MULTISPECIES: hydrogen peroxide-inducible genes activator [Pseudoalteromonas]
Protein Classification
hydrogen peroxide-inducible genes activator( domain architecture ID 10444038)
hydrogen peroxide-inducible genes activator OxyR is a lysR-type transcriptional regulator that regulates transcription in response to a low level of cellular H2O2
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| PBP2_OxyR | cd08411 | The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ... |
95-292 | 6.00e-57 | ||||
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. : Pssm-ID: 176103 [Multi-domain] Cd Length: 200 Bit Score: 182.34 E-value: 6.00e-57
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
7-66 | 1.01e-16 | ||||
Bacterial regulatory helix-turn-helix protein, lysR family; : Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 72.80 E-value: 1.01e-16
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| Name | Accession | Description | Interval | E-value | |||||
| PBP2_OxyR | cd08411 | The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ... |
95-292 | 6.00e-57 | |||||
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176103 [Multi-domain] Cd Length: 200 Bit Score: 182.34 E-value: 6.00e-57
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| PRK11151 | PRK11151 | DNA-binding transcriptional regulator OxyR; Provisional |
7-248 | 2.61e-44 | |||||
DNA-binding transcriptional regulator OxyR; Provisional Pssm-ID: 182999 [Multi-domain] Cd Length: 305 Bit Score: 152.88 E-value: 2.61e-44
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| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
6-277 | 3.92e-44 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 151.17 E-value: 3.92e-44
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
94-292 | 1.79e-27 | |||||
LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 460931 [Multi-domain] Cd Length: 205 Bit Score: 105.83 E-value: 1.79e-27
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| LysR_Sec_metab | NF040786 | selenium metabolism-associated LysR family transcriptional regulator; LysR family ... |
7-278 | 1.09e-17 | |||||
selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations. Pssm-ID: 468737 [Multi-domain] Cd Length: 298 Bit Score: 81.51 E-value: 1.09e-17
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
7-66 | 1.01e-16 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 72.80 E-value: 1.01e-16
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| PRK10086 | PRK10086 | DNA-binding transcriptional regulator DsdC; |
14-106 | 5.51e-07 | |||||
DNA-binding transcriptional regulator DsdC; Pssm-ID: 182231 [Multi-domain] Cd Length: 311 Bit Score: 50.00 E-value: 5.51e-07
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| Name | Accession | Description | Interval | E-value | |||||
| PBP2_OxyR | cd08411 | The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ... |
95-292 | 6.00e-57 | |||||
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176103 [Multi-domain] Cd Length: 200 Bit Score: 182.34 E-value: 6.00e-57
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| PRK11151 | PRK11151 | DNA-binding transcriptional regulator OxyR; Provisional |
7-248 | 2.61e-44 | |||||
DNA-binding transcriptional regulator OxyR; Provisional Pssm-ID: 182999 [Multi-domain] Cd Length: 305 Bit Score: 152.88 E-value: 2.61e-44
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| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
6-277 | 3.92e-44 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 151.17 E-value: 3.92e-44
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
94-292 | 1.79e-27 | |||||
LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 460931 [Multi-domain] Cd Length: 205 Bit Score: 105.83 E-value: 1.79e-27
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| PBP2_LTTR_substrate | cd05466 | The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ... |
96-277 | 3.08e-26 | |||||
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Pssm-ID: 176102 [Multi-domain] Cd Length: 197 Bit Score: 102.29 E-value: 3.08e-26
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| LysR_Sec_metab | NF040786 | selenium metabolism-associated LysR family transcriptional regulator; LysR family ... |
7-278 | 1.09e-17 | |||||
selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations. Pssm-ID: 468737 [Multi-domain] Cd Length: 298 Bit Score: 81.51 E-value: 1.09e-17
|
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
7-66 | 1.01e-16 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 72.80 E-value: 1.01e-16
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| PRK11242 | PRK11242 | DNA-binding transcriptional regulator CynR; Provisional |
8-244 | 3.61e-16 | |||||
DNA-binding transcriptional regulator CynR; Provisional Pssm-ID: 183051 [Multi-domain] Cd Length: 296 Bit Score: 76.92 E-value: 3.61e-16
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| PRK12682 | PRK12682 | transcriptional regulator CysB-like protein; Reviewed |
8-251 | 3.17e-14 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 183679 [Multi-domain] Cd Length: 309 Bit Score: 71.56 E-value: 3.17e-14
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| PBP2_CidR | cd08438 | The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ... |
96-277 | 4.70e-14 | |||||
