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Search results 5801 to 5900 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
IPR046135
Name: Protein of unknown function DUF6137
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000709) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the neomycin biosynthetic gene cluster from Streptomyces fradiae ATCC 10745 = DSM 40063 and appears to be predominantly found in bacteria [ ].
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Protein Domain
IPR046134
Name: Protein of unknown function DUF6131
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses.
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Protein Domain
IPR046133
Name: Protein of unknown function DUF6130
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is mainly found in bacteria. There are two conserved sequence motifs: NLRI and HVTVDD.
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Protein Domain
IPR046130
Name: Protein of unknown function DUF6127
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found predominantly in bacteria.
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Protein Domain
IPR010183
Name: Bacteriophage lambda, Recombination protein bet
Type: Family
Description: This entry represents Recombination protein bet from Bacteriophage lambda (Bet, also known as red-beta). Bet functions in general recombination and in the late, rolling-circle mode of lambda DNA replication. It has a function similar to that of E.coli recT. It is a single-stranded DNA binding protein that can promote renaturation of DNA [ , , ]. Members of this protein family are found in tailed bacteriophagues and bacterial prophagues.
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Protein Domain
IPR022787
Name: D-proline reductase (dithiol), PrdB protein
Type: Family
Description: Members of this family form the PrdB subunit, usually a selenoprotein, in the D-proline reductase complex. The usual pathway is conversion of L-protein to D-proline by a racemase, then use of D-proline as an electron acceptor coupled to ATP generation under anaerobic conditions [ ].
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Protein Domain
IPR022167
Name: Protein of unknown function DUF3698
Type: Family
Description: This domain family is found in eukaryotes, and is typically between 89 and 105 amino acids in length.
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Protein Domain
IPR022169
Name: Protein of unknown function DUF3701
Type: Family
Description: This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with .
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Protein Domain
IPR046129
Name: Protein of unknown function DUF6126
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000663) is described by MIBiG as an example of the following biosynthetic class, terpene. It includes a member from the hopene biosynthetic gene cluster from Streptomyces coelicolor A3(2) and appears to be predominantly found in Actinobacteria [ , ].
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Protein Domain
IPR046126
Name: Protein of unknown function DUF6123
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Firmicutes.
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Protein Domain
IPR046125
Name: Protein of unknown function DUF6122
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is mainly found in bacteria. There are two conserved sequence motifs: HYG and RCSI.
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Protein Domain
IPR046124
Name: Protein of unknown function DUF6121
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is mainly in Actinobacteria.
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Protein Domain
IPR046123
Name: Protein of unknown function DUF6120
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found predominantly in Firmicutes. There is a conserved MGK sequence motif.
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Protein Domain
IPR046121
Name: Protein of unknown function DUF6118
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Alphaproteobacteria.
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Protein Domain
IPR046120
Name: Protein of unknown function DUF6117
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is mainly found in bacteria.
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Protein Domain
IPR046199
Name: Protein of unknown function DUF6231
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000387) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the mangotoxin biosynthetic gene cluster from Pseudomonas syringae pv. syringae [ , ]. This family appears to be predominantly found in Proteobacteria.
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Protein Domain
IPR046198
Name: Protein of unknown function DUF6230
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001774) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the MS-271 biosynthetic gene cluster from Streptomyces sp [ ]. This family appears to be predominantly found in Actinobacteria. Some members of this family have been identified as putative cholesterol esterases.
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Protein Domain
IPR046197
Name: Protein of unknown function DUF6229
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042 [ ]. This family appears to be predominantly found in bacteria.
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Protein Domain
IPR046196
Name: Protein of unknown function DUF6228
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001042) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the sanglifehrin A biosynthetic gene cluster from Streptomyces flaveolus [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046195
Name: Protein of unknown function DUF6227
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000118) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the pactamycin biosynthetic gene cluster from Streptomyces pactum [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046194
Name: Protein of unknown function DUF6222
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. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp. [ ].
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Protein Domain
IPR046193
Name: Protein of unknown function DUF6221
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046192
Name: Protein of unknown function DUF6220
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001612) is described by MIBiG as an example of the following biosynthetic class, alkaloid. It includes a member from the ambiguine H isonitrile biosynthetic gene cluster from Fischerella ambigua UTEX 1903 [ ]. This family appears to be predominantly found in bacteria.
