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Search results 16301 to 16400 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
IPR015089
Name: Cytochrome b-c1 complex subunit 10
Type: Family
Description: The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is an essential component of the mitochondrial cellular respiratory chain. This family represents the 6.4kDa protein, which may be closely linked to the iron-sulphur protein in the complex and function as an iron-sulphur protein-binding factor [ ].
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Protein Domain
IPR040635
Name: D-ribitol-5-phosphate cytidylyltransferase, C-terminal
Type: Domain
Description: This domain is located at the C-terminal region of ISPD (isoprenoid synthase domain containing protein). Structural homologs can be found in two distinct alpha/beta protein families including the seven-stranded NAD(P) (H)-dependent short-chain dehydrogenases/reductases and five-stranded response regulator proteins involved in bacterial sensing systems [ ].
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Protein Domain
IPR013225
Name: PaaX-like, C-terminal
Type: Domain
Description: This family contains proteins that are similar to the product of the paaX gene of Escherichia coli ( ). This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid [ ].
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Protein Domain
IPR025631
Name: Putative porin-10
Type: Family
Description: This family of membrane β-barrel proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 655 and 722 amino acids in length. is identified by Gene3D as a membrane bound β-barrel. These sequences are putative porins.
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Protein Domain
IPR021098
Name: Bacteriophage P22, Gp10, DNA-stabilising
Type: Family
Description: This entry represents the Bacteriophage P22, Gp10, DNA-stabilising protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.Members of this family are phage proteins involved with stabilising the head assembly unit and condensed DNA within the capsid [ ].
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Protein Domain
IPR021217
Name: Spiroplasma phage 1-C74, Orf10
Type: Family
Description: This entry is represented by Spiroplasma phage 1-C74, Orf10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.Members in this family of proteins are also annotated as Plectrovirus orf 10 transmembrane proteins however currently no function is known.
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Protein Domain
IPR045197
Name: Nuclear pore membrane glycoprotein 210-like
Type: Family
Description: This entry includes Nuclear pore membrane glycoprotein 210 (NUP210) and related proteins from eukaryotes. They are nucleoporins essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity [ ]. This entry also includes some uncharacterised proteins from bacteria and viruses.
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Protein Domain
IPR008425
Name: Cyclin-dependent kinase inhibitor 3
Type: Family
Description: This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a Homo sapiens dual specificity protein phosphatase that dephosphorylates Cdk2 on threonine 160 in a cyclin-dependent manner [ , ].
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Protein Domain
IPR021355
Name: Bacteriophage Syn9, Gp224
Type: Family
Description: This entry is represented by Bacteriophage Syn9, Gp224. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently they have no known function.
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Protein Domain
IPR008416
Name: Baculovirus VP1054
Type: Family
Description: This family consists of several VP1054 proteins from the Baculoviruses. VP1054 (also known as AC54) is a virus structural protein required for nucleocapsid assembly [ ]. It is necessary for localization of the major capsid protein VP39 at the site of nucleocapsid assembly [].
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Protein Domain
IPR021730
Name: Dicarboxylate transport
Type: Domain
Description: In certain bacterial families this protein is expressed from the ydbH gene, and there is a suggestion that this is a form of DctA or dicarboxylate transport protein. Dicarboxylate transport proteins are found in aerobic bacteria which grow on succinate or other C4-dicarboxylates [ ].
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Protein Domain
IPR045509
Name: HD-associated domain
Type: Domain
Description: This entry represents a domain that is found C-terminal to the HD domain found in the EF1143 protein ( ) and O67745_AQUAE ( ) [ , ]. According to the Aravind-Koonin classification of HD-domain proteins, proteins containing this domain belong to cluster 1 [].
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Protein Domain
IPR018720
Name: Domain of unknown function DUF2249
Type: Domain
Description: This domain is found in a number of hypothetical bacterial and archaeal proteins with no known function. It is also found in proteins described as cupin 2 and hemerythrin. It represents a conserved region that shows distant similarity to the SirA protein (see ).
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Protein Domain
IPR031597
Name: KELK-motif containing domain
Type: Domain
Description: KELK is a domain of eukaryotic proteins found in serine/threonine-protein kinase MRCK-type proteins [ ]. The region is low-complexity, but it is not a predicted disordered-binding domain. The name comes from a highly conserved sequence motif within the domain. The function is not known.
