MULTISPECIES: TAXI family TRAP transporter solute-binding subunit [Stutzerimonas]
Protein Classification
TAXI family TRAP transporter solute-binding subunit( domain architecture ID 11493742)
TAXI family TRAP transporter solute-binding subunit is a component of an ATP-independent periplasmic transporter and belongs to type 2 periplasmic-binding fold protein (PBP2) superfamily; the substrate spectrum of TAXI proteins remains to be defined
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| TRAP_TAXI | TIGR02122 | TRAP transporter solute receptor, TAXI family; This family is one of at least three major ... |
28-314 | 9.14e-134 | |||||
TRAP transporter solute receptor, TAXI family; This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds. [Transport and binding proteins, Unknown substrate] : Pssm-ID: 273982 [Multi-domain] Cd Length: 320 Bit Score: 382.45 E-value: 9.14e-134
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| Name | Accession | Description | Interval | E-value | |||||
| TRAP_TAXI | TIGR02122 | TRAP transporter solute receptor, TAXI family; This family is one of at least three major ... |
28-314 | 9.14e-134 | |||||
TRAP transporter solute receptor, TAXI family; This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds. [Transport and binding proteins, Unknown substrate] Pssm-ID: 273982 [Multi-domain] Cd Length: 320 Bit Score: 382.45 E-value: 9.14e-134
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| PBP2_TtGluBP | cd13567 | Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the ... |
28-310 | 6.31e-133 | |||||
Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold; This subgroup includes TtGluBP of TAXI-TRAP family and closely related proteins. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. Pssm-ID: 270285 [Multi-domain] Cd Length: 284 Bit Score: 378.86 E-value: 6.31e-133
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| Imp | COG2358 | TRAP-type uncharacterized transport system, periplasmic component [General function prediction ... |
28-317 | 3.41e-127 | |||||
TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Pssm-ID: 441925 [Multi-domain] Cd Length: 303 Bit Score: 365.32 E-value: 3.41e-127
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| NMT1_3 | pfam16868 | NMT1-like family; |
31-314 | 7.49e-125 | |||||
NMT1-like family; Pssm-ID: 435616 [Multi-domain] Cd Length: 289 Bit Score: 358.87 E-value: 7.49e-125
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
115-191 | 4.36e-05 | |||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 43.86 E-value: 4.36e-05
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| Name | Accession | Description | Interval | E-value | |||||
| TRAP_TAXI | TIGR02122 | TRAP transporter solute receptor, TAXI family; This family is one of at least three major ... |
28-314 | 9.14e-134 | |||||
TRAP transporter solute receptor, TAXI family; This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds. [Transport and binding proteins, Unknown substrate] Pssm-ID: 273982 [Multi-domain] Cd Length: 320 Bit Score: 382.45 E-value: 9.14e-134
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| PBP2_TtGluBP | cd13567 | Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the ... |
28-310 | 6.31e-133 | |||||
Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold; This subgroup includes TtGluBP of TAXI-TRAP family and closely related proteins. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. Pssm-ID: 270285 [Multi-domain] Cd Length: 284 Bit Score: 378.86 E-value: 6.31e-133
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| Imp | COG2358 | TRAP-type uncharacterized transport system, periplasmic component [General function prediction ... |
28-317 | 3.41e-127 | |||||
TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Pssm-ID: 441925 [Multi-domain] Cd Length: 303 Bit Score: 365.32 E-value: 3.41e-127
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| NMT1_3 | pfam16868 | NMT1-like family; |
31-314 | 7.49e-125 | |||||
NMT1-like family; Pssm-ID: 435616 [Multi-domain] Cd Length: 289 Bit Score: 358.87 E-value: 7.49e-125
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| PBP2_TAXI_TRAP | cd13520 | Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic ... |
28-310 | 1.74e-110 | |||||
Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This group includes Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family and closely related proteins. TRAP transporters are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP (substrate-binding protein) of the DctP or TAXI families and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. The substrate-binding domain of TAXI proteins belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and tworeceptor cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270238 [Multi-domain] Cd Length: 285 Bit Score: 322.26 E-value: 1.74e-110
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| PBP2_TAXI_TRAP_like_1 | cd13569 | Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent ... |
28-310 | 5.14e-100 | |||||
Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. Pssm-ID: 270287 [Multi-domain] Cd Length: 283 Bit Score: 295.34 E-value: 5.14e-100
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| PBP2_TAXI_TRAP_like_3 | cd13568 | Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent ... |
28-310 | 1.95e-71 | |||||
Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. Pssm-ID: 270286 [Multi-domain] Cd Length: 289 Bit Score: 222.95 E-value: 1.95e-71
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| PBP2_TAXI_TRAP_like_2 | cd13570 | Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent ... |
32-310 | 3.56e-51 | |||||
Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. Pssm-ID: 270288 [Multi-domain] Cd Length: 281 Bit Score: 170.31 E-value: 3.56e-51
