aliphatic sulfonate ABC transporter substrate-binding protein [Sinorhizobium meliloti]
Protein Classification
aliphatic sulfonate ABC transporter substrate-binding protein( domain architecture ID 11493063)
aliphatic sulfonate ABC transporter substrate-binding protein similar to Bacillus subtilis aliphatic sulfonates-binding protein, part of a binding-protein-dependent transport system for aliphatic sulfonates
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| SsuA_fam | TIGR01728 | ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ... |
41-334 | 2.11e-119 | |||||
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: 345.89 E-value: 2.11e-119
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| Name | Accession | Description | Interval | E-value | |||||
| SsuA_fam | TIGR01728 | ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ... |
41-334 | 2.11e-119 | |||||
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: 345.89 E-value: 2.11e-119
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| PBP2_NrtA_SsuA_CpmA_like | cd01008 | Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ... |
41-256 | 3.05e-59 | |||||
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: 189.81 E-value: 3.05e-59
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| TauA | COG0715 | ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ... |
16-322 | 5.99e-57 | |||||
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 440479 [Multi-domain] Cd Length: 297 Bit Score: 186.75 E-value: 5.99e-57
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| NMT1 | pfam09084 | NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ... |
66-266 | 1.05e-20 | |||||
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: 88.82 E-value: 1.05e-20
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| PRK11553 | PRK11553 | alkanesulfonate transporter substrate-binding subunit; Provisional |
11-325 | 1.28e-20 | |||||
alkanesulfonate transporter substrate-binding subunit; Provisional Pssm-ID: 236929 Cd Length: 314 Bit Score: 90.62 E-value: 1.28e-20
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
62-197 | 2.91e-10 | |||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 59.26 E-value: 2.91e-10
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| Name | Accession | Description | Interval | E-value | ||||||
| SsuA_fam | TIGR01728 | ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ... |
41-334 | 2.11e-119 | ||||||
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: 345.89 E-value: 2.11e-119
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| PBP2_NrtA_SsuA_CpmA_like | cd01008 | Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ... |
41-256 | 3.05e-59 | ||||||
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: 189.81 E-value: 3.05e-59
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| TauA | COG0715 | ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ... |
16-322 | 5.99e-57 | ||||||
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 440479 [Multi-domain] Cd Length: 297 Bit Score: 186.75 E-value: 5.99e-57
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| PBP2_sulfate_ester_like | cd13555 | Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold; This ... |
41-270 | 1.06e-51 | ||||||
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: 172.13 E-value: 1.06e-51
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| TauA | COG4521 | ABC-type taurine transport system, periplasmic component [Inorganic ion transport and ... |
8-339 | 3.09e-38 | ||||||
ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 443595 [Multi-domain] Cd Length: 332 Bit Score: 138.85 E-value: 3.09e-38
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| PBP2_SsuA_like_2 | cd13558 | Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding ... |
72-316 | 3.12e-38 | ||||||
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: 137.03 E-value: 3.12e-38
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| PBP2_SsuA | cd13557 | Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic ... |
41-322 | 1.63e-36 | ||||||
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: 132.80 E-value: 1.63e-36
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| PBP2_SsuA_like_1 | cd13556 | Substrate binding domain of putative sulfonate binding protein, a member of the type 2 ... |
54-305 | 3.49e-35 | ||||||
Substrate binding domain of putative sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily; 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: 270274 Cd Length: 265 Bit Score: 129.13 E-value: 3.49e-35
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| PBP2_taurine | cd13560 | Taurine-binding periplasmic protein; the type 2 periplasmic binding protein fold; This ... |
59-264 | 7.69e-33 | ||||||
Taurine-binding periplasmic 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: 270278 [Multi-domain] Cd Length: 218 Bit Score: 121.64 E-value: 7.69e-33
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| PBP2_SsuA_like_5 | cd13562 | Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ... |
41-250 | 8.18e-30 | ||||||
Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes sulfonate binding domains 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: 270280 [Multi-domain] Cd Length: 215 Bit Score: 113.37 E-value: 8.18e-30
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| PBP2_SsuA_like_6 | cd13563 | Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 ... |
41-250 | 3.01e-29 | ||||||
Putative substrate binding domain of sulfonate binding protein-like, a member of 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: 270281 [Multi-domain] Cd Length: 208 Bit Score: 111.56 E-value: 3.01e-29
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| PBP2_SsuA_like_3 | cd13559 | Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ... |
54-276 | 1.25e-25 | ||||||
Putative substrate binding domain of sulfonate 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: 270277 Cd Length: 258 Bit Score: 103.27 E-value: 1.25e-25
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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 ... |
63-251 | 6.25e-25 | ||||||
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: 100.54 E-value: 6.25e-25
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| NMT1 | pfam09084 | NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ... |