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Protein Domain
IPR018601
Name: Sulfolobus spindle-shape virus 1 F-112 protein-like
Type: Family
Description: This entry is represented by Sulfolobus spindle-shape virus 1 (SSV1), F112 protein [ , ]. This protein adopts a winged helix DNA binding fold containing an intrachain disulfide bond []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
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Protein Domain
IPR004417
Name: Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO
Type: Family
Description: Proteins in this entry catalyse the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. They are closely related to GidA (glucose-inhibited division protein A, also known as MnmG), a protein involved in tRNA modification [ , ] in bacteria and mitochondria.
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Protein Domain
IPR026114
Name: Apolipoprotein F
Type: Family
Description: Human apolipoprotein F (APOF) is a minor apolipoprotein that associates with LDL. It inhibits cholesteryl ester transfer protein (CETP) activity and appears to be an important regulator of cholesterol transport. It also associates to a lesser degree with VLDL, Apo-AI and Apo-AII [ ].
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Protein Domain
IPR044877
Name: Sulfolobus spindle-shape virus 1 F-112 protein-like superfamily
Type: Homologous_superfamily
Description: This entry is represented by Sulfolobus spindle-shape virus 1 (SSV1), F112 protein [ , ]. This protein adopts a winged helix DNA binding fold containing an intrachain disulfide bond []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
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Protein Domain
IPR019542
Name: Enhancer of polycomb-like, N-terminal
Type: Domain
Description: This domain is found at the N-terminal of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes [ ]. It is also present at the N terminus of Jade family proteins.
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Protein Domain
IPR024654
Name: Calcineurin-like phosphoesterase domain, lpxH-type
Type: Domain
Description: This calcineurin-like phosphoesterase domain can be found in some of the bacterial UDP-2,3-diacylglucosamine hydrolases (lpxH), archaeal DNA double-strand break repair protein Mre11 and the N-terminal of the nuclease SbcCD subunit D from bacteria. It can also be found in the eukaryotic vacuolar protein sorting-associated protein 29 (VPS29).
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Protein Domain
IPR011115
Name: SecA DEAD-like, N-terminal
Type: Domain
Description: SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [ , , ]. This domain represents the N-terminal ATP-dependent helicase domain.
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Protein Domain
IPR013666
Name: Pleckstrin-like, plant
Type: Domain
Description: This domain describes a pleckstrin homology (PH)-like region found in several plant proteins, including VAN3-binding protein from Arabidopsis thaliana (also known as FORKED1), a component of the auto-regulatory loop which enables auxin canalisation by recruitment of the PIN1 auxin efflux protein to the cell membrane [ ].
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Protein Domain
IPR027806
Name: Harbinger transposase-derived nuclease domain
Type: Domain
Description: This domain is found in proteins that are related to and are probably endonucleases of the DDE superfamily. Proteins containing this domain include the putative nuclease HARBI1. HARBI1 is a transposase-derived protein that may have nuclease activity potential. It does not have transposase activity [ , ].
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Protein Domain
IPR001640
Name: Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase Lgt
Type: Family
Description: Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase lgt [ ] is an integral membrane enzyme that catalyses the first reaction of the three-step post-translational lipid modification []. It transfers the n-acyl diglyceride group onto what will become the N-terminal cysteine of membrane lipoproteins. This enzyme is an integral membrane protein.
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Protein Domain
IPR016669
Name: Interferon alpha/beta receptor 1
Type: Family
Description: The interferon-alpha/beta receptor 1 family of proteins associates with IFNAR2 to form the type I interferon receptor. Binding of interferons alpha and beta to type I IFNs triggers tyrosine phosphorylation of a number of proteins including JAKs, TYK2, STAT proteins and IFNR alpha- and beta-subunits themselves.
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Protein Domain
IPR028976
Name: CheC-like superfamily
Type: Homologous_superfamily
Description: This superfamily represents a domain found in the CheC-like proteins. In bacteria, CheC is involved in restoration of prestimulus levels of the chemotactic response regulator, CheY-P [ ]. Proteins contain this domain include flagellar motor switch protein FliM/FliY and CheX, both CheY-P phosphatases [, , ].
