extracellular and cell surface molecules [ , ], with consequent effects upon important biological processes. These include modulation of bone cell proliferation [], and growth arrest of breast and prostate cancer cells [, ]. IGFBP4 is abundant in serum, and is expressed in many different tissues. The protein functions as a cardiogenic growth factor in mice -an effect that is IGF-independent, and mediated by inhibition on the canonical Wnt signalling pathway [ ].
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Protein Domain
IPR024984
Name: Protein of unknown function DUF3888
Type: Family
Description: This family of proteins is functionally uncharacterised
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Protein Domain
IPR009368
Name: Protein of unknown function DUF1024
Type: Family
Description: This family consists of several hypothetical proteins, mainly Staphylococcus aureus phage phi proteins which are related to Orf64 from Staphylococcus phage 92 (Bacteriophage 92). The function of this family is unknown.
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Protein Domain
IPR024987
Name: Protein of unknown function DUF3889
Type: Family
Description: This family of proteins is functionally uncharacterised. Proteins in this family are approximately 110 amino acids in length and contain two completely conserved residues (A and Y) that may be functionally important.
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Protein Domain
IPR009371
Name: Type III secretion protein HrpF
Type: Family
Description: The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity [ ].
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Protein Domain
IPR010351
Name: Protein of unknown function DUF943
Type: Family
Description: This family consists of several hypothetical membrane proteins mainly from Enterobacteria.
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Protein Domain
IPR022386
Name: Carbohydrate ABC transporter, N-acetylglucosamine/diacetylchitobiose-binding protein
Type: Family
Description: Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins [ , ].Members of this protein family include the substrate-binding protein diacetylchitobiose binding protein NgcE. NgcE binds both N-acetylglucosamine and the chitin dimer, N,N'-diacetylchitobiose [ ].
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Protein Domain
IPR022389
Name: ParB-related, ThiF-related cassette, protein D
Type: Family
Description: A novel genetic system, often found on plasmids, encodes six major proteins, included a ParB homologue and a ThiF homologue, and is designated PRTRC (ParB-Related, ThiF-Related Cassette). This entry represents PRTRC system protein D.
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Protein Domain
IPR022372
Name: Accessory secretory system protein Asp1
Type: Family
Description: This entry represents Asp1 which, along with SecY2 and SecA2, is part of the accessory secretory protein system [ , ]. This system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to a transport function rather than glycosylation, but its specific molecular role is unknown.
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Protein Domain
IPR010380
Name: Protein of unknown function DUF975
Type: Family
Description: This is a family of uncharacterised bacterial proteins.
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Protein Domain
IPR010382
Name: Protein of unknown function DUF977
Type: Family
Description: This entry consists of several hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR010385
Name: Protein of unknown function DUF982
Type: Family
Description: This family consists of several hypothetical proteins from Proteobacterial species. The function of this family is unknown.
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Protein Domain
IPR022368
Name: Putative thiazole-containing bacteriocin maturation protein
Type: Family
Description: Members of this protein family are found in a three-gene operon in Bacillus anthracis and related Bacillus species, where the other two genes are clearly identified with maturation of a putative thiazole-containing bacteriocin precursor. While there is no detectable pairwise sequence similarity between members of this family and the proposed cyclodehydratases such as SagC of Streptococcus pyogenes (see family ), both families show similarity through PSI-BLAST to ThiF, a protein involved in biosynthesis of the thiazole moiety for thiamine biosynthesis. This family, therefore, may contribute to cyclodehydratase function in heterocycle-containing bacteriocin biosyntheses. In Bacillus licheniformis ATCC 14580, the bacteriocin precursor gene is adjacent to the gene for this protein.
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Protein Domain
IPR010398
Name: Protein of unknown function DUF997
Type: Family
Description: This is a family of predicted bacterial membrane protein with unknown function. This entry includes YhdT, an uncharacterised membrane protein from E. coli [ ].
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Protein Domain
IPR010397
Name: Protein of unknown function DUF996
Type: Family
Description: This is a family of uncharacterised bacterial and archaeal proteins.
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Protein Domain
IPR046397
Name: Pre-baseplate central spike protein Gp5
Type: Family
Description: This entry includes the pre-baseplate central spike protein Gp5 from bacteriophage T4 which is a baseplate central spike complex-associated lysozyme, essential for the localized hydrolysis of bacterial cell wall. This allows the tail tube to penetrate to the host inner membrane, through which the phage DNA is ejected [ , , , ].
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Protein Domain
IPR034391
Name: Cmo-like SPASM domain containing protein
Type: Family
Description: This entry contains non-canonical members of the SPASM/twitch domain containing family, including Cmo, also known as tungsten-containing aldehyde ferredoxin oxidoreductase cofactor-modifying protein [ ] and AdoMet-dependent heme synthase (ahbD) involved in the siroheme-dependent heme b biosynthesis, catalysing the conversion of Fe-coproporphyrin III into heme by the oxidative decarboxylation of two propionate side chains [].
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Protein Domain
IPR012865
Name: Protein of unknown function DUF1642
Type: Family
Description: This entry represents a group of phage and prophage proteins whose function is not known.
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Protein Domain
IPR036838
Name: Ribosomal protein S10 domain superfamily
Type: Homologous_superfamily
Description: Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA [ ]. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.The small ribosomal subunit protein S10 consists of about 100 amino acid residues. In Escherichia coli, S10 is involved in binding tRNA to the ribosome, and also operates as a transcriptional elongation factor [ ]. Experimental evidence [] has revealed that S10 has virtually no groups exposed on the ribosomal surface, and is one of the "split proteins": these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles. S10 belongs to a family of proteins [ ] that includes: bacteria S10; algal chloroplast S10; cyanelle S10; archaebacterial S10; Marchantia polymorpha and Prototheca wickerhamii mitochondrial S10; Arabidopsis thaliana mitochondrial S10 (nuclear encoded); vertebrate S20; plant S20; and yeast URP2.Structurally, the Ribosomal protein S10 domain has a ferrodoxin-like fold, which consists of an alpha+beta sandwich with antiparallel β-sheet.
