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Search results 7901 to 8000 out of 30763 for seed protein

Category restricted to ProteinDomain (x)

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Category: ProteinDomain
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Type Details Score
Protein Domain
IPR011867
Name: Molybdate ABC transporter, permease protein
Type: Family
Description: ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain [].The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ].The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly β-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel β-sheet of armI by a two-fold axis [ , , , , , ].The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [ ]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ].This entry describes the permease protein, ModB, of the molybdate ABC transporter. This system has been characterised in Escherichia coli [ ], Staphylococcus carnosus [] Rhodobacter capsulatus (Rhodopseudomonas capsulata) [] and Azotobacter vinelandii []. Molybdate is chemically similar to sulphate, thiosulphate, and selenate. These related substrates, and sometimes molybdate itself, can be transported by the homologous sulphate receptor. Some apparent molybdenum transport operons include a permease related to this ModB, although less similar than some sulphate permease proteins and not included in this model.
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Protein Domain
IPR011868
Name: Molybdate ABC transporter, ATP-binding protein
Type: Family
Description: ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain [ ].The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ].The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly β-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel β-sheet of armI by a two-fold axis [ , , , , , ].The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [ ]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ].This entry represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulphate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulphate transporter rather than by a specific molybdate transporter.
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Protein Domain
IPR023824
Name: Conserved hypothetical protein CHP04073, exosortase-affiliated
Type: Family
Description: Members of this protein family are found in beta, gamma, and delta proteobacteria, and in the verrucomicrobia. Twenty-two of twenty-four species encountered contain the PEP-CTERM/exosortase system for modulating extracellular polysaccharide biosynthesis production, suggesting a role in protein sorting. There is a distant sequence relationship between a region of this protein of about 100 amino acids and a corresponding region of the very large eukaryotic protein Vps13, associated with vacuolar protein sorting in yeast.
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Protein Domain
IPR011844
Name: Coenzyme PQQ biosynthesis protein PqqF
Type: Family
Description: In the subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA ( ), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases [ ].
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Protein Domain
IPR011842
Name: Coenzyme PQQ biosynthesis protein B
Type: Family
Description: This entry describes coenzyme PQQ biosynthesis protein B, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. Note that this gene appears to be required for PQQ in biosynthesis in Methylobacterium extorquens (under the name pqqG) and in Klebsiella pneumoniae but that the equivalent pqqV in Acinetobacter calcoaceticus is not necessary for heterologous expression of PQQ biosynthesis in Escherichia coli. Based on this latter finding, it is suggested [ ] that PqqB might be a transporter or a PQQ-dependent enzyme rather than a PQQ biosynthesis enzyme [].
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Protein Domain
IPR021220
Name: Protein of unknown function DUF2686
Type: Family
Description: Some members in this family of proteins are annotated as yjfZ however currently no function is known.
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Protein Domain
IPR023883
Name: Conserved hypothetical protein CHP03980, redox-disulphide
Type: Family
Description: Members of this protein family all contain an apparent redox-active disulphide. In at least one family member, a cysteine in the CXXC motif is substituted by a selenocysteine. The family is sometimes found adjacent to (and, on occasion, fused with) members of the hybrid-cluster (prismane) family or the nitrite/sulphite reductase family.
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Protein Domain
IPR021222
Name: Protein of unknown function DUF2714
Type: Family
Description: This family of proteins with unknown function appears to be restricted to Mycoplasmataceae.
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Protein Domain
IPR021223
Name: Abortive phage resistance protein AbiGi
Type: Family
Description: This is a bacterial family of proteins with unknown function. AbiGi is a family of putative type IV toxin-antitoxin system antitoxins. The AbiG abortive phage resistance system affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis [ ].
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Protein Domain
IPR021224
Name: Protein of unknown function DUF2690
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021226
Name: Protein of unknown function DUF2744
Type: Family
Description: This entry represents a family of bacterial and bacteriophage proteins, including the Mycobacteriophage D29 protein Gp29.