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Protein Domain
IPR026404
Name: Radical SAM enzyme, rSAM/lipoprotein system
Type: Family
Description: Members of this protein family are radical SAM enzymes with an additional 4Fe4S cluster-binding C-terminal domain shared with PqqE and many other peptide and protein-modifying radical SAM enzymes. All members occur in the context of a predicted lipoprotein that usually is encoded by an adjacent gene.
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Protein Domain
IPR036785
Name: YkyA-like superfamily
Type: Homologous_superfamily
Description: The YkyA superfamily of proteins contain a lipoprotein signal and a hydrolase domain. They are similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely that they function in pathways important for pathogenicity [ ].
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Protein Domain
IPR022127
Name: Store-operated calcium entry regulator STIMATE/YPL162C
Type: Family
Description: This entry includes STIMATE from animals and uncharacterised vacuolar membrane protein YPL162C from budding yeasts. STIMATE is a ER-resident multi-transmembrane protein that serves as a positive regulator of Ca(2+) influx in vertebrates. It interacts with ER-resident Ca2+ sensor protein STIM1 to promote STIM1 conformational switch [ ].
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Protein Domain
IPR036623
Name: Hemimethylated DNA-binding domain superfamily
Type: Homologous_superfamily
Description: Heat shock protein HspQ, also known as YccV, is an Escherichia coli hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression [ ].This entry represents a YccV-like hemimethylated DNA binding domain superfamily that is found in HspQ and also in longer eukaryotic proteins.
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Protein Domain
IPR022305
Name: Sortase system response regulator
Type: Family
Description: This entry describes a group of DNA-binding response regulator proteins that associate with histidine kinase ( ) to form a two-component system. This system co-occurs with a proteobacterial variant form of the protein sorting transpeptidase called sortase ( ), and a single target protein for the sortase.
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Protein Domain
IPR046799
Name: ROXA-like, winged helix
Type: Domain
Description: This entry represents the C-terminal winged helix domain of ribosomal oxygenases, including ROXA from Escherichia coli, which is reminiscent of WH-domains involved in protein-protein and protein-nucleic acid interactions. However, this domain has an overall negative charge suggesting they do not directly bind nucleic acids [ ].
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Protein Domain
IPR009748
Name: Orthopoxvirus C10L
Type: Family
Description: This family consists of several Orthopoxvirus C10L proteins. C10L viral protein can play an important role in vaccinia virus evasion of the host immune system. It may consist in the blockade of IL-1 receptors by the C10L protein, a homologue of the IL-1 Ra [ ].
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Protein Domain
IPR032305
Name: GTP-binding protein, middle domain
Type: Domain
Description: This entry represents a domain found in a group of GTP-binding proteins. Proteins containing this domain includes GTPase HflX, which associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis [ ]. This function of this domain is not known.
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Protein Domain
IPR015010
Name: Rap1 Myb domain
Type: Domain
Description: Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions [ ].
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Protein Domain
IPR025167
Name: Fusion glycoprotein F0, Isavirus
Type: Family
Description: Fusion between viral and cellular membranes is mediated by viral membrane fusion glycoproteins. This entry represents fusion glycoprotein F0 from the infectious salmon anemia virus (ISAV). The precursor protein F0 is proteolytically cleaved to F1 and F2, which are held together by disulphide bridges [ ].
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Protein Domain
IPR037630
Name: SASH1, SAM domain repeat 2
Type: Domain
Description: This entry represents the SAM (sterile alpha motif) repeat 2 of SASH1, which is a predicted protein-protein interaction domain. SASH1 is a member of the SH3/SAM adapter molecules family and has been identified as a tumour suppressor and critical protein in signal transduction [ , ].
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Protein Domain
IPR010420
Name: CASTOR/POLLUX/SYM8 ion channel, conserved domain
Type: Domain
Description: This entry represents a short region in the middle of proteins that belong to the CASTOR/POLLUX/SYM8 family of ion channels, which are found in plants. They have been implicated in modulating the nuclear membrane envelope potential [ ]. Proteins containing this domain also include uncharacterised bacterial proteins.