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Protein Domain
IPR046191
Name: Protein of unknown function DUF6219
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001575) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the dipeptide aldehydes biosynthetic gene cluster from Ruminococcus sp. 5_1_39BFAA [ ]. This family appears to be predominantly found in bacteria.
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Protein Domain
IPR046190
Name: Protein of unknown function DUF6218
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000696) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the gentamicin biosynthetic gene cluster from Micromonospora echinospora [ , ].
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Protein Domain
IPR046189
Name: Protein of unknown function DUF6217
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001142) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member of the tryptoquialanine biosynthetic gene cluster from Penicillium aethiopicum [ ]. This family appears to be predominantly found in fungi.
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Protein Domain
IPR046188
Name: Protein of unknown function DUF6216
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the yersiniabactin biosynthetic gene cluster from Escherichia coli [ ]. This family appears to be predominantly found in Proteobacteria.
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Protein Domain
IPR046187
Name: Protein of unknown function DUF6215
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001856) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the caniferolide A biosynthetic gene cluster from Streptomyces caniferus [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046186
Name: Protein of unknown function DUF6214
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001782) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the spiroindimicin A biosynthetic gene cluster from Streptomyces sp. SCSIO 03032 [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046185
Name: Protein of unknown function DUF6213
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. It includes a member from the lavendiol biosynthetic gene cluster from Streptomyces lavendulae [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046184
Name: Protein of unknown function DUF6212
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000801) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the galactoglucan biosynthetic gene cluster from Sinorhizobium meliloti [ ]. This family appears to be predominantly found in proteobacteria.
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Protein Domain
IPR046183
Name: Protein of unknown function DUF6211
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. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [ ].
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Protein Domain
IPR046182
Name: Protein of unknown function DUF6210
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001448) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the malacidin A biosynthetic gene cluster from uncultured bacterium [ ]. This family appears to be predominantly found in bacteria.
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Protein Domain
IPR046181
Name: Protein of unknown function DUF6209
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC00001940) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the pyxidicycline A biosynthetic gene cluster from Pyxidicoccus fallax [ ]. This family appears to be predominantly found in bacteria.
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Protein Domain
IPR046180
Name: Protein of unknown function DUF6208
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000976) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the curacin A biosynthetic gene cluster from Moorea producens 3L [ , ]. This family appears to be predominantly found in Cyanobacteria.
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Protein Domain
IPR046179
Name: Protein of unknown function DUF6188
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. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [ ]. This family appears to be predominantly found in bacteria.
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Protein Domain
IPR046178
Name: Protein of unknown function DUF6187
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. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp. [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046177
Name: Protein of unknown function DUF6186
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001215) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the conglobatin biosynthetic gene cluster from Streptomyces conglobatus [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046176
Name: Protein of unknown function DUF6185
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001485) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the 3-demethylchuangxinmycin biosynthetic gene cluster from Actinoplanes tsinanensis [ ]. This family appears to be predominantly found in Actinobacteria.
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Protein Domain
IPR046175
Name: Protein of unknown function DUF6177
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000360) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the GE81112 biosynthetic gene cluster from Streptomyces sp. L-49973 and appears to be predominantly found in Actinobacteria [ ].
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Protein Domain
IPR046174
Name: Protein of unknown function DUF6176
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000198) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide. It includes a member from the arenimycin A biosynthetic gene cluster from Salinispora arenicola CNB527 [ , ].
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Protein Domain
IPR046173
Name: Protein of unknown function DUF6175
Type: Family
Description: This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are typically between 316 and 421 amino acids in length.
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Protein Domain
IPR046172
Name: Protein of unknown function DUF6174
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is predominantly found in bacteria.
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Protein Domain
IPR046171
Name: Protein of unknown function DUF6173
Type: Family
Description: This family of proteins is functionally uncharacterised. Proteins in this entry are mainly found in Proteobacteria.
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Protein Domain
IPR046170
Name: Protein of unknown function DUF6172
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found mostly in Proteobacteria. There is a conserved KRER sequence motif.
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Protein Domain
IPR046169
Name: Protein of unknown function DUF6171
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is primarly found in bacteria and viruses.
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Protein Domain
IPR046168
Name: Protein of unknown function DUF6170
Type: Family
Description: This family of proteins is functionally uncharacterised. Most proteins in this family are found in Gammaproteobacteria.
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Protein Domain
IPR046167
Name: Protein of unknown function DUF6169
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Bacteroidetes.
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Protein Domain
IPR046166
Name: Protein of unknown function DUF6168
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Bacteroidetes.