66-266 | 1.05e-20 | ||||||
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: 88.82 E-value: 1.05e-20
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| PRK11553 | PRK11553 | alkanesulfonate transporter substrate-binding subunit; Provisional |
11-325 | 1.28e-20 | ||||||
alkanesulfonate transporter substrate-binding subunit; Provisional Pssm-ID: 236929 Cd Length: 314 Bit Score: 90.62 E-value: 1.28e-20
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| PBP2_SsuA_like_4 | cd13561 | Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ... |
41-252 | 3.59e-20 | ||||||
Putative substrate binding domain of sulfonate 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: 270279 [Multi-domain] Cd Length: 212 Bit Score: 87.43 E-value: 3.59e-20
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| PBP2_NrtA_CpmA_like | cd13553 | Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 ... |
66-256 | 2.72e-19 | ||||||
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: 84.94 E-value: 2.72e-19
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| PBP2_ThiY_THI5_like | cd13564 | Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway ... |
66-256 | 1.63e-17 | ||||||
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: 79.85 E-value: 1.63e-17
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| PBP2_DszB | cd13554 | Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 ... |
69-285 | 5.97e-17 | ||||||
Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes DszB, which converts 2'-hydroxybiphenyl-2-sulfinate to 2-hydroxybiphenyl and sulfinate at the rate-limiting step of the microbial dibenzothiophene desulfurization pathway. The overall fold of DszB is highly similar to those of periplasmic substrate-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. 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. The DszB protein 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. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270272 [Multi-domain] Cd Length: 246 Bit Score: 79.09 E-value: 5.97e-17
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| tauA | PRK11480 | taurine transporter substrate binding subunit; Provisional |
63-266 | 2.11e-16 | ||||||
taurine transporter substrate binding subunit; Provisional Pssm-ID: 183158 Cd Length: 320 Bit Score: 78.88 E-value: 2.11e-16
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| PBP2_ThiY | cd13651 | Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway ... |
66-251 | 2.19e-14 | ||||||
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: 71.23 E-value: 2.19e-14
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| PBP2_TAXI_TRAP | cd13520 | Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic ... |
41-215 | 1.26e-13 | ||||||
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: 70.34 E-value: 1.26e-13
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| Imp | COG2358 | TRAP-type uncharacterized transport system, periplasmic component [General function prediction ... |
80-273 | 1.32e-12 | ||||||
TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Pssm-ID: 441925 [Multi-domain] Cd Length: 303 Bit Score: 67.56 E-value: 1.32e-12
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| PBP2_PhnD_like | cd01071 | Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ... |
62-211 | 4.27e-12 | ||||||
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: 65.36 E-value: 4.27e-12
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| PhnD | COG3221 | ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion ... |
62-215 | 9.53e-12 | ||||||
ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 442454 [Multi-domain] Cd Length: 250 Bit Score: 64.17 E-value: 9.53e-12
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| 3A0109s03R | TIGR01098 | phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are ... |
9-213 | 4.20e-11 | ||||||
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: 62.37 E-value: 4.20e-11
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| Phosphonate-bd | pfam12974 | ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ... |
62-211 | 6.20e-11 | ||||||
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: 61.90 E-value: 6.20e-11
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
62-197 | 2.91e-10 | ||||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 59.26 E-value: 2.91e-10
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| TRAP_TAXI | TIGR02122 | TRAP transporter solute receptor, TAXI family; This family is one of at least three major ... |
11-214 | 3.50e-10 | ||||||
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: 60.42 E-value: 3.50e-10
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| PBP2_Cystine_like_1 | cd13713 | Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ... |
127-214 | 2.74e-08 | ||||||
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold; This group contains uncharacterized periplasmic cystine-binding domain of 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. Likewise, 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: 270431 [Multi-domain] Cd Length: 218 Bit Score: 53.44 E-value: 2.74e-08
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| PBP2_TAXI_TRAP_like_1 | cd13569 | Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent ... |
125-215 | 2.85e-08 | ||||||
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: 54.20 E-value: 2.85e-08
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| PBP2_TtGluBP | cd13567 | Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the ... |
128-215 | 1.32e-07 | ||||||
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: 52.21 E-value: 1.32e-07
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| PBP2_Cae31940 | cd13649 | Substrate binding domain of an uncharacterized protein similar to ABC-type transporter for ... |
66-217 | 3.59e-07 | ||||||
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: 50.22 E-value: 3.59e-07
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| PBP2_PnhD_4 | cd13574 | Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ... |
88-195 | 3.02e-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: 270292 [Multi-domain] Cd Length: 250 Bit Score: 47.69 E-value: 3.02e-06
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