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Protein Domain
IPR023889
Name: TOMM system kinase/cyclase fusion protein
Type: Family
Description: This entry represents a family of proteins of around 1350 in length. They are found in multiple species of Burkholderia, in Acidovorax avenae subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1, and in multiple copies in Sorangium cellulosum, in genomic neighbourhoods that include a cyclodehydratase/docking scaffold fusion protein and a member of the thiazole/oxazole modified metabolite (TOMM) precursor family. The proteins have a kinase domain in their N-terminal 300 amino acids, followed by a cyclase homology domain, followed by regions without named domain definitions. They are probable bacteriocin-like metabolite biosynthesis proteins.
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Protein Domain
IPR021228
Name: BREX system ATP-binding protein BrxD
Type: Family
Description: This is a family of proteins found in bacterial proteins associated with Bacteriophage Exclusion (BREX) system, a defense system that allows bacteriophage adsorption but blocks phage DNA replication [ ]. This family represents the ATP-binding protein BrxD [].
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Protein Domain
IPR021229
Name: Protein of unknown function DUF2800
Type: Family
Description: This is a family of uncharacterised proteins found in bacteria and viruses.
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Protein Domain
IPR033207
Name: Centriolar coiled-coil protein of 110kDa
Type: Family
Description: CCP110 is a centriole protein implicated in the regulation of cell division [ ], centrosome duplication [], centriole length [, ] and in the suppression of ciliogenesis [, ]. Its levels and localization to the centrosome are tightly regulated in a cell cycle dependent manner []. CP110 has been shown to interact with two calcium-binding proteins, centrin and calmodulin (CaM), to regulate cytokinesis [].
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Protein Domain
IPR021213
Name: Protein of unknown function DUF2567
Type: Family
Description: This is a bacterial family of proteins with unknown function.
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Protein Domain
IPR021214
Name: Protein of unknown function DUF2568
Type: Family
Description: One member in this family is annotated as yrdB which is part of a four gene operon however currently no function is known.
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Protein Domain
IPR021215
Name: Protein of unknown function DUF2752
Type: Family
Description: This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
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Protein Domain
IPR021216
Name: Protein of unknown function DUF2722
Type: Family
Description: This eukaryotic family of proteins has no known function.
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Protein Domain
IPR021218
Name: Protein of unknown function DUF2784
Type: Family
Description: This is a family of uncharacterised protein. The function is not known however it is conserved in Bacteria.
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Protein Domain
IPR021219
Name: Protein of unknown function DUF2703
Type: Family
Description: This family of protein has no known function.
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Protein Domain
IPR021200
Name: Conserved hypothetical integral membrane protein
Type: Family
Description: This entry represents a family of putative integral membrane proteins that have an especially well-conserved region near the C terminus with an invariant tyrosine. The function of this family is unknown.
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Protein Domain
IPR011889
Name: Bacterial surface protein 26-residue repeat
Type: Repeat
Description: This entry describes a tandem peptide repeat sequence of 25 or 26 residues, found in predicted surface proteins (often lipoproteins) mainly from Listeria monocytogenes, Listeria innocua, Enterococcus faecalis (Streptococcus faecalis), Lactobacillus plantarum, Mycoplasma spp., Helicobacter hepaticus, and other species.
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Protein Domain
IPR021262
Name: Protein of unknown function DUF2839
Type: Family
Description: This bacterial family of unknown function appear to be restricted to Cyanobacteria.
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Protein Domain
IPR021263
Name: Protein of unknown function DUF2840
Type: Family
Description: This bacterial family of proteins have no known function.
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Protein Domain
IPR021265
Name: Protein of unknown function DUF2842
Type: Family
Description: This bacterial family of proteins have no known function.