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Protein Domain
IPR046165
Name: Protein of unknown function DUF6167
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Actinobacteria.
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Protein Domain
IPR046164
Name: Protein of unknown function DUF6166
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. There are two conserved sequence motifs: GDRTIDG and VVANF.
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Protein Domain
IPR046163
Name: Protein of unknown function DUF6165
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 129 and 147 amino acids in length.
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Protein Domain
IPR046162
Name: Protein of unknown function DUF6164
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found primarly in Proteobacteria.
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Protein Domain
IPR046161
Name: Protein of unknown function DUF6163
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found mostly in Alphaproteobacteria.
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Protein Domain
IPR046160
Name: Protein of unknown function DUF6162
Type: Family
Description: This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Proteobacteria.
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Protein Domain
IPR020566
Name: Histidine biosynthesis bifunctional protein HisB
Type: Family
Description: This entry represents the histidine biosynthesis bifunctional protein HisB [ , ], which contains an N-terminal histidinol phosphate phosphatase () and a C-terminal imidazoleglycerol-phosphate dehydratase ( ) [ ]. HisB catalyses steps 6 and 8 of L-histidine biosynthesis. The N-terminal histidinol phosphate phosphatase domain folds into a single domain that has similarity to the haloacid dehalogenase (HAD) enzyme family, with a zinc ion stabilising the conformation of an extended loop [].
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Protein Domain
IPR024619
Name: Protein of unknown function DUF3860
Type: Family
Description: This protein family includes hypothetical protein (JCVI_PEP_1096688149193) whose crystal structure has been solved PDB:2OD5. The hypothetical protein is from an environmental metagenome (unidentified marine microbe).
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Protein Domain
IPR012609
Name: Sporulation stage V, protein M
Type: Family
Description: This family consists of the stage V sporulation (SpoV) proteins of Bacillus subtilis which includes SpoVM. SpoVM is an small, 26 residue-long protein that is produced in the mother cell chamber of the sporangium during the process of sporulation in B. subtilis. SpoVM forms an amphipathic α-helix and is recruited to the polar septum shortly after the sporangium undergoes asymmetric division. The function of SpoVM depends on proper subcellular localisation [ ].
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Protein Domain
IPR000625
Name: Anti-repression trans-activator protein, REV protein
Type: Family
Description: REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [ ] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].
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Protein Domain
IPR000686
Name: Fanconi anaemia group C protein
Type: Family
Description: Fanconi anemia (FA) is a human disorder characterized by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. It is required for the monoubiquitylation of FANCD2 and FANCI heterodimer. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24 [ , ].This entry represents FANCC [ ].
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Protein Domain
IPR009013
Name: Attachment protein shaft domain superfamily
Type: Homologous_superfamily
Description: The attachment proteins in adenoviruses and reoviruses display structural similarity, indicating similar cell-surface receptor binding strategies, even though these viruses differ from one another in design, capsid composition and genome composition [ , ]. The dsDNA adenoviruses are responsible for diseases such as pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised, while the dsRNA reoviruses are responsible for mild respiratory or gastrointestinal infections. The attachment proteins play a pivotal role in disease patterns through their selective recognition of cell-surface receptors. The fibre protein and the sigma 1 protein act as attachment proteins in adenoviruses and reoviruses, respectively. The attachment proteins are homo-trimeric, and contain a long, thin central shaft, or tail domain, and a C-terminal head domain that plays an important role in cell attachment. The structure of the shaft or tail domain reveals a triple β-spiral that is formed by interlocking β-hairpin repeat units.
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Protein Domain
IPR036630
Name: Head decoration protein D superfamily
Type: Homologous_superfamily
Description: Bacteriophage lambda head decoration protein D stabilises the head shell after the rearrangement of GP7 subunits of the head shell lattice that accompanies expansion of the head. There are approximately 420 copies of protein D per mature phage.Head decoration protein D structure has a β-clip fold, which consists of a double-stranded ribbon sharply bent in two places where the ribbon ends form incomplete barrel.
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Protein Domain
IPR012663
Name: Conserved hypothetical protein CHP02450, tryptophan-rich
Type: Family
Description: Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo.