68-209 | 3.74e-06 | ||||||
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: 47.28 E-value: 3.74e-06
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| NMT1_2 | pfam13379 | NMT1-like family; This family is closely related to the pfam09084 family. |
34-265 | 4.04e-06 | ||||||
NMT1-like family; This family is closely related to the pfam09084 family. Pssm-ID: 463863 Cd Length: 254 Bit Score: 47.34 E-value: 4.04e-06
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| SBP_bac_3 | pfam00497 | Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ... |
124-225 | 6.89e-06 | ||||||
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 425719 [Multi-domain] Cd Length: 221 Bit Score: 46.52 E-value: 6.89e-06
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| NMT1_3 | pfam16868 | NMT1-like family; |
128-202 | 7.78e-06 | ||||||
NMT1-like family; Pssm-ID: 435616 [Multi-domain] Cd Length: 289 Bit Score: 46.86 E-value: 7.78e-06
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| PBP2_GltI_DEBP | cd13688 | Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ... |
127-195 | 1.05e-05 | ||||||
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic binding protein fold; This subfamily represents the periplasmic-binding protein component of ABC transporter specific for carboxylic amino acids, including GtlI from Escherichia coli. The aspartate-glutamate binding 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: 270406 [Multi-domain] Cd Length: 238 Bit Score: 46.09 E-value: 1.05e-05
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| PBP2_TAXI_TRAP_like_3 | cd13568 | Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent ... |
128-197 | 1.67e-05 | ||||||
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: 45.76 E-value: 1.67e-05
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| PhnD | TIGR03431 | phosphonate ABC transporter, periplasmic phosphonate binding protein; This model is a subset ... |
9-211 | 1.73e-05 | ||||||
phosphonate ABC transporter, periplasmic phosphonate binding protein; This model is a subset of the broader subfamily of phosphate/phosphonate binding protein ABC transporter components, TIGR01098. In this model all members of the seed have support from genomic context for association with pathways for the metabolims of phosphonates, particularly the C-P lyase system, GenProp0232. This model includes the characterized phnD gene from E. coli. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function. Pssm-ID: 132472 [Multi-domain] Cd Length: 288 Bit Score: 45.81 E-value: 1.73e-05
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| PBP2_Atu4678_like | cd13696 | The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ... |
87-211 | 5.90e-05 | ||||||
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: 43.91 E-value: 5.90e-05
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| PBP2_GluR0 | cd00997 | Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ... |
128-197 | 7.41e-05 | ||||||
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate receptor domain GluR0. These domains are found in the GluR0 proteins that have been shown to function as prokaryotic L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. The GluR0 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: 270218 [Multi-domain] Cd Length: 218 Bit Score: 43.48 E-value: 7.41e-05
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| PBP2_Ca3427_like | cd13637 | The conserved hypothetical protein Ca3427 exhibits the type 2 periplasmic-binding protein fold; ... |
41-149 | 1.29e-04 | ||||||
The conserved hypothetical protein Ca3427 exhibits the type 2 periplasmic-binding protein fold; This group includes the Ca3427 protein from candida albicans, which is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8, and other related hypothetical proteins. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Ca3427 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. 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. Pssm-ID: 270355 Cd Length: 273 Bit Score: 42.94 E-value: 1.29e-04
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| PBP2_PnhD_3 | cd13573 | Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ... |
70-154 | 1.61e-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: 270291 [Multi-domain] Cd Length: 253 Bit Score: 42.46 E-value: 1.61e-04
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| PBP2_PnhD_1 | cd13571 | Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ... |
88-150 | 2.74e-04 | ||||||
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding components 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: 270289 [Multi-domain] Cd Length: 253 Bit Score: 41.86 E-value: 2.74e-04
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| PBP2_Bug_TTT | cd07012 | Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains ... |
129-223 | 3.57e-04 | ||||||
Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold; The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter. Pssm-ID: 270234 Cd Length: 291 Bit Score: 41.69 E-value: 3.57e-04
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| PBP2_HisK | cd13704 | The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ... |
129-199 | 5.92e-04 | ||||||
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein; This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain 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 through their function as an initial high-affinity binding component. 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. Pssm-ID: 270422 [Multi-domain] Cd Length: 220 Bit Score: 40.65 E-value: 5.92e-04
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| PBP2_Ngo0372_TcyA | cd13711 | Substrate binding domain of ABC transporters involved in cystine import; the type 2 ... |
129-199 | 7.12e-04 | ||||||
Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold; This subgroup includes cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette transporters from Neisseria gonorrhoeae and Bacillus subtilis and their related proteins. 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. Likewise, 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: 270429 [Multi-domain] Cd Length: 222 Bit Score: 40.36 E-value: 7.12e-04
