MULTISPECIES: ABC transporter substrate-binding protein [Bacillus]
Protein Classification
ABC transporter substrate-binding protein( domain architecture ID 10194896)
ABC transporter substrate-binding protein functions as the initial receptor in the ABC transport of one or more from a variety of substrates including sugars, ions, peptides, and drugs, among others; belongs to the type 2 periplasmic binding protein (PBP2) fold superfamily
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| PBP2_Cystine_like_1 | cd13713 | Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ... |
37-253 | 2.61e-118 | ||||
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: 337.33 E-value: 2.61e-118
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| Name | Accession | Description | Interval | E-value | |||||
| PBP2_Cystine_like_1 | cd13713 | Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ... |
37-253 | 2.61e-118 | |||||
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: 337.33 E-value: 2.61e-118
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
38-256 | 6.91e-84 | |||||
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: 250.28 E-value: 6.91e-84
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| SBP_bac_3 | pfam00497 | Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ... |
39-252 | 4.98e-77 | |||||
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: 232.57 E-value: 4.98e-77
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| 3A0103s03R | TIGR01096 | lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ... |
19-252 | 3.35e-64 | |||||
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino acids, peptides and amines] Pssm-ID: 273440 [Multi-domain] Cd Length: 250 Bit Score: 201.05 E-value: 3.35e-64
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
37-252 | 2.56e-63 | |||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 197.55 E-value: 2.56e-63
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| PRK11260 | PRK11260 | cystine ABC transporter substrate-binding protein; |
1-253 | 2.51e-62 | |||||
cystine ABC transporter substrate-binding protein; Pssm-ID: 183061 [Multi-domain] Cd Length: 266 Bit Score: 196.87 E-value: 2.51e-62
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| Name | Accession | Description | Interval | E-value | |||||
| PBP2_Cystine_like_1 | cd13713 | Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ... |
37-253 | 2.61e-118 | |||||
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: 337.33 E-value: 2.61e-118
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
38-256 | 6.91e-84 | |||||
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: 250.28 E-value: 6.91e-84
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| PBP2_peptides_like | cd13530 | Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ... |
37-251 | 8.41e-80 | |||||
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: 239.46 E-value: 8.41e-80
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| PBP2_Cystine_like | cd13626 | Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ... |
38-253 | 1.96e-77 | |||||
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: 233.75 E-value: 1.96e-77
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| SBP_bac_3 | pfam00497 | Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ... |
39-252 | 4.98e-77 | |||||
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: 232.57 E-value: 4.98e-77
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| PBP2_mlr5654_like | cd13702 | Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ... |
35-252 | 2.93e-72 | |||||
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which serve as initial receptors in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group 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: 270420 [Multi-domain] Cd Length: 223 Bit Score: 220.65 E-value: 2.93e-72
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| PBP2_Arg_Lys_His | cd13624 | Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ... |
46-252 | 1.43e-71 | |||||
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: 218.52 E-value: 1.43e-71
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| PBP2_HisJ_LAO | cd13703 | Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; ... |
35-252 | 1.02e-68 | |||||
Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; the type 2 periplasmic-binding protein fold; This subgroup includes the periplasmic-binding proteins, HisJ and LAO, that serve as initial receptors in the ABC transport of histidine and lysine-arginine-ornithine amino acids. They are belong 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: 270421 [Multi-domain] Cd Length: 229 Bit Score: 211.72 E-value: 1.02e-68
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| PBP2_HisJ_LAO_like | cd01001 | Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ... |
35-252 | 2.97e-67 | |||||
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and related proteins; the type 2 periplasmic-binding protein fold; This family comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong 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: 270222 [Multi-domain] Cd Length: 228 Bit Score: 207.92 E-value: 2.97e-67
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| PBP2_FliY | cd13712 | Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ... |
39-253 | 1.52e-65 | |||||
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic binding protein fold; This group contains cystine binding domain FliY and its 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: 270430 [Multi-domain] Cd Length: 219 Bit Score: 203.39 E-value: 1.52e-65
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| 3A0103s03R | TIGR01096 | lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ... |