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Protein Domain
IPR036626
Name: Head-to-tail joining protein W superfamily
Type: Homologous_superfamily
Description: GpW is a 68 residue protein known to be present in phage particles. Extracts of phage-infected cells lacking GpW contain DNA-filled heads, and active tails, but no infectious virions. GpW is required for the addition of GpFII to the head, which is, in turn, required for the attachment of tails. Since GpFII and tails are known to be attached at the connector, GpW is also likely to assemble at this site. The addition of GpW to filled heads increases the DNase resistance of the packaged DNA, suggesting that GpW either forms a plug at the connector to prevent ejection of the DNA, or binds directly to the DNA. The large number of positively charged residues in GpW (its calculated pI is 10.8) is consistent with a role in DNA interaction [ ].The structure of GpW has an α-β(2)-alpha fold with antiparallel hairpin.
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Protein Domain
IPR000696
Name: Peptidase A6, nodavirus coat protein
Type: Family
Description: Aspartic peptidases, also known as aspartyl proteases ([intenz:3.4.23.-]), are widely distributed proteolytic enzymes [, , ] known to exist in vertebrates, fungi, plants, protozoa, bacteria, archaea, retroviruses and some plant viruses. All known aspartic peptidases are endopeptidases. A water molecule, activated by two aspartic acid residues, acts as the nucleophile in catalysis. Aspartic peptidases can be grouped into five clans, each of which shows a unique structural fold [].Peptidases in clan AA are either bilobed (family A1 or the pepsin family) or are a homodimer (all other families in the clan, including retropepsin from HIV-1/AIDS) [ ]. Each lobe consists of a single domain with a closed β-barrel and each lobe contributes one Asp to form the active site. Most peptidases in the clan are inhibited by the naturally occurring small-molecule inhibitor pepstatin [].Clan AC contains the single family A8: the signal peptidase 2 family. Members of the family are found in all bacteria. Signal peptidase 2 processes the premurein precursor, removing the signal peptide. The peptidase has four transmembrane domains and the active site is on the periplasmic side of the cell membrane. Cleavage occurs on the amino side of a cysteine where the thiol group has been substituted by a diacylglyceryl group. Site-directed mutagenesis has identified two essential aspartic acid residues which occur in the motifs GNXXDRX and FNXAD (where X is a hydrophobic residue) [ ]. No tertiary structures have been solved for any member of the family, but because of the intramembrane location, the structure is assumed not to be pepsin-like.Clan AD contains two families of transmembrane endopeptidases: A22 and A24. These are also known as "GXGD peptidases"because of a common GXGD motif which includes one of the pair of catalytic aspartic acid residues. Structures are known for members of both families and show a unique, common fold with up to nine transmembrane regions [ ]. The active site aspartic acids are located within a large cavity in the membrane into which water can gain access [].Clan AE contains two families, A25 and A31. Tertiary structures have been solved for members of both families and show a common fold consisting of an α-β-alpha sandwich, in which the beta sheet is five stranded [ , ].Clan AF contains the single family A26. Members of the clan are membrane-proteins with a unique fold. Homologues are known only from bacteria. The structure of omptin (also known as OmpT) shows a cylindrical barrel containing ten beta strands inserted in the membrane with the active site residues on the outer surface [ ].There are two families of aspartic peptidases for which neither structure nor active site residues are known and these are not assigned to clans. Family A5 includes thermopsin, an endopeptidase found only in thermophilic archaea. Family A36 contains sporulation factor SpoIIGA, which is known to process and activate sigma factor E, one of the transcription factors that controls sporulation in bacteria [ ].This group of proteins, which include the Nodavirus coat precusor endopeptidases, are aspartic peptidases that belong to the MEROPS peptidase family A6 (clan AB).Nodaviruses are small, icosahedral viruses, pathogenic to insects and mammals. A virus particle consists of a single virion, within which is packaged two RNA stands, RNA1 and RNA2.Nodavirus coat precursor endopeptidase (also known as protein alpha) is the only protein encoded by RNA2. During the process of virion assembly, this precursor is cleaved into coat proteins beta and gamma. RNA1 encodes two proteins, at least one of which is involved in RNA replication. The relatively uncomplicated nature of their structural protein and RNA constituents make the nodaviruses a good virus model [ ].The 3D structure of the capsid protein has been determined by X-ray crystallography to 2.8A resolution []. The structure contains a β-barreldomain, with a prominent protrusion composed largely of β-sheet. This protrusion, together with similar protrusions from neighbouring subunits,forms a prominent trigonal pyramid with quasi-3-fold symmetry [ ]. Twoα-helices extend toward the interior of the particle [ ].