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Protein Domain
IPR011434
Name: Putative host cell surface-exposed lipoprotein Ltp-like, HTH region
Type: Domain
Description: This entry represents a domain found as 1 to 5 copies in proteins from bacteria and virus, including Putative host cell surface-exposed lipoprotein from Streptococcus phage TP-J34 (Ltp, ), a superinfection exclusion protein. This domain shows a three-helix bundle belonging to the HTH superfamily [ ].
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Protein Domain
IPR021170
Name: DnaJ homologue subfamily C member 10
Type: Family
Description: This group represents ER-resident disulfide reductase protein ERdj5, also known as DnaJ homologue subfamily C member 10. It is a endoplasmic reticulum co-chaperone, involved both in the correct folding of proteins that form obligatory non-native disulfides and degradation of misfolded proteins [ , , , ].
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Protein Domain
IPR008427
Name: Extracellular membrane protein, CFEM domain
Type: Domain
Description: The CFEM domain is a fungal-specific domain that contains eight cysteines and is found in some proteins with proposed roles in fungal pathogenesis [ ].The structure of the CFEM domain containing protein 'Surface antigen protein 2' from Candida albicans ( ) has been solved [ ].
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Protein Domain
IPR021300
Name: Integrating conjugative element protein, PFL4695
Type: Family
Description: This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE.
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Protein Domain
IPR045670
Name: Domain of unknown function DUF5916
Type: Domain
Description: This entry represents an uncharacterised domain found mostly in bacterial proteins. In CBM9 domain containing proteins, this domain is C-terminal to the CBM9 domain. According to BOCTOPUS prediction this region has a membrane barrel topology, which suggests that proteins containing this domain maybe novel carbohydrate channels.
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Protein Domain
IPR045784
Name: Radical SAM domain-containing protein, N-terminal
Type: Domain
Description: This presumed domain is found at the N terminus of radical SAM proteins from bacteria and archaea. Proteins containing this domain are thought to catalyse diverse reactions, including methylations, isomerization, ring formation, anaerobic oxidation and protein radical formation [ ]. The function of this domain is unknown.
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Protein Domain
IPR031567
Name: Sin1, middle CRIM domain
Type: Domain
Description: CRIM is a domain in the middle of Sin1 protein that is important in the substrate recognition of TORC2. It is conserved from yeast to humans. TOR is a serine/threonine-specific protein kinase and forms functionally distinct protein complexes referred to as TORC1 and TORC2 [ ].
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Protein Domain
IPR006964
Name: NUDE domain
Type: Domain
Description: This entry represents the conserved region of NUDE proteins. Proteins containing this domain are homologues of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.
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Protein Domain
IPR028435
Name: Plakophilin/Delta catenin
Type: Family
Description: The p120 subfamily of armadillo-related proteins includes deta-catenin, Splicing regulator ARVCF, p0071/plakophilin-4, and plakophilins 1-3 [ ]. These proteins are involved in mediating cell-cell adhesion. Besides their junctional localisation, these proteins can be found in the cytoplasm and nucleus where they play additional roles [, , ].
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Protein Domain
IPR028426
Name: Huntingtin family
Type: Family
Description: The huntingtin family consists of huntingtin proteins, including Dictyostelium HD protein homologue. Abnormalities in the huntingtin protein (Htt) are associated with Huntington's disease [], but despite its importance the function of Htt is largely unknown. In Dictyostelium discoideum Htt is required for normal chemotaxis and cytokinesis [].
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Protein Domain
IPR019454
Name: Putative cell-wall binding lipoprotein YkyA-like
Type: Family
Description: The YkyA family of proteins contain a lipoprotein signal and a hydrolase domain. They are similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely that they function in pathways important for pathogenicity [ ].
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Protein Domain
IPR032866
Name: Prokaryotic Ubiquitin
Type: Family
Description: This entry represents a Ubiquitin-superfamily protein that is present across several bacterial lineages, and found in gene neighbourhoods with components of the ubiquitin modification system such as the E1, E2 and JAB proteins, and a novel α-helical protein, which is predicted to be enzymatic [ ].
