energy-coupling factor ABC transporter permease similar to cobalt transport protein CbiM which is a seven-transmembrane protein and the substrate-specific component of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import
Ribosome biogenesis protein, C-terminal; This family represents the C-terminal domain of some ...
17-37
6.13e-03
Ribosome biogenesis protein, C-terminal; This family represents the C-terminal domain of some putative ribosome biogenesis proteins in archaea. It has also been identified in the eukaryotic protein Tsr3, which is involved in ribosomal RNA biogenesis.
The actual alignment was detected with superfamily member pfam04034:
Pssm-ID: 474903 Cd Length: 127 Bit Score: 35.86 E-value: 6.13e-03
cobalamin biosynthesis protein CbiM; A cutoff of 200 bits for trusted orthologs of cbiM is ...
31-231
6.25e-78
cobalamin biosynthesis protein CbiM; A cutoff of 200 bits for trusted orthologs of cbiM is suggested. Scores lower than 200 but higher than 20 may be considered sufficient to call a protein cobalamin biosynthesis protein CbiM-related.The seed alignment for this model is a cluster of very closely related proteins from Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, Methanococcus jannaschii, and Salmonella typhimurium, each of which has greater than 50% identity to all the others. The ortholog from Salmonella is the source of the gene symbol cbiM for this set.In Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Methanococcus jannaschii, a second homolog of cbiM is also found. These cbiM-related proteins appear to represent a distinct but less well-conserved orthologous group. Still more distant homologs include sll0383 from Synechocystis sp. and HI1621 from Haemophilus influenzae; the latter protein, from a species that does not synthesize cobalamin, is the most divergent member of the group. The functions of and relationships among the set of proteins homologous to cbiM have not been determined. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 272919 Cd Length: 214 Bit Score: 234.31 E-value: 6.25e-78
Cobalt uptake substrate-specific transmembrane region; This family of proteins forms part of ...
32-231
3.83e-44
Cobalt uptake substrate-specific transmembrane region; This family of proteins forms part of the cobalt-transport complex in prokaryotes, CbiMNQO. CbiMNQO and NikMNQO are the most widespread groups of microbial transporters for cobalt and nickel ions and are unusual uptake systems as they consist of eg two transmembrane components (CbiM and CbiQ), a small membrane-bound component (CbiN) and an ATP-binding protein (CbiO) but no extracytoplasmic solute-binding protein. Similar components constitute the nickel transporters with some variability in the small membrane-bound component, either NikN or NikL, which are not similar to CbiN at the sequence level. CbiM is the substrate-specific component of the complex and is a seven-transmembrane protein. The CbiMNQO and NikMNQO systems form part of the coenzyme B12 biosynthesis pathway. The NikM protein is pfam10670.
Pssm-ID: 460375 [Multi-domain] Cd Length: 202 Bit Score: 147.72 E-value: 3.83e-44
Ribosome biogenesis protein, C-terminal; This family represents the C-terminal domain of some ...
17-37
6.13e-03
Ribosome biogenesis protein, C-terminal; This family represents the C-terminal domain of some putative ribosome biogenesis proteins in archaea. It has also been identified in the eukaryotic protein Tsr3, which is involved in ribosomal RNA biogenesis.
Pssm-ID: 461139 Cd Length: 127 Bit Score: 35.86 E-value: 6.13e-03
cobalamin biosynthesis protein CbiM; A cutoff of 200 bits for trusted orthologs of cbiM is ...
31-231
6.25e-78
cobalamin biosynthesis protein CbiM; A cutoff of 200 bits for trusted orthologs of cbiM is suggested. Scores lower than 200 but higher than 20 may be considered sufficient to call a protein cobalamin biosynthesis protein CbiM-related.The seed alignment for this model is a cluster of very closely related proteins from Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, Methanococcus jannaschii, and Salmonella typhimurium, each of which has greater than 50% identity to all the others. The ortholog from Salmonella is the source of the gene symbol cbiM for this set.In Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Methanococcus jannaschii, a second homolog of cbiM is also found. These cbiM-related proteins appear to represent a distinct but less well-conserved orthologous group. Still more distant homologs include sll0383 from Synechocystis sp. and HI1621 from Haemophilus influenzae; the latter protein, from a species that does not synthesize cobalamin, is the most divergent member of the group. The functions of and relationships among the set of proteins homologous to cbiM have not been determined. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 272919 Cd Length: 214 Bit Score: 234.31 E-value: 6.25e-78
Cobalt uptake substrate-specific transmembrane region; This family of proteins forms part of ...
32-231
3.83e-44
Cobalt uptake substrate-specific transmembrane region; This family of proteins forms part of the cobalt-transport complex in prokaryotes, CbiMNQO. CbiMNQO and NikMNQO are the most widespread groups of microbial transporters for cobalt and nickel ions and are unusual uptake systems as they consist of eg two transmembrane components (CbiM and CbiQ), a small membrane-bound component (CbiN) and an ATP-binding protein (CbiO) but no extracytoplasmic solute-binding protein. Similar components constitute the nickel transporters with some variability in the small membrane-bound component, either NikN or NikL, which are not similar to CbiN at the sequence level. CbiM is the substrate-specific component of the complex and is a seven-transmembrane protein. The CbiMNQO and NikMNQO systems form part of the coenzyme B12 biosynthesis pathway. The NikM protein is pfam10670.
Pssm-ID: 460375 [Multi-domain] Cd Length: 202 Bit Score: 147.72 E-value: 3.83e-44
Ribosome biogenesis protein, C-terminal; This family represents the C-terminal domain of some ...
17-37
6.13e-03
Ribosome biogenesis protein, C-terminal; This family represents the C-terminal domain of some putative ribosome biogenesis proteins in archaea. It has also been identified in the eukaryotic protein Tsr3, which is involved in ribosomal RNA biogenesis.
Pssm-ID: 461139 Cd Length: 127 Bit Score: 35.86 E-value: 6.13e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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