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Protein Domain
IPR024629
Name: Mitochondrial homologous recombination protein 1
Type: Family
Description: Saccharomyces cerevisiae Mhr1 promotes homologous DNA pairing and functions as a mitochondrial recombinase that mediates the predominant form of mtDNA replication and acts in mtDNA segregation and the repair of mtDNA double-stranded breaks (DSBs) [ , ]. This entry also includes the Mhr1 homologue, ML67, from Neurospora crassa. Both Mhr1 and ML67 have been shown to be localised on the mitoribosomal large subunit [].
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Protein Domain
IPR024691
Name: Micronemal protein 1, galectin-like domain
Type: Domain
Description: MIC1 is released as part of a complex by Toxoplasma gondii prior to invasion. The complex, which consists of MIC4-MIC1-MIC6, participates in host cell attachment and penetration, and is critical in invasion [ ]. MIC1 is a lactose-binding lectin [] required for the complex to leave the early compartments of the secretory pathway [].This entry represents the C-terminal domain of MIC1, which has a galectin-like fold that interacts with and stabilises MIC6, providing a mechanism for an exit from the early secretory compartments and trafficking of the complex to micronemes [ ].
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Protein Domain
IPR022037
Name: Protein of unknown function DUF3606
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
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Protein Domain
IPR022036
Name: Protein of unknown function DUF3605
Type: Family
Description: This family of proteins is found mostly in fungi, including N-acetylglucosamine-induced protein 1 (Gig1) from Candida albicans. Gig1 plays a role in the N-acetylglucosamine metabolic pathway [ ].
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Protein Domain
IPR022024
Name: Protein of unknown function DUF3602
Type: Family
Description: This domain family is found in eukaryotes, and is typically between 78 and 89 amino acids in length. This entry include protein Par32 from Saccharomyces cerevisiae. Par32 is hyperphosphorylated after treatment with rapamycin in a TAP42-dependent manner [ ]. It is also involved in resistance to cisplatin [].
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Protein Domain
IPR022028
Name: Protein of unknown function DUF3604
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are typically between 621 and 693 amino acids in length.
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Protein Domain
IPR036657
Name: DNA-binding protein Tfx superfamily, archaea
Type: Homologous_superfamily
Description: This entry represents a superfamily of Tfx DNA-binding proteins, which is restricted to the archaea. TfX has a 2-layer alpha/beta topology. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
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Protein Domain
IPR009032
Name: Vpu protein cytoplasmic domain superfamily
Type: Homologous_superfamily
Description: The human immunodeficiency virus type 1 Vpu transmembrane protein is required for the induction of degradation human CD4 receptor degradation in the endoplasmic reticulum, and for the enhancement of virus particle release from the plasma membrane of infected cells. The cytoplasmic domain of Vpu directly interacts with the CD4 receptor, targeting it for proteasome degradation [ ]. The cytoplasmic domain encompasses the C-terminal half of the 81-residue protein, and is comprised of a few helical turns without an apparent hydrophobic core [].
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Protein Domain
IPR022018
Name: ARF GTPase-activating protein GIT1, C-terminal
Type: Domain
Description: This entry represents the C-terminal domain of the ARF GTPase-activating protein GIT1. GIT1 is an ArfGAP and scaffolding protein regulating cell adhesion and migration [ ]. To perform this function, it localises p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C-terminal and the LD motifs of paxillin. The C-terminal folds into a four helix bundle.
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Protein Domain
IPR012683
Name: Conserved hypothetical protein CHP02302, transmembrane
Type: Family
Description: Members of this family are found predominantly in the alphaproteobacteria and bacteroidetes. Each has 2-3 predicted transmembrane helices near the N terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted to be outside the membrane. Bradyrhizobium japonicum contains two tandem copies that are, together, homologous to the single members found in other species.
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Protein Domain
IPR010022
Name: Protein of unknown function XkdX
Type: Family
Description: This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
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Protein Domain
IPR024668
Name: GA-binding protein alpha subunit, N-terminal
Type: Domain
Description: GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats). This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded β-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [ ].
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Protein Domain
IPR022072
Name: Protein of unknown function DUF3624
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.
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Protein Domain
IPR022074
Name: Protein of unknown function DUF3626
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 374 amino acids in length.
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Protein Domain
IPR022079
Name: Protein of unknown function DUF3629
Type: Family
Description: This family of proteins is found in eukaryotes. Proteins in this family are typically between 256 and 292 amino acids in length.