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Protein Domain
IPR021267
Name: Protein of unknown function DUF2844
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021268
Name: Protein of unknown function DUF2845
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021269
Name: Protein of unknown function DUF2848
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR033231
Name: Secreted and transmembrane protein 1
Type: Family
Description: Secreted and transmembrane protein 1 (SECTM1), also known as protein K-12, has been identified as a ligand for CD7, an immunoglobulin superfamily molecule with a role in T- and NK-cell activation and cytokine production [ ]. SECTM1 is a potent costimulatory ligand for T cell proliferation and is induced by IFN-gamma [, , ].The human genome contains only one SECTM gene, while the mouse genome contains two (SECTM1A and SECTM1B) [ ].
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Protein Domain
IPR021250
Name: Protein of unknown function DUF2789
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021251
Name: Protein of unknown function DUF2793
Type: Family
Description: This family of proteins currently has no known function.
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Protein Domain
IPR021252
Name: Protein of unknown function DUF2794
Type: Family
Description: This is a bacterial family of proteins with unknown function.
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Protein Domain
IPR021253
Name: Protein of unknown function DUF2796
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021254
Name: Protein of unknown function DUF2806
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021256
Name: Protein of unknown function DUF2808
Type: Family
Description: This family of proteins with unknown function are mostly from Cyanobacteria.
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Protein Domain
IPR021257
Name: Protein of unknown function DUF2809
Type: Family
Description: Some members in this family of proteins are annotated as yjgA however currently no function for the protein is known.
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Protein Domain
IPR021259
Name: Protein of unknown function DUF2817
Type: Family
Description: This family of proteins has no known function.
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Protein Domain
IPR035888
Name: Myotubularin-related protein 3, PH-GRAM domain
Type: Domain
Description: MTMR3 is a member of the myotubularin dual specificity protein phosphatase gene family. MTMR3 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro [ ]. The protein can self-associate and also form heteromers with MTMR4 [].Both MTMR3 and MTMR4 contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, a coiled-coil region, and a C-terminal lipid-binding FYVE domain which binds phosphotidylinositol-3-phosphate. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome [ ]. Six of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules []. This entry represents the PH-GRAM domain of myotubularin-related protein 3.
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Protein Domain
IPR021240
Name: Protein of unknown function DUF2776
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021242
Name: Protein of unknown function DUF2799
Type: Family
Description: Some members in this family of proteins are annotated as yfiL which has no known function.
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Protein Domain
IPR021243
Name: Protein of unknown function DUF2804
Type: Family
Description: This is a family of proteins with unknown function.
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Protein Domain
IPR021244
Name: Protein of unknown function DUF2802
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021245
Name: Protein of unknown function DUF2790
Type: Family
Description: This family of proteins with unknown function appear to be restricted to Pseudomonadaceae.
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Protein Domain
IPR021246
Name: Protein of unknown function DUF2797
Type: Family
Description: This family of proteins has no known function.
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Protein Domain
IPR021247
Name: Protein of unknown function DUF2785
Type: Family
Description: Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family has no known function.
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Protein Domain
IPR021248
Name: Protein of unknown function DUF2787
Type: Family
Description: This family of proteins, predominantly found in Gammaproteobacteria, has no known function. The conserved hypothetical protein VC1805 from Vibrio cholerae is included in this entry. VC1805 adopts a monomeric assembly, showing an unusual topology with a flat seven-stranded anti-parallel β-sheet and two helices located on the same side of the sheet. It has some structural homology with the human protein p32 and binds to the complement protein C1q, which suggests a possible role in the adherence of the bacteria to the intestinal wall [ ].
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Protein Domain
IPR021249
Name: Protein of unknown function DUF2788
Type: Family
Description: This bacterial family of proteins have no known function.
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Protein Domain
IPR021230
Name: Protein of unknown function DUF2810
Type: Family
Description: This is a bacterial family of uncharacterised proteins. This entry contains YibL ( ), which comigrates with the mature 50S ribosome subunit. It either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [ ].
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Protein Domain
IPR021231
Name: Protein of unknown function DUF2811
Type: Family
Description: This is a bacterial family of uncharacterised proteins.