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176129 [Multi-domain] Cd Length: 197 Bit Score: 69.51 E-value: 4.70e-14
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| PBP2_LTTR_like_4 | cd08440 | TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
96-277 | 5.25e-14 | |||||
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176131 [Multi-domain] Cd Length: 197 Bit Score: 69.09 E-value: 5.25e-14
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| PBP2_Nac | cd08433 | The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ... |
96-264 | 1.34e-13 | |||||
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176124 Cd Length: 198 Bit Score: 68.01 E-value: 1.34e-13
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| rbcR | CHL00180 | LysR transcriptional regulator; Provisional |
2-181 | 1.66e-13 | |||||
LysR transcriptional regulator; Provisional Pssm-ID: 177082 [Multi-domain] Cd Length: 305 Bit Score: 69.66 E-value: 1.66e-13
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| PBP2_LTTR_aromatics_like | cd08414 | The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ... |
96-245 | 4.61e-12 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Pssm-ID: 176106 [Multi-domain] Cd Length: 197 Bit Score: 63.68 E-value: 4.61e-12
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| PRK09986 | PRK09986 | LysR family transcriptional regulator; |
6-244 | 4.90e-11 | |||||
LysR family transcriptional regulator; Pssm-ID: 182183 [Multi-domain] Cd Length: 294 Bit Score: 62.05 E-value: 4.90e-11
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| PBP2_LTTR_like_2 | cd08427 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
97-283 | 1.58e-10 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176118 [Multi-domain] Cd Length: 195 Bit Score: 59.51 E-value: 1.58e-10
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| PRK09906 | PRK09906 | DNA-binding transcriptional regulator HcaR; Provisional |
7-164 | 2.11e-10 | |||||
DNA-binding transcriptional regulator HcaR; Provisional Pssm-ID: 182137 [Multi-domain] Cd Length: 296 Bit Score: 60.55 E-value: 2.11e-10
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| PRK12680 | PRK12680 | LysR family transcriptional regulator; |
6-151 | 2.88e-10 | |||||
LysR family transcriptional regulator; Pssm-ID: 183677 [Multi-domain] Cd Length: 327 Bit Score: 60.41 E-value: 2.88e-10
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| PBP2_GbpR | cd08435 | The C-terminal substrate binding domain of galactose-binding protein regulator contains the ... |
96-277 | 3.45e-10 | |||||
The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176126 [Multi-domain] Cd Length: 201 Bit Score: 58.44 E-value: 3.45e-10
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| PBP2_MleR | cd08437 | The substrate binding domain of LysR-type transcriptional regulator MleR which required for ... |
97-249 | 3.50e-10 | |||||
The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176128 Cd Length: 198 Bit Score: 58.50 E-value: 3.50e-10
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| PRK11139 | PRK11139 | DNA-binding transcriptional activator GcvA; Provisional |
19-149 | 2.00e-09 | |||||
DNA-binding transcriptional activator GcvA; Provisional Pssm-ID: 182990 [Multi-domain] Cd Length: 297 Bit Score: 57.55 E-value: 2.00e-09
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| PBP2_LTTR_like_6 | cd08423 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
96-281 | 3.53e-09 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176115 [Multi-domain] Cd Length: 200 Bit Score: 55.68 E-value: 3.53e-09
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| PRK12683 | PRK12683 | transcriptional regulator CysB-like protein; Reviewed |
8-168 | 5.57e-09 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 237172 [Multi-domain] Cd Length: 309 Bit Score: 56.20 E-value: 5.57e-09
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| PRK11716 | PRK11716 | HTH-type transcriptional activator IlvY; |
29-153 | 5.90e-09 | |||||
HTH-type transcriptional activator IlvY; Pssm-ID: 236961 [Multi-domain] Cd Length: 269 Bit Score: 55.98 E-value: 5.90e-09
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| PBP2_PAO1_like | cd08412 | The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ... |
96-281 | 8.84e-09 | |||||
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Pssm-ID: 176104 [Multi-domain] Cd Length: 198 Bit Score: 54.47 E-value: 8.84e-09
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| PBP2_LTTR_like_3 | cd08436 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
96-250 | 1.56e-08 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176127 [Multi-domain] Cd Length: 194 Bit Score: 53.76 E-value: 1.56e-08
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| PRK12684 | PRK12684 | CysB family HTH-type transcriptional regulator; |
9-168 | 4.68e-08 | |||||
CysB family HTH-type transcriptional regulator; Pssm-ID: 237173 [Multi-domain] Cd Length: 313 Bit Score: 53.44 E-value: 4.68e-08
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| PBP2_YofA_SoxR_like | cd08442 | The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ... |
114-249 | 4.86e-08 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176133 Cd Length: 193 Bit Score: 52.22 E-value: 4.86e-08