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| TauA | COG0715 | ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ... |
40-191 | 1.41e-12 | |||||
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 440479 [Multi-domain] Cd Length: 297 Bit Score: 66.95 E-value: 1.41e-12
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| PhnD | COG3221 | ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion ... |
120-223 | 3.61e-09 | |||||
ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 442454 [Multi-domain] Cd Length: 250 Bit Score: 56.47 E-value: 3.61e-09
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| PBP2_NrtA_SsuA_CpmA_like | cd01008 | Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ... |
55-189 | 3.64e-09 | |||||
Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This family represents the periplasmic binding proteins involved in nitrate, alkanesulfonate, and bicarbonate transport. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. Other closest homologs involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB) are also included in this family. After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270229 [Multi-domain] Cd Length: 212 Bit Score: 55.76 E-value: 3.64e-09
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| Phosphonate-bd | pfam12974 | ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ... |
71-230 | 3.73e-08 | |||||
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake. Pssm-ID: 432911 [Multi-domain] Cd Length: 243 Bit Score: 53.42 E-value: 3.73e-08
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| PBP2_ThiY_THI5_like_1 | cd13652 | Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 ... |
121-189 | 7.26e-08 | |||||
Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 periplasmic binding protein fold; This subfamily is phylogenetically similar to ThiY, which is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270370 [Multi-domain] Cd Length: 217 Bit Score: 52.00 E-value: 7.26e-08
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| PBP2_ThiY | cd13651 | Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway ... |
39-170 | 1.77e-07 | |||||
Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway intermediates; a member of the type 2 periplasmic binding fold superfamily; ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport , as well as THI5 which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes. After binding the ligand, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270369 [Multi-domain] Cd Length: 214 Bit Score: 50.82 E-value: 1.77e-07
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| PBP2_PhnD_like | cd01071 | Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ... |
92-189 | 2.71e-07 | |||||
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily; This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270232 [Multi-domain] Cd Length: 253 Bit Score: 50.72 E-value: 2.71e-07
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| PBP2_NrtA_CpmA_like | cd13553 | Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 ... |
108-189 | 7.29e-07 | |||||
Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes nitrate (NrtA) and bicarbonate (CmpA) receptors. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270271 [Multi-domain] Cd Length: 212 Bit Score: 49.11 E-value: 7.29e-07
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| PBP2_PnhD_3 | cd13573 | Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ... |
61-165 | 1.46e-06 | |||||
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270291 [Multi-domain] Cd Length: 253 Bit Score: 48.63 E-value: 1.46e-06
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| Periplasmic_Binding_Protein_Type_2 | cd00648 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
35-200 | 6.60e-06 | |||||
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences. Pssm-ID: 270214 [Multi-domain] Cd Length: 196 Bit Score: 46.03 E-value: 6.60e-06
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| PBP2_sulfate_ester_like | cd13555 | Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold; This ... |
107-263 | 9.72e-06 | |||||
Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270273 Cd Length: 268 Bit Score: 46.17 E-value: 9.72e-06
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| PBP2_ThiY_THI5_like | cd13564 | Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway ... |
118-229 | 1.12e-05 | |||||
Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway intermediates and similar proteins; the type 2 periplasmic binding protein fold; ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270282 [Multi-domain] Cd Length: 214 Bit Score: 45.57 E-value: 1.12e-05
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| 3A0109s03R | TIGR01098 | phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are ... |
99-203 | 2.91e-05 | |||||
phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other, related binding components for closely related substances such as phosphate and phosphite. A number of members of this family are found in genomic contexts with components of selenium metabolic processes suggestive of a role in selenate or other selenium-compound transport. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232) has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates. [Transport and binding proteins, Anions] Pssm-ID: 273442 [Multi-domain] Cd Length: 254 Bit Score: 44.65 E-value: 2.91e-05
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
115-191 | 4.36e-05 | |||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 43.86 E-value: 4.36e-05
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| SsuA_fam | TIGR01728 | ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ... |