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Protein Domain
IPR021232
Name: Protein of unknown function DUF2735
Type: Family
Description: Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed.
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Protein Domain
IPR021233
Name: Protein of unknown function DUF2783
Type: Family
Description: This is a bacterial family of uncharacterised protein.
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Protein Domain
IPR021234
Name: Protein of unknown function DUF2827
Type: Family
Description: This is a family of uncharacterised proteins found mostly in Burkholderia.
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Protein Domain
IPR021235
Name: Protein of unknown function DUF2637
Type: Family
Description: This family of proteins has no known function.
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Protein Domain
IPR021238
Name: Protein of unknown function DUF2620
Type: Family
Description: This is a bacterial family of proteins with unknown function.
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Protein Domain
IPR021239
Name: Protein of unknown function DUF2625
Type: Family
Description: Some members in this family of proteins are annotated as ybfG however currently no function is known.
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Protein Domain
IPR021290
Name: Protein of unknown function DUF2861
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021292
Name: Protein of unknown function DUF2863
Type: Family
Description: This bacterial family of proteins have no known function.
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Protein Domain
IPR021293
Name: Protein of unknown function DUF2865
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021294
Name: Protein of unknown function DUF2866
Type: Family
Description: This bacterial family of proteins have no known function.
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Protein Domain
IPR021295
Name: Protein of unknown function DUF2867
Type: Family
Description: This family contains uncharacterized proteins, including the single-pass membrane protein YbjT from Escherichia coliwhich has an N-terminal NAD(P)-binding domain.
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Protein Domain
IPR021296
Name: Protein of unknown function DUF2868
Type: Family
Description: Some members in this family of proteins with unknown function are annotated as putative membrane proteins. However, this cannot be confirmed.
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Protein Domain
IPR021298
Name: Cilia- and flagella-associated protein 298
Type: Family
Description: This entry includes a group of cilia- and flagella-associated protein, including Kur from zebrafish and C21orf59 from humans. Kur has been shown to play a dual role in cilia motility and polarization [ ].Primary ciliary dyskinesia (PCD) is caused when defects of motile cilia lead to chronic airway infections, male infertility, and situs abnormalities. Mutations in the C21orf59 gene cause ciliary dyskinesia, primary, 26 (CILD26) [ ].
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Protein Domain
IPR021299
Name: Protein of unknown function DUF2871
Type: Family
Description: This family of proteins has no known function.
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Protein Domain
IPR021280
Name: Protein of unknown function DUF2723
Type: Family
Description: This family is conserved in bacteria. The function is not known.
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Protein Domain
IPR021283
Name: Protein of unknown function DUF2612
Type: Family
Description: This is a phage protein family expressed from a range of Proteobacteria species. The function is not known.
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Protein Domain
IPR021284
Name: Protein of unknown function DUF2750
Type: Family
Description: This family is conserved in Proteobacteria. The function is not known.
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Protein Domain
IPR033253
Name: Cilia- and flagella-associated protein 45
Type: Family
Description: Cilia- and flagella-associated protein 45, also known as coiled-coil domain-containing protein 19 (CCDC19) or nasopharyngeal epithelium specific protein (NESG1), has been identified in humans as a tumour suppressor [ , ]. It activates the expression of miR-184, which suppresses the expression of C-Myc, a key oncogenic transcription factor.
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Protein Domain
IPR021270
Name: Protein of unknown function DUF2849
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021271
Name: Protein of unknown function DUF2850
Type: Family
Description: This family of proteins with unknown function appear to be restricted to Vibrionaceae.
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Protein Domain
IPR021272
Name: Protein of unknown function DUF2851
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021273
Name: Protein of unknown function DUF2852
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021274
Name: Protein of unknown function DUF2853
Type: Family
Description: This bacterial family of proteins has no known function.
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Protein Domain
IPR021276
Name: Protein of unknown function DUF2855
Type: Family
Description: This family of proteins has no known function.