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| PBP2_CysL_like | cd08420 | C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ... |
96-297 | 2.28e-07 | |||||
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176112 [Multi-domain] Cd Length: 201 Bit Score: 50.18 E-value: 2.28e-07
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| cbl | PRK12679 | HTH-type transcriptional regulator Cbl; |
15-149 | 2.46e-07 | |||||
HTH-type transcriptional regulator Cbl; Pssm-ID: 183676 [Multi-domain] Cd Length: 316 Bit Score: 51.35 E-value: 2.46e-07
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| PRK11233 | PRK11233 | nitrogen assimilation transcriptional regulator; Provisional |
24-247 | 5.19e-07 | |||||
nitrogen assimilation transcriptional regulator; Provisional Pssm-ID: 183045 [Multi-domain] Cd Length: 305 Bit Score: 50.07 E-value: 5.19e-07
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| PRK10086 | PRK10086 | DNA-binding transcriptional regulator DsdC; |
14-106 | 5.51e-07 | |||||
DNA-binding transcriptional regulator DsdC; Pssm-ID: 182231 [Multi-domain] Cd Length: 311 Bit Score: 50.00 E-value: 5.51e-07
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| PBP2_GltC_like | cd08434 | The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ... |
79-288 | 6.72e-07 | |||||
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176125 [Multi-domain] Cd Length: 195 Bit Score: 48.69 E-value: 6.72e-07
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| PRK13348 | PRK13348 | HTH-type transcriptional regulator ArgP; |
8-145 | 8.22e-07 | |||||
HTH-type transcriptional regulator ArgP; Pssm-ID: 237357 [Multi-domain] Cd Length: 294 Bit Score: 49.58 E-value: 8.22e-07
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| PRK10094 | PRK10094 | HTH-type transcriptional activator AllS; |
10-245 | 4.26e-06 | |||||
HTH-type transcriptional activator AllS; Pssm-ID: 182237 [Multi-domain] Cd Length: 308 Bit Score: 47.49 E-value: 4.26e-06
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| PBP2_BudR | cd08451 | The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ... |
96-174 | 8.99e-06 | |||||
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176142 [Multi-domain] Cd Length: 199 Bit Score: 45.63 E-value: 8.99e-06
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| PBP2_Nitroaromatics_like | cd08417 | The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ... |
126-215 | 1.01e-05 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176109 [Multi-domain] Cd Length: 200 Bit Score: 45.28 E-value: 1.01e-05
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| PRK09791 | PRK09791 | LysR family transcriptional regulator; |
1-146 | 1.10e-05 | |||||
LysR family transcriptional regulator; Pssm-ID: 182077 [Multi-domain] Cd Length: 302 Bit Score: 46.29 E-value: 1.10e-05
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| PRK15421 | PRK15421 | HTH-type transcriptional regulator MetR; |
7-297 | 6.81e-05 | |||||
HTH-type transcriptional regulator MetR; Pssm-ID: 185319 [Multi-domain] Cd Length: 317 Bit Score: 43.85 E-value: 6.81e-05
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| PRK03601 | PRK03601 | HTH-type transcriptional regulator HdfR; |
10-77 | 7.49e-05 | |||||
HTH-type transcriptional regulator HdfR; Pssm-ID: 235137 [Multi-domain] Cd Length: 275 Bit Score: 43.47 E-value: 7.49e-05
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| PRK03635 | PRK03635 | ArgP/LysG family DNA-binding transcriptional regulator; |
8-56 | 1.62e-04 | |||||
ArgP/LysG family DNA-binding transcriptional regulator; Pssm-ID: 235144 [Multi-domain] Cd Length: 294 Bit Score: 42.45 E-value: 1.62e-04
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| PRK14997 | PRK14997 | LysR family transcriptional regulator; Provisional |
4-172 | 7.75e-04 | |||||
LysR family transcriptional regulator; Provisional Pssm-ID: 184959 [Multi-domain] Cd Length: 301 Bit Score: 40.36 E-value: 7.75e-04
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| cysB | PRK12681 | HTH-type transcriptional regulator CysB; |
7-99 | 1.11e-03 | |||||
HTH-type transcriptional regulator CysB; Pssm-ID: 183678 [Multi-domain] Cd Length: 324 Bit Score: 39.88 E-value: 1.11e-03
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| PRK09801 | PRK09801 | LysR family transcriptional regulator; |
1-100 | 2.02e-03 | |||||
LysR family transcriptional regulator; Pssm-ID: 182085 [Multi-domain] Cd Length: 310 Bit Score: 39.25 E-value: 2.02e-03
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| PBP2_ToxR | cd08465 | The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ... |
124-182 | 2.49e-03 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176154 Cd Length: 200 Bit Score: 38.44 E-value: 2.49e-03
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| PBP2_DntR_NahR_LinR_like | cd08459 | The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ... |
129-215 | 3.90e-03 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 176148 [Multi-domain] Cd Length: 201 Bit Score: 37.94 E-value: 3.90e-03
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| PRK15092 | PRK15092 | DNA-binding transcriptional repressor LrhA; Provisional |
10-149 | 4.26e-03 | |||||
DNA-binding transcriptional repressor LrhA; Provisional Pssm-ID: 237907 [Multi-domain] Cd Length: 310 Bit Score: 38.09 E-value: 4.26e-03
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