TonB dependent receptor having a carboxypeptidase regulatory-like domain, may act as a channel to allow import of extracellular nutrients, such as iron-siderophore complexes or non-Fe compounds
TonB-dependent receptor; This model represents a family of TonB-dependent outer-membrane ...
114-927
2.60e-60
TonB-dependent receptor; This model represents a family of TonB-dependent outer-membrane receptors which are found mainly in Xanthomonas and Caulobacter. These appear to represent the expansion of a paralogous family in that the 22 X. axonopodis (21 in X. campestris) and 18 C. crescentus sequences are more closely related to each other than any of the many TonB-dependent receptors found in other species. In fact, the Crescentus and Xanthomonas sequences are inseparable on a phylogenetic tree using a PAM-weighted neighbor-joining method, indicating that one of the two genuses may have acquired this set of receptors from the other. The mechanism by which this family is shared between Xanthomonas, a gamma proteobacterial plant pathogen and Caulobacter, an alpha proteobacterial aquatic organism is unclear. [Transport and binding proteins, Porins]
The actual alignment was detected with superfamily member TIGR01782:
Pssm-ID: 273804 [Multi-domain] Cd Length: 845 Bit Score: 221.05 E-value: 2.60e-60
CarboxypepD_reg-like domain; This domain family is found in bacteria, archaea and eukaryotes, ...
25-119
1.79e-15
CarboxypepD_reg-like domain; This domain family is found in bacteria, archaea and eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam07715 and pfam00593.
:
Pssm-ID: 433425 [Multi-domain] Cd Length: 88 Bit Score: 72.24 E-value: 1.79e-15
TonB-dependent receptor; This model represents a family of TonB-dependent outer-membrane ...
114-927
2.60e-60
TonB-dependent receptor; This model represents a family of TonB-dependent outer-membrane receptors which are found mainly in Xanthomonas and Caulobacter. These appear to represent the expansion of a paralogous family in that the 22 X. axonopodis (21 in X. campestris) and 18 C. crescentus sequences are more closely related to each other than any of the many TonB-dependent receptors found in other species. In fact, the Crescentus and Xanthomonas sequences are inseparable on a phylogenetic tree using a PAM-weighted neighbor-joining method, indicating that one of the two genuses may have acquired this set of receptors from the other. The mechanism by which this family is shared between Xanthomonas, a gamma proteobacterial plant pathogen and Caulobacter, an alpha proteobacterial aquatic organism is unclear. [Transport and binding proteins, Porins]
Pssm-ID: 273804 [Multi-domain] Cd Length: 845 Bit Score: 221.05 E-value: 2.60e-60
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
141-927
1.43e-39
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore.
Pssm-ID: 238657 [Multi-domain] Cd Length: 635 Bit Score: 156.46 E-value: 1.43e-39
CarboxypepD_reg-like domain; This domain family is found in bacteria, archaea and eukaryotes, ...
25-119
1.79e-15
CarboxypepD_reg-like domain; This domain family is found in bacteria, archaea and eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam07715 and pfam00593.
Pssm-ID: 433425 [Multi-domain] Cd Length: 88 Bit Score: 72.24 E-value: 1.79e-15
TonB-linked outer membrane protein, SusC/RagA family; This model describes a distinctive clade ...
25-173
2.28e-11
TonB-linked outer membrane protein, SusC/RagA family; This model describes a distinctive clade among the TonB-linked outer membrane proteins (OMP). Members of this family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 alone. Published descriptions of members of this family are available for RagA from Porphyromonas gingivalis, SusC from Bacteroides thetaiotaomicron, and OmpW from Bacteroides caccae. Members form pairs with members of the SusD/RagB family (pfam07980). Transporter complexes including these outer membrane proteins are likely to import large degradation products of proteins (e.g. RagA) or carbohydrates (e.g. SusC) as nutrients, rather than siderophores. [Transport and binding proteins, Unknown substrate]
Pssm-ID: 274948 [Multi-domain] Cd Length: 981 Bit Score: 68.00 E-value: 2.28e-11
Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity, or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families.