19-252 | 3.35e-64 | |||||
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino acids, peptides and amines] Pssm-ID: 273440 [Multi-domain] Cd Length: 250 Bit Score: 201.05 E-value: 3.35e-64
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
37-252 | 2.56e-63 | |||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 197.55 E-value: 2.56e-63
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| PRK11260 | PRK11260 | cystine ABC transporter substrate-binding protein; |
1-253 | 2.51e-62 | |||||
cystine ABC transporter substrate-binding protein; Pssm-ID: 183061 [Multi-domain] Cd Length: 266 Bit Score: 196.87 E-value: 2.51e-62
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| PBP2_GlnH | cd00994 | Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ... |
37-253 | 2.84e-60 | |||||
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; This periplasmic substrate-binding component serves as an initial receptor in the ABC transport of glutamine in bacteria and eukaryota. GlnH 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: 270216 [Multi-domain] Cd Length: 218 Bit Score: 189.79 E-value: 2.84e-60
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| PBP2_Ngo0372_TcyA | cd13711 | Substrate binding domain of ABC transporters involved in cystine import; the type 2 ... |
37-256 | 3.00e-60 | |||||
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: 189.82 E-value: 3.00e-60
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| PBP2_AatB_like | cd00996 | Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ... |
48-253 | 1.51e-59 | |||||
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: 188.17 E-value: 1.51e-59
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| PBP2_Arg_STM4351 | cd13700 | Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding ... |
39-252 | 1.25e-56 | |||||
Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding protein fold; This group includes domains similar to Escherichia coli arginine third transport system. STM4351 is the high arginine specific periplasmic-binding protein of ABC transport system. STM4351 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: 270418 [Multi-domain] Cd Length: 222 Bit Score: 180.72 E-value: 1.25e-56
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| PBP2_YxeM | cd13709 | Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ... |
36-256 | 2.46e-55 | |||||
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein fold; This group contains cystine-binding domain (YxeM) of a periplasmic receptor-dependent ATP-binding cassette transporter and its closely 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: 270427 [Multi-domain] Cd Length: 227 Bit Score: 177.54 E-value: 2.46e-55
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| PBP2_MidA_like | cd01004 | Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ... |
36-251 | 1.12e-54 | |||||
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 periplasmic binding protein fold; This subgroup includes the periplasmic binding component of ABC transporter involved in uptake of mimosine MidA and its similar proteins. This periplasmic binding 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: 270225 [Multi-domain] Cd Length: 230 Bit Score: 175.89 E-value: 1.12e-54
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| PBP2_HisK | cd13704 | The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ... |
46-252 | 1.07e-53 | |||||
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: 173.15 E-value: 1.07e-53
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| PBP2_Cys_DEBP_like | cd01000 | Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ... |
48-252 | 6.54e-49 | |||||
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: 161.32 E-value: 6.54e-49
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| PBP2_Dsm1740 | cd13629 | Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ... |
37-252 | 2.38e-48 | |||||
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily includes the periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), 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 PBPII 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: 270347 [Multi-domain] Cd Length: 221 Bit Score: 159.27 E-value: 2.38e-48
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| PBP2_ml15202_like | cd13701 | Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ... |
46-252 | 2.91e-48 | |||||
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which are involved in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group 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: 270419 [Multi-domain] Cd Length: 227 Bit Score: 159.55 E-value: 2.91e-48
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| PBP2_BsGlnH | cd13689 | Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ... |
48-253 | 8.75e-48 | |||||
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: 158.16 E-value: 8.75e-48
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| glnH | PRK09495 | glutamine ABC transporter periplasmic protein; Reviewed |
18-253 | 1.02e-44 | |||||
glutamine ABC transporter periplasmic protein; Reviewed Pssm-ID: 236540 [Multi-domain] Cd Length: 247 Bit Score: 151.05 E-value: 1.02e-44
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| PBP2_GluB | cd13690 | Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ... |
53-253 | 2.94e-43 | |||||
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein fold; This group includes periplasmic glutamate-binding domain GluB from Corynebacterium efficiens and its related proteins. The GluB 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: 270408 [Multi-domain] Cd Length: 231 Bit Score: 146.64 E-value: 2.94e-43