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Protein Domain
IPR042210
Name: Glycoprotein VP7, domain 2
Type: Homologous_superfamily
Description: Glycoprotein VP7, also known as outer shell glycoprotein, is a serotype-specific antigen, and is the major neutralisation antigen. It is found in the dsRNA rotaviruses.This superfamily represents the domain 2 found in glycoprotein VP7, it consists of 8 beta strands arranged into a jelly-roll beta sandwich.
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Protein Domain
IPR017566
Name: NrfD
Type: Family
Description: Members of this protein family are NrfD, a highly hydrophobic protein encoded in the nrf operon, which encodes cytochrome c nitrite reductase. This multiple haem-containing enzyme can reduce nitrite to ammonia. Members belong to a broader protein family, which also contains an NrfD-related subunit of polysulphide reductase.
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Protein Domain
IPR025525
Name: hAT-like transposase, RNase-H fold
Type: Domain
Description: This domain is found as part of an RNase-H fold section in a number of hAT-like transposases, such as protein DAYSLEEPER (At3g42170) from Arabidopsis [ ]. Protein DAYSLEEPER is essential for plant development and can also regulate global gene expression []. This entry also includes some uncharacterised fungal proteins.
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Protein Domain
IPR019380
Name: Casein kinase substrate, phosphoprotein PP28
Type: Domain
Description: This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II [ ].
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Protein Domain
IPR017730
Name: Chaperonin ClpB
Type: Family
Description: Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family of ATPases associated with various cellular activities ( ). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins [ , ].
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Protein Domain
IPR013272
Name: Vps72/YL1, C-terminal
Type: Domain
Description: This domain is found at the C terminus in proteins of the Vps72/YL1 family [ , ], in which it represents a proline-rich domain []. These proteins are involved in chromatin remodelling [, ]. This domain is also found in proteins that do not belong to the Vps72/YL1 family.
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Protein Domain
IPR011116
Name: SecA Wing/Scaffold
Type: Domain
Description: SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner. This domain is composed of two C-terminal alpha helical subdomains: the wing and scaffold subdomains.
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Protein Domain
IPR007651
Name: Lipin, N-terminal
Type: Domain
Description: Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [ , ].
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Protein Domain
IPR003594
Name: Histidine kinase/HSP90-like ATPase
Type: Domain
Description: This domain is found in several ATP-binding proteins, including: histidine kinase [ ], DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins. The fold of this domain consists of two layers, alpha/beta, which contains an 8-stranded mixed β-sheet.
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Protein Domain
IPR015260
Name: Syntaxin 6, N-terminal
Type: Domain
Description: This domain is found in the N-terminal of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Its exact function has not been determined, though it is known that it regulates the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport [].
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Protein Domain
IPR015168
Name: SsuA/THI5-like
Type: Domain
Description: This domain is found in NMT1/THI5 family proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [ , , ]. This domain is also found in aliphatic sulfonates-binding protein SsuA, which is part of a transport system for aliphatic sulfonates [].
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Protein Domain
IPR018219
Name: Thiol peroxidase conserved site
Type: Conserved_site
Description: Escherichia coli protein Tpx [ ] is an antioxidant protein with a thiol peroxidase activity. It acts as an antioxidant enzyme by removing peroxides within the catalase- and peroxidase-deficient periplasmic space of E. coli. It is a small protein of 18kDa whose sequence is wellconserved in other bacterial species.
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Protein Domain
IPR038193
Name: Mistic superfamily
Type: Homologous_superfamily
Description: Mistic is an integral membrane protein that folds autonomously into the membrane [ ]. It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations [].
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Protein Domain
IPR005902
Name: Putative DNA-binding protein, HU-related
Type: Family
Description: This family of proteins is related to, but longer than, DNA-binding protein HU. It contains a distinctive domain architecture when compared to HU and related histone-like DNA-binding. Members include, so far, a protein from Bacteroides fragilis and ten from Porphyromonas gingivalis (Bacteroides gingivalis). Both species are oral pathogens.
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Protein Domain
IPR029488
Name: Hemingway/CFA97
Type: Family
Description: Drosophila Hemingway (Hmw) is required for motile cilia function and sperm flagella assembly [ ]. The human orthologue, known as cilia- and flagella-associated protein 97 (CFAP97) or KIAA1430, localises to the primary cilium []. Another member of this family is the uncharacterised protein CFAP97D1/2 (CFAP97 domain-containing protein 1/2).