116-189 | 9.42e-05 | |||||
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins. [Transport and binding proteins, Other] Pssm-ID: 130789 [Multi-domain] Cd Length: 288 Bit Score: 43.50 E-value: 9.42e-05
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| PBP2_SsuA_like_2 | cd13558 | Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding ... |
107-189 | 9.59e-05 | |||||
Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270276 Cd Length: 267 Bit Score: 43.04 E-value: 9.59e-05
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| NMT1 | pfam09084 | NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ... |
103-167 | 1.25e-04 | |||||
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine.3]. They are regulated by thiamine. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor. Pssm-ID: 430398 [Multi-domain] Cd Length: 216 Bit Score: 42.59 E-value: 1.25e-04
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| PBP2_SsuA | cd13557 | Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic ... |
121-189 | 1.65e-04 | |||||
Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes the sulfonate binding domains SsuA found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270275 Cd Length: 275 Bit Score: 42.66 E-value: 1.65e-04
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| PBP2_PnhD_4 | cd13574 | Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ... |
28-173 | 2.75e-04 | |||||
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270292 [Multi-domain] Cd Length: 250 Bit Score: 41.53 E-value: 2.75e-04
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| PBP2_Cae31940 | cd13649 | Substrate binding domain of an uncharacterized protein similar to ABC-type transporter for ... |
34-220 | 4.47e-04 | |||||
Substrate binding domain of an uncharacterized protein similar to ABC-type transporter for thiamin biosynthetic pathway intermediates; a member of the type 2 periplasmic binding fold superfamily; This subfamily includes the periplamic-binding protein Cae31940 which is phylogenetically similar to the ThiY/THI5 family. ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, They interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270367 Cd Length: 223 Bit Score: 40.98 E-value: 4.47e-04
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| PBP2_Atu4678_like | cd13696 | The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ... |
99-195 | 5.54e-04 | |||||
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Agrobacterium tumefaciens and its related proteins. The putative Atu4678-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270414 [Multi-domain] Cd Length: 227 Bit Score: 40.44 E-value: 5.54e-04
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
121-239 | 1.18e-03 | |||||
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]; Pssm-ID: 440596 [Multi-domain] Cd Length: 223 Bit Score: 39.58 E-value: 1.18e-03
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| PBP2_AA_binding_like_1 | cd13625 | Substrate-binding domain of putative amino acid-binding protein; the type 2 ... |
121-236 | 1.96e-03 | |||||
Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold; This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270343 [Multi-domain] Cd Length: 230 Bit Score: 38.89 E-value: 1.96e-03
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| PBP2_PnhD_2 | cd13572 | Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ... |
97-172 | 2.08e-03 | |||||
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270290 [Multi-domain] Cd Length: 249 Bit Score: 38.83 E-value: 2.08e-03
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| PBP2_Cystine_like | cd13626 | Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ... |
115-191 | 2.47e-03 | |||||
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein fold; Cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Also, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270344 [Multi-domain] Cd Length: 219 Bit Score: 38.45 E-value: 2.47e-03
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| PBP2_BsGlnH | cd13689 | Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ... |
115-200 | 3.55e-03 | |||||
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 periplasmic-bindig protein fold; This group includes periplasmic glutamine-binding domain GlnP from Bacillus subtilis and its related proteins. The GlnP domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270407 [Multi-domain] Cd Length: 229 Bit Score: 38.37 E-value: 3.55e-03
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| PBP2_BztA | cd13692 | Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type ... |
121-165 | 5.84e-03 | |||||
Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type 2 periplasmic binding protein fold; BztA is the periplamic-binding protein component of ABC transporter specific for carboxylic amino acids, glutamine and asparagine. The BZtA domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270410 [Multi-domain] Cd Length: 236 Bit Score: 37.61 E-value: 5.84e-03
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| PBP2_Ala | cd13628 | Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ... |
74-191 | 8.16e-03 | |||||
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 periplasmic binding protein; This periplasmic substrate component serves as an initial receptor in the ABC transport of glutamine in eubacteria and archaea. After binding the alanine with high affinity, this domain Interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. This alanine specific domain belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270346 [Multi-domain] Cd Length: 219 Bit Score: 37.06 E-value: 8.16e-03
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