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| PRK15007 | PRK15007 | arginine ABC transporter substrate-binding protein; |
19-254 | 7.18e-43 | |||||
arginine ABC transporter substrate-binding protein; Pssm-ID: 184969 [Multi-domain] Cd Length: 243 Bit Score: 146.33 E-value: 7.18e-43
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| PBP2_BvgS_HisK_like | cd01007 | The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ... |
36-252 | 1.77e-42 | |||||
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: 144.21 E-value: 1.77e-42
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| PBP2_Atu4678_like | cd13696 | The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ... |
36-252 | 1.96e-42 | |||||
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: 144.44 E-value: 1.96e-42
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| PBP2_GlnP | cd13619 | Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ... |
46-251 | 3.20e-42 | |||||
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily; Periplasmic glutamine binding domain GlnP serves as an initial receptor in the ABC transport of glutamine in eubacteria. GlnP 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: 270337 [Multi-domain] Cd Length: 220 Bit Score: 143.61 E-value: 3.20e-42
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| PRK15437 | PRK15437 | histidine ABC transporter substrate-binding protein HisJ; Provisional |
36-258 | 3.01e-41 | |||||
histidine ABC transporter substrate-binding protein HisJ; Provisional Pssm-ID: 185334 [Multi-domain] Cd Length: 259 Bit Score: 142.48 E-value: 3.01e-41
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| PBP2_OccT_like | cd13699 | Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding ... |
35-252 | 7.29e-41 | |||||
Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding protein fold; This group includes periplasmic octopine-binding protein and related proteins. This group 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 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: 270417 [Multi-domain] Cd Length: 211 Bit Score: 139.82 E-value: 7.29e-41
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| PRK15010 | PRK15010 | lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT; |
1-259 | 1.47e-39 | |||||
lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT; Pssm-ID: 184972 [Multi-domain] Cd Length: 260 Bit Score: 138.21 E-value: 1.47e-39
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| PBP2_AA_binding_like_1 | cd13625 | Substrate-binding domain of putative amino acid-binding protein; the type 2 ... |
46-251 | 2.08e-39 | |||||
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: 136.74 E-value: 2.08e-39
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| PBP2_ArtJ | cd00999 | The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold ... |
37-251 | 4.68e-38 | |||||
The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold protein superfamily; An arginine-binding protein found in Chlamydiae trachomatis (CT-ArtJ) and pneumoniae (CPn-ArtJ) and its closely related proteins. CT- and CPn-ArtJ are shown to have different immunogenic properties despite a high sequence similarity. The ArtJ proteins display the type 2 periplasmic binding fold organized in two alpha-beta domains with arginine-binding region at their interface. Pssm-ID: 270220 [Multi-domain] Cd Length: 223 Bit Score: 132.83 E-value: 4.68e-38
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| PBP2_SMa0082_like | cd01072 | The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ... |
48-254 | 4.01e-37 | |||||
The substrate-binding domain of putatuve 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 Sinorhizobium meliloti and its related proteins. The putative SMa0082-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: 270233 [Multi-domain] Cd Length: 238 Bit Score: 130.85 E-value: 4.01e-37
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| PBP2_Ala | cd13628 | Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ... |
46-251 | 8.90e-35 | |||||
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: 124.50 E-value: 8.90e-35
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| PBP2_Arg_3 | cd13622 | Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ... |
39-252 | 1.35e-34 | |||||
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding fold; This subgroup is similar to the HisJ-like family that comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong 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: 270340 [Multi-domain] Cd Length: 222 Bit Score: 123.95 E-value: 1.35e-34
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| PBP2_GltI_DEBP | cd13688 | Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ... |
48-252 | 1.50e-34 | |||||
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: 124.29 E-value: 1.50e-34
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| PBP2_TcyK | cd13710 | Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding ... |
36-257 | 8.62e-33 | |||||
Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding protein fold; This group contains periplasmic cystine-binding domain (TcyK) of an ATP-binding cassette transporter from Bacillus subtilus and its closely 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: 270428 [Multi-domain] Cd Length: 233 Bit Score: 119.71 E-value: 8.62e-33
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| PBP2_Ehub_like | cd01002 | Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 ... |
47-251 | 1.36e-30 | |||||
Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 periplasmic binding protein fold; This family represents the periplasmic substrate-binding component of ABC transport systems that involved in uptake of osmoprotectants (also termed compatible solutes) such as ectoine and hydroxyectoine. To counteract the efflux of water, bacteria and archaea accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. 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: 270223 [Multi-domain] Cd Length: 242 Bit Score: 113.91 E-value: 1.36e-30
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| PBP2_YfhD_N | cd01009 | The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ... |
45-253 | 1.20e-29 | |||||
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes the solute binding domain YfhD_N. These domains are found in the YfhD proteins that are predicted to function as lytic transglycosylases that cleave the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin in peptidoglycan, while the YfhD_N domain might act as an auxiliary or regulatory subunit. In addition to periplasmic solute binding domain, they have an SLT domain, typically found in soluble lytic transglycosylases, and a C-terminal low complexity domain. The YfhD proteins might have been recruited to create localized cell wall openings required for transport of large substrates such as DNA. 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: 270230 [Multi-domain] Cd Length: 223 Bit Score: 111.15 E-value: 1.20e-29
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| PBP2_AA_binding_like_2 | cd13627 | Substrate-binding domain of putative amino acid-binding protein; the type 2 ... |
38-249 | 5.50e-29 | |||||
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: 270345 [Multi-domain] Cd Length: 243 Bit Score: 109.80 E-value: 5.50e-29
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| PBP2_polar_AA | cd13693 | Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic ... |
46-251 | 7.29e-29 | |||||
Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of putative polar amino acid ABC transporter. The polar amino-acid 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: 270411 [Multi-domain] Cd Length: 228 Bit Score: 109.33 E-value: 7.29e-29
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| PBP2_GltS | cd13620 | Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ... |
41-250 | 1.43e-28 | |||||
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily; This family comprises of the periplasmic-binding protein component (GltS) of an ABC transporter specific for glutamate or arginine from Lactococcus lactis, as well as its closely related proteins. The GltS 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: 270338 [Multi-domain] Cd Length: 227 Bit Score: 108.58 E-value: 1.43e-28
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| PBP2_Cysteine | cd13694 | Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ... |
36-252 | 4.46e-28 | |||||
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein fold; This subfamily comprises of the periplasmic-binding protein component of ABC transporter specific for cysteine and its closely related proteins. The cysteine-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: 270412 [Multi-domain] Cd Length: 229 Bit Score: 107.05 E-value: 4.46e-28
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| PBP2_GluR0 | cd00997 | Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ... |
48-253 | 1.30e-27 | |||||
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: 105.50 E-value: 1.30e-27
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| PBP2_HisGluGlnArgOpine | cd13698 | Substrate binding domain of ABC-type histidine/glutamate/glutamine/arginine/opine transporter; ... |
36-252 | 6.96e-27 | |||||
Substrate binding domain of ABC-type histidine/glutamate/glutamine/arginine/opine transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic-binding component of His/Glu/Gln/Arg/Opine ATP-binding cassette transport system. This substrate-binding 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 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: 270416 [Multi-domain] Cd Length: 214 Bit Score: 103.53 E-value: 6.96e-27
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| PBP2_Peb1a_like | cd13691 | Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 ... |
56-251 | 5.16e-26 | |||||
Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic aspartate/glutamate binding domain Peb1a and its closely related protein. The Peb1a is an important virulence factor in the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonization. The Peb1a 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: 270409 [Multi-domain] Cd Length: 228 Bit Score: 101.76 E-value: 5.16e-26
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| PBP2_PheC | cd01069 | Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ... |
36-252 | 1.76e-25 | |||||
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes cyclohexadienyl dehydratase PheC. These proteins catalyze the decarboxylation of prephenate to phenylpyruvate in the alternative phenylalanine biosynthesis pathway in some proteobacteria and archaea. The PheC 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. Since they the PheC proteins are so similar to periplasmic binding proteins, (PBP), it is evolutionarily plausible that several pre-existing PBP proteins might have been recruited to perform the enzymatic function. Pssm-ID: 270231 [Multi-domain] Cd Length: 232 Bit Score: 100.49 E-value: 1.76e-25
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| PBP2_YckB | cd01003 | Substrate binding domain of an ABC cystine transporter; the type 2 periplasmic binding protein ... |
41-253 | 3.33e-25 | |||||