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Protein Domain
IPR026845
Name: Neurexophilin/NXPE
Type: Family
Description: This entry includes neurexophilin and NXPE proteins. Neurexophilins form a family of related glycoproteins that are proteolytically processed after synthesis and bind to alpha-neurexins. The structure and characteristics of neurexophilins indicate that they function as neuropeptides that may signal via alpha-neurexins [ ].NXPE is a glycoprotein with unknown function.
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Protein Domain
IPR024293
Name: SAC3 helical domain
Type: Domain
Description: This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [ ].
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Protein Domain
IPR036266
Name: SecA, Wing/Scaffold superfamily
Type: Homologous_superfamily
Description: SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner. This domain is composed of two C-terminal alpha helical subdomains: the wing and scaffold subdomains.
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Protein Domain
IPR022176
Name: Apolipoprotein B100 C-terminal
Type: Domain
Description: This domain is found in the C terminus of some apolipoprotein B100 (ApoB100) proteins. It is approximately 60 amino acids in length and contains two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport [ ].
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Protein Domain
IPR039002
Name: Hydrogenase maturation factor HybF
Type: Family
Description: Bacterial membrane-bound nickel-dependent hydrogenases require a number of accessory proteins which are involved in their maturation [ ]. Escherichia coli has two accessory proteins that share protein sequence similarity, HypA and HybF []. This entry represents HybF, which is involved in the maturation of isoenzymes 1 and 2 [].
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Protein Domain
IPR022376
Name: PQQ-dependent catabolism-associated CXXCW motif
Type: Family
Description: This entry represents proteins with a CXXXCW motif, consistent with a possible role in redox cofactor binding. These proteins show strong relationships by phylogenetic profiling and conserved gene neighbourhoods with a transport system for alcohols metabolised by PQQ-dependent enzymes. Members of this protein family are mostly found in Proteobacteria.
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Protein Domain
IPR009232
Name: EB-1 binding
Type: Domain
Description: This region at the C terminus of the APC proteins binds the microtubule-associating protein EB-1 [ ]. At the C terminus of the alignment is also a PDZ-binding domain. A short motif in the middle of the region appears to be found in the APC2 proteins (e.g. ).
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Protein Domain
IPR046226
Name: Domain of unknown function DUF6259
Type: Domain
Description: This domain is mainly found in bacterial proteins and is functionally uncharacterised. However, some proteins containing this domain are putative glycoside hydrolases and this domain has some overlaps with clan family members of CL0058. Proteins containing this domain are typically between 678 and 749 amino acids in length.
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Protein Domain
IPR036890
Name: Histidine kinase/HSP90-like ATPase superfamily
Type: Homologous_superfamily
Description: This domain superfamily is found in several ATP-binding proteins, including: histidine kinase [ ], DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins. The fold of this domain consists of two layers, alpha/beta, which contains an 8-stranded mixed β-sheet.
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Protein Domain
IPR022570
Name: Betacoronavirus, lineage A, NSP1
Type: Family
Description: This entry represents the N-terminal region of the betacoronavirus polyprotein, which contains non-structural protein 1 (Nsp1) from betacoronavirus lineage A. This protein is important for viral replication and pathogenesis [ , ]. It suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling.
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Protein Domain
IPR044122
Name: UPF0261 domain
Type: Domain
Description: This entry represents the uncharacterised UPF0261 domain. It is present at the N terminus of the tomato resistance protein Tm-1, which inhibits replication complex formation through its binding to tomato mosaic virus (ToMV) replication proteins. It contains an ATP-binding site required for interaction with ToMV proteins [ , ].
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Protein Domain
IPR007348
Name: CopC domain
Type: Domain
Description: Copper resistance protein C (CopC) is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm [ ].The structure of CopC consists of a Greek key beta barrel fold [ ].
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Protein Domain
IPR032371
Name: Domain of unknown function DUF4873
Type: Domain
Description: This entry consists mostly of a standalone domain found in short uncharacterised proteins from various high GC Gram-positive bacteria, primarily Mycobacterium species. However, in some proteins, such as the Rv0943c protein from Mycobacterium tuberculosis H37Rv, this domain is found at the C terminus, following the FAD/NAD(P)-binding domain ( ).