Pssm-ID: 200604 [Multi-domain] Cd Length: 76 Bit Score: 42.51 E-value: 4.53e-05
TonB-dependent receptor; This model represents a family of TonB-dependent outer-membrane ...
114-927
2.60e-60
TonB-dependent receptor; This model represents a family of TonB-dependent outer-membrane receptors which are found mainly in Xanthomonas and Caulobacter. These appear to represent the expansion of a paralogous family in that the 22 X. axonopodis (21 in X. campestris) and 18 C. crescentus sequences are more closely related to each other than any of the many TonB-dependent receptors found in other species. In fact, the Crescentus and Xanthomonas sequences are inseparable on a phylogenetic tree using a PAM-weighted neighbor-joining method, indicating that one of the two genuses may have acquired this set of receptors from the other. The mechanism by which this family is shared between Xanthomonas, a gamma proteobacterial plant pathogen and Caulobacter, an alpha proteobacterial aquatic organism is unclear. [Transport and binding proteins, Porins]
Pssm-ID: 273804 [Multi-domain] Cd Length: 845 Bit Score: 221.05 E-value: 2.60e-60
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
141-927
1.43e-39
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore.
Pssm-ID: 238657 [Multi-domain] Cd Length: 635 Bit Score: 156.46 E-value: 1.43e-39
Outer membrane protein beta-barrel family; This family includes proteins annotated as TonB ...
460-925
2.39e-19
Outer membrane protein beta-barrel family; This family includes proteins annotated as TonB dependent receptors. But it is also likely to contain other membrane beta barrel proteins of other functions.
Pssm-ID: 434300 [Multi-domain] Cd Length: 407 Bit Score: 91.57 E-value: 2.39e-19
CarboxypepD_reg-like domain; This domain family is found in bacteria, archaea and eukaryotes, ...
25-119
1.79e-15
CarboxypepD_reg-like domain; This domain family is found in bacteria, archaea and eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam07715 and pfam00593.
Pssm-ID: 433425 [Multi-domain] Cd Length: 88 Bit Score: 72.24 E-value: 1.79e-15
TonB-linked outer membrane protein, SusC/RagA family; This model describes a distinctive clade ...
25-173
2.28e-11
TonB-linked outer membrane protein, SusC/RagA family; This model describes a distinctive clade among the TonB-linked outer membrane proteins (OMP). Members of this family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 alone. Published descriptions of members of this family are available for RagA from Porphyromonas gingivalis, SusC from Bacteroides thetaiotaomicron, and OmpW from Bacteroides caccae. Members form pairs with members of the SusD/RagB family (pfam07980). Transporter complexes including these outer membrane proteins are likely to import large degradation products of proteins (e.g. RagA) or carbohydrates (e.g. SusC) as nutrients, rather than siderophores. [Transport and binding proteins, Unknown substrate]
Pssm-ID: 274948 [Multi-domain] Cd Length: 981 Bit Score: 68.00 E-value: 2.28e-11
TonB-dependent Receptor Plug Domain; The Plug domain has been shown to be an independently ...
133-236
3.12e-10
TonB-dependent Receptor Plug Domain; The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors. It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel.
Pssm-ID: 462243 [Multi-domain] Cd Length: 107 Bit Score: 58.05 E-value: 3.12e-10
TonB-dependent siderophore receptor; This subfamily model encompasses a wide variety of ...
580-927
4.83e-08
TonB-dependent siderophore receptor; This subfamily model encompasses a wide variety of TonB-dependent outer membrane siderophore receptors. It has no overlap with TonB receptors known to transport other substances, but is likely incomplete due to lack of characterizations. It is likely that genuine siderophore receptors will be identified which score below the noise cutoff to this model at which point the model should be updated. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins]
Pssm-ID: 273805 [Multi-domain] Cd Length: 651 Bit Score: 57.04 E-value: 4.83e-08
Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity, or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families.
Pssm-ID: 200604 [Multi-domain] Cd Length: 76 Bit Score: 42.51 E-value: 4.53e-05
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.
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