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Protein Domain
IPR009214
Name: Protein of unknown function DUF1129
Type: Family
Description: There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
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Protein Domain
IPR012863
Name: Protein of unknown function DUF1636
Type: Family
Description: The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
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Protein Domain
IPR012861
Name: Protein of unknown function DUF1634
Type: Family
Description: This family contains many hypothetical bacterial and archaeal proteins. A few members of this family are annotated as being putative transmembrane proteins, and the region in question in fact contains many hydrophobic residues.
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Protein Domain
IPR036823
Name: Ribosomal protein S7 domain superfamily
Type: Homologous_superfamily
Description: Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [ , ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [ , ].Ribosomal protein S7 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S7 is known to bind directly to part of the 3'end of 16Sribosomal RNA. It belongs to a family of ribosomal proteins which have been grouped on the basis of sequence similarities [, ].This entry represents the S7 structural domain superfamily, which consists of a bundle of six helices and an extended beta hairpin between helices 3 and 4, with two or more RNA-binding sites on its surface [ ].
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Protein Domain
IPR009223
Name: Adenomatous polyposis coli protein repeat
Type: Repeat
Description: This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). In the human protein many cancer-linked SNPs are found near the first three occurrences of the motif. These repeats bind beta-catenin [ ].
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Protein Domain
IPR024842
Name: Triple repetitive-sequence of QXXK/R protein
Type: Family
Description: TRIQK is a small protein family that is conserved across vertebrates. It is named after the characteristic triple repeat of the sequence QXXK/R that is shared by all family members [ ]. The proteins are localised to the endoplasmic reticulum membrane. They may play a role in cell growth and the maintenance of cell morphology [].
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Protein Domain
IPR009225
Name: Bacteriophage head completion protein GpL
Type: Family
Description: This entry represents the head completion protein GpL found in bacteriophages and prophages. GpL allows the completion of filled heads by rendering newly packaged DNA in the heads resistant to DNase. The protein is thought to bind to DNA filled capsids [ ].
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Protein Domain
IPR012873
Name: Protein of unknown function DUF1672
Type: Family
Description: This family is composed of hypothetical bacterial proteins of unknown function.
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Protein Domain
IPR012872
Name: Protein of unknown function DUF1670
Type: Family
Description: The hypothetical eukaryotic proteins found in this family are of unknown function.
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Protein Domain
IPR024830
Name: Glucocorticoid modulatory element-binding protein 1/2
Type: Family
Description: Glucocorticoid modulatory element-binding (GMEB) proteins 1 and 2 are homologous sequences that form a heteromeric complex that binds to glucocorticoid modulatory elements and increases sensitivity to low concentrations of glucocorticoids [ , ]. The GMEB1/2 complex is also an essential auxiliary factor for the replication of parvoviruses, critically regulating the viral nickase during infection []. GMEB1 has been shown to inhibit caspase, preventing hypoxia- and oxidative stress-induced neuronal apoptosis []. This entry also includes Transcription regulator spe-44 from Caenorhabditis elegans, a transcription factor that controls spermatogenesis and sperm cell fate by regulation of sperm gene expression, highly similar to the mammalian GMEB1/2 [].
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Protein Domain
IPR024836
Name: Janus kinase and microtubule-interacting protein
Type: Family
Description: Janus kinase and microtubule interacting proteins (JAKMIPs) are predominantly expressed in neural tissues and lymphoid organs. Three family members have been identified, termed JAKMIP1-3. They contain an N-terminal region that targets the protein to microtubule polymers and a C-terminal region that is able to associate with Janus kinase (Jak) family members, such as Tyk2 or Jak1 [ ]. The proteins may have a role in Jak signalling and regulation of microtubule cytoskeleton rearrangements.JAKMIP1 has also been shown to interact with GABA(B) receptor R1 subunits [ ], and may be involved in microtubule-dependent transport of the GABA-B receptor [].
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Protein Domain
IPR012840
Name: Anaerobic ribonucleoside-triphosphate reductase activating protein
Type: Family
Description: This enzyme is a member of the radical-SAM family. It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, ) and presumably fulfils the identical function as NrdG [ , ], which utilises S-adenosyl methionine, an iron-sulphur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centred radical in NrdD [].
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Protein Domain
IPR009205
Name: Predicted archaeal flagellar protein C
Type: Family
Description: Members of this family are encoded by archaeal flagellar operons, and are therefore predicted to be involved in archaeal flagellar assembly, but their specific role is unknown [ ]. In several archaea, the flagellin genes are followed immediately by the genes encoding flagellar accessory proteins flaCDEFGHIJ. They may have a role in translocation, secretion, or assembly of the flagellum. FlaC has been shown to be membrane-associated.Archaeal flagella, found in all the main groupings of archaea, differ from eubacterial flagella in both structure and composition, although some archaeal flagellar proteins show similarity to the eubacterial proteins involved in the pilus biogenesis/type II and IV secretory pathways [ , , , , ].
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Protein Domain
IPR009253
Name: Protein of unknown function DUF905
Type: Family
Description: This family consists of several short hypothetical proteobacterial proteins of unknown function.
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Protein Domain
IPR022231
Name: Protein of unknown function DUF3757
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 154 amino acids in length.
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Protein Domain
IPR022230
Name: Protein of unknown function DUF3756
Type: Family
Description: This domain family is found in viruses, and is approximately 40 amino acids in length.
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