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Protein Domain
IPR044533
Name: FCS-Like Zinc finger 1/2/3
Type: Family
Description: This entry represents a group of plant FCS-Like Zinc finger-containing proteins, including FLZ1-3 from Arabidopsis. They are DUF581 proteins that may act as an adapter to facilitate the interaction of SnRK1 complex with effector proteins, conferring tissue- and stimulus-type specific differences in the SnRK1 regulation pathway [ ].
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Protein Domain
IPR015116
Name: Cdc42 binding domain-like
Type: Domain
Description: This entry represents the Cdc42 (a GTPase) binding domain. The domain is largely unstructured in the absence of Cdc42 [ ]. Proteins containing this domain include the tyrosine-protein kinase sid-3 [], the ERBB receptor feedback inhibitor 1, the activated CDC42 kinase 1 and the probable tyrosine-protein kinase kin-25.
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Protein Domain
IPR040509
Name: CdiI, C-terminal
Type: Domain
Description: This is the C-terminal domain of Contact-dependent growth inhibition immunity (CdiI) proteins present in Enterobacter cloacae. CdiI proteins neutralize CdiA-CT toxins to protect toxin-producing cells from auto-inhibition. Structural homology searches reveal that Enterobacter cloacae's CdiI is most similar to the Whirly family of single-stranded DNA-binding protein [ ].
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Protein Domain
IPR039796
Name: MIP18 family
Type: Family
Description: MIP18 is a component of the cytosolic iron-sulfur protein assembly (CIA) complex, a multiprotein complex that mediates the incorporation of iron-sulfur cluster into extramitochondrial Fe/S proteins [ , , ]. This entry includes MIP18 and its homologues, such as YHR122W from S. cerevisiae [] and AE7 from plants [].
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Protein Domain
IPR010488
Name: Zeta toxin domain
Type: Domain
Description: This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein [ ]. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].
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Protein Domain
IPR008562
Name: Autographa californica nuclear polyhedrosis virus (AcMNPV), C42
Type: Family
Description: This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101 (also known as Protein C42) [ ]. It plays a role in host nuclear actin polymerization by recruiting p78/73 protein that is capable of activating an actin-related protein 2/3 complex to initiate nuclear actin polymerization [].
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Protein Domain
IPR018536
Name: Chromophore lyase CpcS/CpeS
Type: Family
Description: This entry represents the CpcS/CpeS biliprotein lyase family, which have been shown to covalently attach chromophores to cystiene residue(s) of phycobiliproteins [ , ]. In the chromatically adapting cyanobacterium Fremyella diplosiphon, the proteins have been shown to be induced by green light, as part of the cpeCDESTR operon [].
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Protein Domain
IPR031761
Name: Folded gastrulation, N-terminal domain
Type: Domain
Description: This is the N-terminal domain of the folded gastrulation protein. Folded gastrulation is required for morphogenic movements during gastrulation and nervous system development. It may act as a secreted signal and activate the G protein alpha subunit. This domain may be the G protein-coupled receptor ligand [ , ].
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Protein Domain
IPR041346
Name: DR2241, 4Fe-4S iron-sulfur cluster binding domain
Type: Domain
Description: This is the C-terminal domain found in Deinococcus radiodurans protein DR2241 (a Ribosomal protein S2-related protein). This domain has been shown to harbour the sequence motifs CxxC and CxxxC which bind a [4Fe-4S] iron-sulphur cluster. Together with the preceding domain, it is heavily involved in the tetramer formation [].
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Protein Domain
IPR018823
Name: Putative ER transporter, 6TM, N-terminal
Type: Domain
Description: This domain is found in proteins conserved in fungi. Their function is not known. This entry represents the N-terminal half of some member proteins which contain the DUF2421 domain ( ) at their C terminus. These proteins are putative endoplasmic reticulum tranpsorters, with a total of 12 TMs.
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Protein Domain
IPR041511
Name: Putative DNA-binding domain
Type: Domain
Description: This is a putative DNA-binding protein dimerization domain found bacterial proteins such as CD3330, (a transposon-related DNA-binding protein from Clostridium difficile). Crystal structure analysis suggests that CD3330 N terminus is involved in dimer formation and also in crystal packing but the C terminus is open to solvent [ ].