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Protein Domain
IPR021277
Name: Protein of unknown function DUF2610
Type: Family
Description: This family of proteins is functionally uncharacterised. They are predicted to contain a ribbon-helix-helix fold, so may function as DNA-binding proteins.
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Protein Domain
IPR021279
Name: Protein of unknown function DUF2721
Type: Family
Description: This family is conserved in bacteria. The function is not known.
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Protein Domain
IPR045287
Name: Protein IN CHLOROPLAST ATPASE BIOGENESIS
Type: Family
Description: This entry represents a group of plant proteins, including PAB (Protein IN CHLOROPLAST ATPASE BIOGENESIS) from Arabidopsis. PAB is a chloroplastic chaperone that functions downstream of chaperonin 60 (Cpn60)-mediated CF1gamma subunit folding to promote its assembly into the catalytic core of the chloroplast ATP synthase [ ].
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Protein Domain
IPR035900
Name: Colicin E immunity protein superfamily
Type: Homologous_superfamily
Description: This family includes bacterial colicin and pyocin immunity proteins [ , ]. These immunity proteins can bind specifically to the DNase-type colicins and pyocins and inhibit their bactericidal activity. The 1.8-angstrom crystal structure of the ImmE7 protein consists of four antiparallel α-helices []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. Pyocin protects a cell that harbours the plasmid ColE2 encoding colicin E2 against colicin E2; it is thus essential both for autonomous replication and colicin E2 immunity [].
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Protein Domain
IPR023911
Name: Uncharacterised protein family, AIR synthase-related
Type: Family
Description: This entry represents AIR-synthase related proteins. It also matches the C-terminal of MSMEG_0567 from Mycobacterium smegmatis. The N-terminal of MSMEG_0567 is a GNAT family N-acetyltransferase and resemble the full length of sll0787 from Synechocystis sp. PCC 6803.
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Protein Domain
IPR011924
Name: Lipoprotein releasing system, ATP-binding protein
Type: Family
Description: This entry represents LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane [ ]. The LolCDE complex differs mechanistically from all other ABC transporters as it is not involved in the transmembrane transport of substrates [].
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Protein Domain
IPR011925
Name: Lipoprotein-releasing system transmembrane protein LolC/E
Type: Family
Description: This entry describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC [ ].The LolCDE complex releases lipoproteins from the inner membrane, thereby initiating lipoprotein sorting to the outer membrane. The LolCDE complex in Escherichia coli is composed of two copies of an ATPase subunit, LolD, and one copy each of integral membrane subunits LolC and LolE [ ]. TheLolCDE complex releases the lipoproteins in the periplasm, where they form a complex with LolA. The LolA-lipoprotein complex crosses the periplasm to reach the outer membrane, where LolB incorporates the lipoprotein into the outer membrane. LolA is involved in the interaction with membrane subunit LolC, whereas no interaction has been observed with LolE. This observations indicate that LolC and LolE may play different roles in the lipoprotein transfer despite their structural resemblance [ , ].
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Protein Domain
IPR011927
Name: Stage V sporulation protein D
Type: Family
Description: This entry describes the SpoVD family of homologues of the cell division protein FtsI, a penicillin binding protein. This family is restricted to Bacillus subtilis and related Gram-positive species with known or suspected endospore formation capability. In these species, the functional equivalent of FtsI is desginated PBP-2B, a paralog of SpoVD.
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Protein Domain
IPR011737
Name: Conserved hypothetical protein CHP02206, TP0381
Type: Family
Description: This entry represents a family of hydrophobic proteins with seven predicted transmembrane alpha helices. Members are found in Bacillus subtilis (ywaF), TP0381 from Treponema pallidum (TP0381), Streptococcus pyogenes, Rhodococcus erythropolis, etc.