Substrate binding domain of an ABC cystine transporter; the type 2 periplasmic binding protein fold; Periplasmic cystine-binding domain (YckB) of an ATP-binding cassette (ABC) transporter from Bacillus subtilis and its 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 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: 270224 [Multi-domain] Cd Length: 229 Bit Score: 99.65 E-value: 3.33e-25
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| MltF | COG4623 | Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ... |
45-253 | 5.00e-24 | |||||
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, Signal transduction mechanisms]; Pssm-ID: 443662 [Multi-domain] Cd Length: 421 Bit Score: 99.75 E-value: 5.00e-24
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| PBP2_BvgS_D2 | cd13707 | The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ... |
39-251 | 2.75e-23 | |||||
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein; This group contains the second domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS 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: 270425 [Multi-domain] Cd Length: 221 Bit Score: 94.21 E-value: 2.75e-23
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| PBP2_HisK_like_1 | cd13706 | Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This ... |
41-252 | 1.08e-21 | |||||
Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This group includes 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: 270424 [Multi-domain] Cd Length: 219 Bit Score: 89.93 E-value: 1.08e-21
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| PBP2_Mlr3796_like | cd13695 | The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic ... |
48-237 | 1.05e-20 | |||||
The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Mesorhizobium loti and its related proteins. The putative Mlr3796-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: 270413 [Multi-domain] Cd Length: 232 Bit Score: 87.62 E-value: 1.05e-20
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| PRK10859 | PRK10859 | membrane-bound lytic murein transglycosylase MltF; |
1-253 | 2.25e-18 | |||||
membrane-bound lytic murein transglycosylase MltF; Pssm-ID: 236778 [Multi-domain] Cd Length: 482 Bit Score: 84.16 E-value: 2.25e-18
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| PBP2_ArtJ_like | cd13697 | Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding ... |
60-252 | 9.85e-17 | |||||
Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding protein fold; The ArtJ 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: 270415 [Multi-domain] Cd Length: 228 Bit Score: 76.80 E-value: 9.85e-17
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| PBP2_BvgS_like_1 | cd13708 | Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is ... |
36-251 | 1.04e-16 | |||||
Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS 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: 270426 [Multi-domain] Cd Length: 220 Bit Score: 76.40 E-value: 1.04e-16
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| PRK10797 | PRK10797 | glutamate and aspartate transporter subunit; Provisional |
48-256 | 3.04e-14 | |||||
glutamate and aspartate transporter subunit; Provisional Pssm-ID: 236763 [Multi-domain] Cd Length: 302 Bit Score: 71.05 E-value: 3.04e-14
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| PBP2_BztA | cd13692 | Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type ... |
49-192 | 7.17e-13 | |||||
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: 66.12 E-value: 7.17e-13
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| PRK11917 | PRK11917 | bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed |
56-251 | 8.11e-13 | |||||
bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed Pssm-ID: 183381 [Multi-domain] Cd Length: 259 Bit Score: 66.48 E-value: 8.11e-13
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| TauA | COG0715 | ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ... |
59-237 | 8.19e-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: 63.87 E-value: 8.19e-12
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| PBP2_AA_binding_like_3 | cd13621 | Substrate-binding domain of putative amino acid-binding protein; the type 2 ... |
48-256 | 1.10e-11 | |||||
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: 270339 [Multi-domain] Cd Length: 229 Bit Score: 62.83 E-value: 1.10e-11
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| PBP2_AA_hypothetical | cd13623 | Substrate-binding domain of putative amino-acid transport system; the type 2 periplasmic ... |
55-250 | 1.32e-11 | |||||
Substrate-binding domain of putative amino-acid transport system; 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: 270341 [Multi-domain] Cd Length: 220 Bit Score: 62.30 E-value: 1.32e-11
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| PhnD | COG3221 | ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion ... |
65-251 | 6.95e-10 | |||||
ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 442454 [Multi-domain] Cd Length: 250 Bit Score: 58.01 E-value: 6.95e-10
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| PBP2_iGluR_NMDA | cd13687 | The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ... |
60-251 | 9.32e-10 | |||||
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; The ligand-binding domain of the ionotropic NMDA subtype is structurally homologous to the periplasmic-binding fold type II superfamily, while the N-terminal domain belongs to the periplasmic-binding fold type I. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. Pssm-ID: 270405 [Multi-domain] Cd Length: 239 Bit Score: 57.26 E-value: 9.32e-10
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| PBP2_iGluR_NMDA_Nr2 | cd13718 | The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
80-251 | 1.54e-09 | |||||