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Protein Domain
IPR046039
Name: Protein of unknown function DUF5997
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001814) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the ulleungmycin biosynthetic gene cluster from Streptomyces sp. KCB13F003 [ ].
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Protein Domain
IPR046038
Name: Protein of unknown function DUF5996
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000434) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the SW-163C biosynthetic gene cluster from Streptomyces sp. SNA15896 [ ].
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Protein Domain
IPR046037
Name: Protein of unknown function DUF5995
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000354) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This includes a protein from the friulimicin A biosynthetic gene cluster from Actinoplanes friuliensis [ ].
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Protein Domain
IPR046036
Name: Protein of unknown function DUF5994
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC) mainly found in actinobacteria. This BGC (BGC0000202) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family contains a protein found in the azicemicin B biosynthetic gene cluster from Kibdelosporangium sp. MJ126-NF4 [ ]. The function of this protein is unknown.
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Protein Domain
IPR046035
Name: Protein of unknown function DUF5993
Type: Family
Description: This family of integral membrane proteins is found primarily in proteobacteria.
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Protein Domain
IPR046034
Name: Protein of unknown function DUF5992
Type: Family
Description: This family of uncharacterised proteins is found in bacteria.
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Protein Domain
IPR046033
Name: Protein of unknown function DUF5991
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001890) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). The exemplar is the amphi-enterobactin 1 biosynthetic gene cluster from Vibrio campbellii [ ].
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Protein Domain
IPR046032
Name: Protein of unknown function DUF5990
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001048) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide), polyketide, and saccharide. This family includes a protein in the tallysomycin A biosynthetic gene cluster from Streptoalloteichus hindustanus [ ]. Some members of this family have been annotated as monooxygenase, but this could not be confirmed.
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Protein Domain
IPR046031
Name: Protein of unknown function DUF5989
Type: Family
Description: This family of proteins is primarily found mainly in bacteria. Proteins in this family are integral membrane proteins that are approximately 50 amino acids in length. There is a C-terminal conserved APFIY sequence motif. This family may have distant partial similarity to PF02694 suggesting this may be a transporter protein.
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Protein Domain
IPR046030
Name: Protein of unknown function DUF5988
Type: Family
Description: This family of proteins is found in bacteria. There are two conserved sequence motifs: GGP and YEHF.
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Protein Domain
IPR022060
Name: Protein of unknown function DUF3616
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are typically between 335 and 392 amino acids in length. There is a conserved GLRGPV sequence motif.
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Protein Domain
IPR022062
Name: Protein of unknown function DUF3618
Type: Family
Description: This domain family is found in bacteria, and is approximately 50 amino acids in length.
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Protein Domain
IPR022061
Name: Protein of unknown function DUF3617
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important.
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Protein Domain
IPR022064
Name: Protein of unknown function DUF3619
Type: Family
Description: This protein is found in bacteria. Proteins in this family are about 140 amino acids in length. This protein has two conserved sequence motifs: AAR and DDLP.
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Protein Domain
IPR022069
Name: Protein of unknown function DUF3622
Type: Family
Description: This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
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Protein Domain
IPR046029
Name: Protein of unknown function DUF5987
Type: Family
Description: This family of uncharacterised proteins is found in actinobacteria. Many protein in this family are annotated as regulator, but the source of this annotation is uncertain.
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Protein Domain
IPR046028
Name: Protein of unknown function DUF5986
Type: Family
Description: This family of proteins is found mainly in Firmicutes. Proteins in this family are typically between 235 and 254 amino acids in length. There is a single completely conserved residue R that may be functionally important.
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Protein Domain
IPR010090
Name: Phage tail tape measure protein
Type: Domain
Description: This entry represents a reasonably well conserved core region of a family of phage tail proteins. The member from phage TP901-1 was characterised as a tail length tape measure protein in that a shortened form of the protein leads to phage with proportionately shorter tails [ ].
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Protein Domain
IPR046027
Name: Protein of unknown function DUF5985
Type: Family
Description: This family of uncharacterised proteins is found mainly in bacteria. Proteins in this family are approximately 90 amino acids in length and contain three transmembrane helices.
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Protein Domain
IPR046026
Name: Protein of unknown function DUF5984
Type: Family
Description: This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000838) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the flexirubin biosynthetic gene cluster from Flavobacterium johnsoniae. This protein has no known function.
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