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Protein Domain
IPR023728
Name: Small heat shock protein IbpA
Type: Family
Description: Small heat shock proteins IbpA associate with aggregated proteins, together with IbpB, to stabilise and protect them from irreversible denaturation and extensive proteolysis during heat shock and oxidative stress. Aggregated proteins bound to the IbpAB complex are more efficiently refolded and reactivated by the ATP-dependent chaperone systems ClpB and DnaK/DnaJ/GrpE. Its activity is ATP-independent[ ], [].These proteins form homomultimers of about 100-150 subunits at optimal growth temperatures. The conformation changes to monomers at high temperatures or high ionic concentrations. Proteins in this entry belong to the small heat shock protein (HSP20) family.
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Protein Domain
IPR011748
Name: Uncharacterised protein family, phage tail-like
Type: Domain
Description: This entry describes a region of sequence similarity shared by a number of uncharacterised proteins in bacterial genomes, including Geobacter sulfurreducens PCA, Rhizobium loti (Mesorhizobium loti), Streptomyces coelicolor (strain A3(2)), Gloeobacter violaceus PCC 7421, and Myxococcus xanthus. In all cases, the genomic region resembles a phage tail region, based on tentative identifications of neighbouring genes. A region of this domain resembles a region of , another phage tail protein model.
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Protein Domain
IPR011740
Name: Protein of unknown function DUF2460
Type: Family
Description: The entry represents a number of conserved hypothetical proteins. Their genes are often, though not always, encoded in apparent phage-derived regions of bacterial chromosomes. The Rhodobacter capsulatus sequence is apparently part of the gene transfer agent [see Fig.1, in ].
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Protein Domain
IPR011725
Name: Coenzyme PQQ biosynthesis protein A
Type: Family
Description: This entry describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product [ ].
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Protein Domain
IPR011728
Name: Polyhydroxyalkanoic acid inclusion protein PhaP
Type: Family
Description: This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage [ ].
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Protein Domain
IPR011755
Name: Conserved hyptothetical protein CHP02269, MYXXA
Type: Family
Description: This family consists of at least 9 paralogues in Myxococcus xanthus, a member of the Deltaproteobacteria. One appears truncated toward the N terminus; the others are predicted lipoproteins. The function is unknown.
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Protein Domain
IPR011754
Name: Myxococcus xanthus paralogous protein 2268
Type: Family
Description: This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.
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Protein Domain
IPR011751
Name: Myxococcus xanthus paralogous protein 2265
Type: Family
Description: This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus (strain DK 1622). Members are about 200 amino acids in length. No other homologuess are known; the function is unknown.
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Protein Domain
IPR021111
Name: Hexameric tyrosine-coordinated heme protein (HTHP)
Type: Family
Description: Hexameric tyrosine-coordinated heme protein (HTHP) is from the marine bacterium Silicibacter pomeroyi and has peroxidase and catalase activity. HTHP consists of six monomers which each binds a solvent accessible heme group and is stabilised by the interaction of three neighbouring monomers [ ]. The heme iron is penta-coordinated with a tyrosine residue as proximal ligand [].
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Protein Domain
IPR045147
Name: AT-rich interactive domain-containing protein 3
Type: Family
Description: This entry represents a group of transcription factors, including ARID3A/B/C from humans and protein dead ringer (Retn) from Drosophila melanogaster. ARID3A (also known as E2FBP1 or Bright) is involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation [ , ]. ARID3B has been linked to malignant neuroblastoma []. Retn is regulator of the late development of longitudinal glia []. Mutations in the Drosophila retn gene lead to female behavioral defects and alter a limited set of neurons in the CNS. Retn also affects a male behavioral pathway activated by fruM [].
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Protein Domain
IPR045140
Name: SHC SH2 domain-binding protein 1-like
Type: Family
Description: This entry includes SHC SH2 domain-binding protein 1 (Shcbp1) and related proteins, including protein nessun dorma (also known as Nesd) from Drosophila melanogaster. Shcbp1 is expressed in proliferating cells and is an important component of FGF (fibroblast growth factor) signalling in neural progenitor cells [ ]. Nesd is part of the centralspindlin complex, a key regulator of cytokinesis [].