The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. Pssm-ID: 270436 [Multi-domain] Cd Length: 283 Bit Score: 57.35 E-value: 1.54e-09
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| PBP2_iGluR_non_NMDA_like | cd13685 | The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ... |
47-252 | 4.37e-09 | |||||
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors including AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) receptors (GluR1-4), kainate receptors (GluR5-7 and KA1/2), and orphan receptors delta 1/2. iGluRs form tetrameric ligand-gated ion channels, which are concentrated at postsynaptic sites in excitatory synapses where they fulfill a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine#binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I. Pssm-ID: 270403 [Multi-domain] Cd Length: 252 Bit Score: 55.65 E-value: 4.37e-09
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| PBP2_PhnD_like | cd01071 | Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ... |
33-235 | 1.94e-08 | |||||
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: 53.80 E-value: 1.94e-08
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| 3A0109s03R | TIGR01098 | phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are ... |
1-153 | 2.15e-08 | |||||
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: 53.51 E-value: 2.15e-08
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| PBP2_NrtA_SsuA_CpmA_like | cd01008 | Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ... |
78-237 | 4.82e-08 | |||||
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: 51.90 E-value: 4.82e-08
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| PBP2_iGluR_ligand_binding | cd00998 | The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ... |
48-252 | 1.07e-07 | |||||
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic binding protein type II superfamily; This subfamily represents the ligand binding of ionotropic glutamate receptors. iGluRs are heterotetrameric ion channels that comprises of three functionally distinct subtypes based on their pharmacology and structural similarities: AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid), NMDA (N-methyl-D-aspartate), and kainate receptors. All three types of channels are also activated by the physiological neurotransmitter, glutamate. iGluRs are concentrated at postsynaptic sites, where they exert a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I. Pssm-ID: 270219 [Multi-domain] Cd Length: 243 Bit Score: 51.61 E-value: 1.07e-07
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| TauA | COG4521 | ABC-type taurine transport system, periplasmic component [Inorganic ion transport and ... |
124-241 | 2.43e-07 | |||||
ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 443595 [Multi-domain] Cd Length: 332 Bit Score: 51.03 E-value: 2.43e-07
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| PBP2_iGluR_Kainate | cd13714 | Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ... |
57-252 | 4.24e-07 | |||||
Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as 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. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR 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: 270432 [Multi-domain] Cd Length: 251 Bit Score: 49.84 E-value: 4.24e-07
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| PBP2_DszB | cd13554 | Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 ... |
121-185 | 9.72e-07 | |||||
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: 48.66 E-value: 9.72e-07
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| GluR_Plant | cd13686 | Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily ... |
46-252 | 1.07e-06 | |||||
Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily contains the glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as 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. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR 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: 270404 [Multi-domain] Cd Length: 232 Bit Score: 48.29 E-value: 1.07e-06
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| Periplasmic_Binding_Protein_Type_2 | cd00648 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
58-187 | 1.44e-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: 47.57 E-value: 1.44e-06
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| Lig_chan-Glu_bd | pfam10613 | Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ... |
53-130 | 2.29e-06 | |||||
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060. Pssm-ID: 463166 [Multi-domain] Cd Length: 111 Bit Score: 45.20 E-value: 2.29e-06
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| NMT1 | pfam09084 | NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ... |
51-241 | 2.56e-06 | |||||
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: 47.21 E-value: 2.56e-06
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| PBP2_NrtA_CpmA_like | cd13553 | Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 ... |
73-235 | 4.52e-06 | |||||
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: 46.42 E-value: 4.52e-06
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| PBP2_MxaJ | cd13531 | Methanol oxidation system protein MoxJ; the type 2 periplasmic binding fold; This predicted ... |
59-241 | 5.04e-06 | |||||
Methanol oxidation system protein MoxJ; the type 2 periplasmic binding fold; This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. Other evidence also suggests that MoxJ is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. MoxJ may be both, a component of a periplasmic enzyme that converts methanol to formaldehyde and a component of an ABC transporter that delivers the resulting formaldehyde to the cell's interior. Pssm-ID: 270249 Cd Length: 242 Bit Score: 46.31 E-value: 5.04e-06