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Protein Domain
IPR019665
Name: Putative oxidoreductase/dehydrogenase, Rossmann-like domain
Type: Domain
Description: This entry represents an NAD/NADP-binding domain with a core Rossmann-type fold, found in an uncharacterised protein family thought to be putative NADP oxidoreductase coenzyme F420-dependent proteins and/or NAD-dependent glycerol-3-phosphate dehydrogenase-like proteins. This Rossmann-fold domain consists of 3-layers alpha/beta/alpha, where the six beta strands are parallel in the order 321456.
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Protein Domain
IPR042108
Name: GTPase HflX, N-terminal domain superfamily
Type: Homologous_superfamily
Description: This domain represents the N-terminal region of GTP-binding HflX-like proteins [ , ]. These proteins interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP []. The N-terminal region is necessary for stability of the whole protein, its structure is composed of four parallel β-strand and four α-helices.
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Protein Domain
IPR044922
Name: DUF2063, N-terminal superfamily
Type: Homologous_superfamily
Description: This superfamily represents the N-terminal part of uncharacterised proteins, including a Neisseria protein ( , ) which comprises an α-helical bundle with 4 main helices. From genomic context and the fold of the C-terminal part, it is suggested that this protein is involved in transcriptional regulation [ ].
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Protein Domain
IPR004963
Name: Pectinacetylesterase/NOTUM
Type: Family
Description: This family includes protein Notum from animals and pectinacetylesterase (PAE) from plants. Notum is a carboxylesterase that removes an essential palmitoleate moiety from Wnt proteins. Notum constitutes the first known extracellular protein deacylase [ , ]. PAEs catalyse the deacetylation of pectin, a major compound of primary cell walls [, ].
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Protein Domain
IPR023582
Name: Impact family
Type: Family
Description: The Impact protein is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea [ ].
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Protein Domain
IPR006977
Name: Yip1 domain
Type: Domain
Description: This entry contains proteins belonging to the Yip1 family and represents the Yip1 domain. The Yip1 integral membrane domain contains four transmembrane α-helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a Golgi protein involved in vesicular transport that interacts with GTPases [ ].
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Protein Domain
IPR006911
Name: Armadillo repeat-containing domain
Type: Domain
Description: This domain contains armadillo-like repeats [ ]. Proteins containing this domain interact with numerous other proteins, through these interactions they are involved in a wide variety of processes including carcinogenesis [], control of cellular ageing and survival [], regulation of circadian rhythm [] and lysosomal sorting of G protein-coupled receptors [].
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Protein Domain
IPR038306
Name: CagS superfamily
Type: Homologous_superfamily
Description: This superfamily represents CAG pathogenicity island protein 13 (CagS) from Helicobacter pylori. The gene lies just downstream of the cluster whose protein-products resemble those of the Vibrio proteins that form the structural core of T4SS. The exact function of CagS is not known [ ]. This superfamily consists of four α-helices.
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Protein Domain
IPR032776
Name: CECR6/TMEM121 family
Type: Family
Description: This family includes Cat eye syndrome critical region protein 6 (also known as TMEM121B), a protein which has been identified in a screen for candidate genes for the developmental disorder Cat Eye Syndrome (CES) [ ]. It also includes the TMEM121 transmembrane proteins. The function of this family is unknown.
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Protein Domain
IPR038663
Name: Bacteriophage PRD1, P5 C-terminal domain superfamily
Type: Homologous_superfamily
Description: The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. P5 is an elongated multidomain trimer. The C-terminal fragment of P5 appears to contain the residues responsible for the trimerization of the protein, whereas the smaller N-terminal part mediates the interaction with protein P31 [ , ].
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Protein Domain
IPR024425
Name: Cell wall-active antibiotics response LiaF-like, C-terminal
Type: Domain
Description: This domain is found in various prokaryotic proteins, including cell wall-active antibiotic response proteins. This entry includes protein product of the yvqF gene, LiaF, located immediately upstream of vraS. It is associated with glycopeptide resistance in Staphylococcus aureus [ ]. This domain has been described as Toast_rack from its structural resemblance.
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