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Protein Domain
IPR045131
Name: CDGSH iron-sulfur domain-containing protein 1/2
Type: Family
Description: Proteins in this family contain the CDGSH-type zinc finger. Interestingly, they do not contain any zinc ions, but rather iron contained in a 2Fe-2S (iron-sulfur) cluster. The conserved sequence C-X-C-X(2)-(S/T)-X(3)-P-X-C-D-G-(S/A/T)-H is a defining feature of this unique family of proteins and is likely involved in iron binding [ ]. They play an important part in the proliferation of breast cancer cells and tumour formation []. CISD1 (also known as mitoNEET) is a mitochondrial protein that plays an important part in mitochondrial bioenergetics. It also plays a part in insulin regulation, inflammation and autophagy []. CISD2 (also known as NAF-1) can be found in endoplasmic reticulum (ER) and mitochondrial outer membrane []. It regulates autophagy [].Mutations of the CISD2 gene cause Wolfram syndrome 2 (WFS2), a rare disorder characterized by juvenile-onset insulin-dependent diabetes mellitus with optic atrophy [ ].
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Protein Domain
IPR045188
Name: PH domain containing protein Boi1/Boi2-like
Type: Family
Description: This entry represents a group of PH domain containing proteins, including Boi1/2 from budding yeasts and PKHJ1/Sesquipedalian1-2/PKHA3 from humans. Budding yeast Boi1/2 are involved in polar growth and required for fusion of secretory vesicles with plasma membrane at sites of polarised growth [ ]. Sesquipedalian-1/2 are inositol polyphosphate phosphatase interacting proteins required for receptor recycling from endosomes, both to the trans-Golgi network and to the plasma membrane []. PKHA3 plays a role in regulation of vesicular cargo transport from the trans-Golgi network to the plasma membrane []. It regulates Golgi phosphatidylinositol 4-phosphate (PtdIns4P) levels and activates the PtdIns4P phosphatase activity of SACM1L when it binds PtdIns4P in 'trans' configuration [].
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Protein Domain
IPR045181
Name: Heavy metal binding protein HIPP-like
Type: Family
Description: This entry represents a group of heavy metal binding proteins mostly from plants, including copper transport proteins CCH/CCS1 and HIPPs (Heavy metal-associated isoprenylated plant proteins) from Arabidopsis. CCH and CCS1 are copper chaperones involved in copper trafficking [ ]. CCH may have additional CTD (carboxy-terminal domain)-mediated plant-specific functions [].HIPPs are metallochaperone-like proteins containing a predicted HMA domain. They may play a role in cadmium detoxification [ ].
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Protein Domain
IPR021192
Name: Uncharacterised conserved protein UCP031578, VanZ/RDD-type
Type: Family
Description: This entry represents an uncharacterised protein with VanZ and RDD domains.
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Protein Domain
IPR045152
Name: Enhancer of mRNA-decapping protein 4-like
Type: Family
Description: Ge-1, also known as EDC4 (enhancer of mRNA-decapping protein 4), is a regulator of mRNA decapping to function in the mRNA P-bodies within the cytoplasm. It has been shown to interact with mTORC1 [ ], coenzyme A synthase [] and MARF1 []. It is also involved in the regulation of immune system [].This entry also includes EDC4 homologues from fungi and plants [ ].
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Protein Domain
IPR045192
Name: Clathrin coat assembly protein AP180-like
Type: Family
Description: Clathrin mediated endocytosis (CME) is a transmembrane cargo and ligand internalisation process that uses a clathrin coat to form vesicles [ ]. During this process, clathrin needs to be connected to the membrane through adapter proteins, such as the main adapter AP2 (adapter protein complex 2) and AP180. AP180 assembles clathrin faster than any other protein examined in vitro []. Mammalian AP180 is only detectable in neurons, where it is strongly enriched within pre-synaptic boutons [, ]. It has been shown that synapses with mutated or disrupted AP180 fail to produce a sufficient number of synaptic vesicles [, ]. This entry includes AP180 and related proteins.
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