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| PBP2_BvgS_D1 | cd13705 | The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ... |
46-251 | 7.06e-06 | |||||
The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein; This group contains the first domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a histidine-kinase (HK), a receiver and a histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS 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: 270423 [Multi-domain] Cd Length: 221 Bit Score: 45.66 E-value: 7.06e-06
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| PBP2_iGluR_NMDA_Nr3 | cd13720 | The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
84-252 | 1.05e-05 | |||||
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. Pssm-ID: 270438 [Multi-domain] Cd Length: 283 Bit Score: 45.61 E-value: 1.05e-05
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| PBP2_iGluR_putative | cd13717 | The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ... |
47-137 | 1.88e-05 | |||||
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as 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. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR 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: 270435 [Multi-domain] Cd Length: 360 Bit Score: 45.37 E-value: 1.88e-05
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| PBP2_iGluR_AMPA_GluR1 | cd13729 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
37-252 | 4.92e-05 | |||||
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR1 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the AMPA receptor subunit GluR1, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Pssm-ID: 270447 [Multi-domain] Cd Length: 260 Bit Score: 43.48 E-value: 4.92e-05
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| PBP2_SsuA_like_2 | cd13558 | Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding ... |
109-213 | 4.92e-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: 43.81 E-value: 4.92e-05
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| PBP2_iGluR_AMPA_GluR4 | cd13727 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
53-252 | 7.79e-04 | |||||
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR4 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the AMPA receptor subunit GluR4, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I.The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Pssm-ID: 270445 [Multi-domain] Cd Length: 259 Bit Score: 40.02 E-value: 7.79e-04
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| Phosphonate-bd | pfam12974 | ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ... |
84-235 | 1.46e-03 | |||||
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: 39.17 E-value: 1.46e-03
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| PBP2_iGluR_delta_1 | cd13730 | The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the ... |
45-200 | 1.50e-03 | |||||
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the delta1 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRdelta2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. Pssm-ID: 270448 [Multi-domain] Cd Length: 257 Bit Score: 39.17 E-value: 1.50e-03
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| PBP2_iGluR_delta_like | cd13716 | The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of ... |
45-141 | 2.06e-03 | |||||
The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of iGluRs belongs to the periplasmic-binding fold type I. Although the delta receptors are members of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. Pssm-ID: 270434 [Multi-domain] Cd Length: 257 Bit Score: 38.67 E-value: 2.06e-03
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| PBP2_SsuA_like_5 | cd13562 | Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ... |
98-188 | 3.56e-03 | |||||
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: 37.87 E-value: 3.56e-03
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| SsuA_fam | TIGR01728 | ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ... |
110-240 | 4.19e-03 | |||||
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: 37.73 E-value: 4.19e-03
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| Imp | COG2358 | TRAP-type uncharacterized transport system, periplasmic component [General function prediction ... |
127-249 | 4.50e-03 | |||||
TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Pssm-ID: 441925 [Multi-domain] Cd Length: 303 Bit Score: 37.90 E-value: 4.50e-03
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| PBP2_ThiY_THI5_like | cd13564 | Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway ... |
60-192 | 4.55e-03 | |||||
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: 37.48 E-value: 4.55e-03
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| PBP2_iGluR_kainate_KA2 | cd13725 | The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a ... |
77-141 | 5.24e-03 | |||||
The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the KA2 subunit of kainate receptor. While this ligand-binding domain is structurally homologous to the periplasmic binding fold type II superfamily, the N_terminal domain of kainate receptors belongs to the periplasmic-binding fold type I. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. Pssm-ID: 270443 [Multi-domain] Cd Length: 250 Bit Score: 37.38 E-value: 5.24e-03
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| NMT1_3 | pfam16868 | NMT1-like family; |
127-244 | 7.59e-03 | |||||
NMT1-like family; Pssm-ID: 435616 [Multi-domain] Cd Length: 289 Bit Score: 37.23 E-value: 7.59e-03
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