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| PBP2_PnhD_2 | cd13572 | Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ... |
36-216 | 8.11e-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: 270290 [Multi-domain] Cd Length: 249 Bit Score: 40.37 E-value: 8.11e-04
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| TctC | COG3181 | Tripartite-type tricarboxylate transporter, extracytoplasmic receptor component TctC [Energy ... |
129-223 | 1.01e-03 | ||||||
Tripartite-type tricarboxylate transporter, extracytoplasmic receptor component TctC [Energy production and conversion]; Pssm-ID: 442414 Cd Length: 324 Bit Score: 40.51 E-value: 1.01e-03
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| PBP2_Cys_DEBP_like | cd01000 | Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ... |
114-240 | 1.08e-03 | ||||||
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold; This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins. The cysteine and aspartate-glutamate binding domains belong 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: 270221 [Multi-domain] Cd Length: 228 Bit Score: 39.98 E-value: 1.08e-03
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| Periplasmic_Binding_Protein_Type_2 | cd00648 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
41-218 | 1.31e-03 | ||||||
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: 39.48 E-value: 1.31e-03
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| PBP2_Cystine_like | cd13626 | Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ... |
71-197 | 1.33e-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: 39.61 E-value: 1.33e-03
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| OpuAC | pfam04069 | Substrate binding domain of ABC-type glycine betaine transport system; Part of a high affinity ... |
59-274 | 1.42e-03 | ||||||
Substrate binding domain of ABC-type glycine betaine transport system; Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis. The family member OpuBC is closely related, and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine. L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA). Pssm-ID: 397954 [Multi-domain] Cd Length: 257 Bit Score: 39.62 E-value: 1.42e-03
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| PBP2_TRAP_BpDctp6_7 | cd13602 | Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ... |
136-200 | 2.05e-03 | ||||||
Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold; DctP6 and DctP7 groups of the TRAP transporters that involved in pyroglutamic acid transport. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain 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. Pssm-ID: 270320 [Multi-domain] Cd Length: 300 Bit Score: 39.52 E-value: 2.05e-03
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| PBP2_peptides_like | cd13530 | Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ... |
129-209 | 2.39e-03 | ||||||
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, 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 majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 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. Pssm-ID: 270248 [Multi-domain] Cd Length: 217 Bit Score: 38.77 E-value: 2.39e-03
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| PBP2_BvgS_HisK_like | cd01007 | The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ... |
129-199 | 2.71e-03 | ||||||
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins; This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane spanning sensor-kinase and a cytoplasmic response regulator. It serves as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. The N-terminal sensing domain of the sensor kinase detects extracellular signals, such as small molecule ligands and ions, which then modulate the catalytic activity of the cytoplasmic kinase domain through a phosphorylation cascade. The periplasmic sensor domain 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: 270228 [Multi-domain] Cd Length: 220 Bit Score: 38.67 E-value: 2.71e-03
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| PBP2_AatB_like | cd00996 | Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ... |
129-166 | 3.34e-03 | ||||||
Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong to the type 2 periplasmic binding fold protein superfamily; This subfamily includes periplasmic binding domain of ATP-binding cassette transporter-like systems that serve as initial receptors in the ABC transport of amino acids and their derivatives in eubacteria. 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. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The Abp proteins belong to the PBPI 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: 270217 [Multi-domain] Cd Length: 227 Bit Score: 38.33 E-value: 3.34e-03
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| PBP2_Arg_Lys_His | cd13624 | Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ... |
129-197 | 3.98e-03 | ||||||
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold; This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ 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: 270342 [Multi-domain] Cd Length: 219 Bit Score: 38.24 E-value: 3.98e-03
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| PotD | COG0687 | Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; |
10-110 | 6.12e-03 | ||||||
Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Pssm-ID: 440451 [Multi-domain] Cd Length: 348 Bit Score: 37.97 E-value: 6.12e-03
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| PBP2_BsGlnH | cd13689 | Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ... |
125-200 | 8.54e-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: 37.21 E-value: 8.54e-03
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| PBP2_BCP_2 | cd13643 | Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline ... |
164-229 | 9.33e-03 | ||||||
Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system-like; the type 2 periplasmic-binding protein fold; This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as glycine betaine, proline betaine, choline, and carnitine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain 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. Pssm-ID: 270361 [Multi-domain] Cd Length: 283 Bit Score: 37.27 E-value: 9.33e-03
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