transcriptional regulator, LysR family [Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111]
Protein Classification
LysR family transcriptional regulator( domain architecture ID 11426520)
LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic binding proteins
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
4-185 | 4.61e-34 | ||||
DNA-binding transcriptional regulator, LysR family [Transcription]; : Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 124.98 E-value: 4.61e-34
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| Periplasmic_Binding_Protein_Type_2 super family | cl21456 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
124-279 | 9.94e-16 | ||||
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. The actual alignment was detected with superfamily member cd08414: Pssm-ID: 473866 [Multi-domain] Cd Length: 197 Bit Score: 74.08 E-value: 9.94e-16
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| Name | Accession | Description | Interval | E-value | ||||
| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
4-185 | 4.61e-34 | ||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 124.98 E-value: 4.61e-34
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| PRK09906 | PRK09906 | DNA-binding transcriptional regulator HcaR; Provisional |
4-189 | 1.57e-26 | ||||
DNA-binding transcriptional regulator HcaR; Provisional Pssm-ID: 182137 [Multi-domain] Cd Length: 296 Bit Score: 106.01 E-value: 1.57e-26
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
7-64 | 1.39e-23 | ||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 91.29 E-value: 1.39e-23
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| PBP2_LTTR_aromatics_like | cd08414 | The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ... |
124-279 | 9.94e-16 | ||||
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: 74.08 E-value: 9.94e-16
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
124-277 | 4.15e-10 | ||||
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: 58.45 E-value: 4.15e-10
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| PBP2_CidR | cd08438 | The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ... |
124-193 | 7.22e-09 | ||||
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: 54.49 E-value: 7.22e-09
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| Name | Accession | Description | Interval | E-value | |||||
| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
4-185 | 4.61e-34 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 124.98 E-value: 4.61e-34
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| PRK09906 | PRK09906 | DNA-binding transcriptional regulator HcaR; Provisional |
4-189 | 1.57e-26 | |||||
DNA-binding transcriptional regulator HcaR; Provisional Pssm-ID: 182137 [Multi-domain] Cd Length: 296 Bit Score: 106.01 E-value: 1.57e-26
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| PRK09986 | PRK09986 | LysR family transcriptional regulator; |
7-256 | 3.46e-25 | |||||
LysR family transcriptional regulator; Pssm-ID: 182183 [Multi-domain] Cd Length: 294 Bit Score: 102.11 E-value: 3.46e-25
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
7-64 | 1.39e-23 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 91.29 E-value: 1.39e-23
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| PRK11242 | PRK11242 | DNA-binding transcriptional regulator CynR; Provisional |
7-72 | 1.07e-18 | |||||
DNA-binding transcriptional regulator CynR; Provisional Pssm-ID: 183051 [Multi-domain] Cd Length: 296 Bit Score: 84.24 E-value: 1.07e-18
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| PBP2_LTTR_aromatics_like | cd08414 | The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ... |
124-279 | 9.94e-16 | |||||
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: 74.08 E-value: 9.94e-16
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| PRK11151 | PRK11151 | DNA-binding transcriptional regulator OxyR; Provisional |
7-72 | 1.79e-14 | |||||
DNA-binding transcriptional regulator OxyR; Provisional Pssm-ID: 182999 [Multi-domain] Cd Length: 305 Bit Score: 72.37 E-value: 1.79e-14
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| rbcR | CHL00180 | LysR transcriptional regulator; Provisional |
7-69 | 7.92e-13 | |||||
LysR transcriptional regulator; Provisional Pssm-ID: 177082 [Multi-domain] Cd Length: 305 Bit Score: 67.74 E-value: 7.92e-13
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| PRK13348 | PRK13348 | HTH-type transcriptional regulator ArgP; |
4-72 | 1.44e-10 | |||||
HTH-type transcriptional regulator ArgP; Pssm-ID: 237357 [Multi-domain] Cd Length: 294 Bit Score: 60.76 E-value: 1.44e-10
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| PBP2_LTTR_like_3 | cd08436 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
138-277 | 1.77e-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: 176127 [Multi-domain] Cd Length: 194 Bit Score: 59.15 E-value: 1.77e-10
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
124-277 | 4.15e-10 | |||||
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: 58.45 E-value: 4.15e-10
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| PBP2_BudR | cd08451 | The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ... |
124-277 | 7.13e-10 | |||||
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: 57.57 E-value: 7.13e-10
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| PRK10341 | PRK10341 | transcriptional regulator TdcA; |
5-73 | 2.32e-09 | |||||
transcriptional regulator TdcA; Pssm-ID: 182391 [Multi-domain] Cd Length: 312 Bit Score: 57.56 E-value: 2.32e-09
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| PRK10094 | PRK10094 | HTH-type transcriptional activator AllS; |
1-72 | 3.71e-09 | |||||
HTH-type transcriptional activator AllS; Pssm-ID: 182237 [Multi-domain] Cd Length: 308 Bit Score: 56.74 E-value: 3.71e-09
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| PBP2_LTTR_substrate | cd05466 | The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ... |
137-273 | 5.31e-09 | |||||
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: 54.91 E-value: 5.31e-09
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| PBP2_CidR | cd08438 | The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ... |
124-193 | 7.22e-09 | |||||
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: 54.49 E-value: 7.22e-09
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| PRK11233 | PRK11233 | nitrogen assimilation transcriptional regulator; Provisional |
7-72 | 1.04e-08 | |||||
nitrogen assimilation transcriptional regulator; Provisional Pssm-ID: 183045 [Multi-domain] Cd Length: 305 Bit Score: 55.46 E-value: 1.04e-08
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| PRK11139 | PRK11139 | DNA-binding transcriptional activator GcvA; Provisional |
9-73 | 1.28e-08 | |||||
DNA-binding transcriptional activator GcvA; Provisional Pssm-ID: 182990 [Multi-domain] Cd Length: 297 Bit Score: 55.23 E-value: 1.28e-08
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| PRK03601 | PRK03601 | HTH-type transcriptional regulator HdfR; |
1-73 | 1.48e-08 | |||||
HTH-type transcriptional regulator HdfR; Pssm-ID: 235137 [Multi-domain] Cd Length: 275 Bit Score: 54.64 E-value: 1.48e-08
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| PRK09791 | PRK09791 | LysR family transcriptional regulator; |
8-72 | 1.15e-07 | |||||
LysR family transcriptional regulator; Pssm-ID: 182077 [Multi-domain] Cd Length: 302 Bit Score: 52.07 E-value: 1.15e-07
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| PRK11074 | PRK11074 | putative DNA-binding transcriptional regulator; Provisional |
12-73 | 2.06e-07 | |||||
putative DNA-binding transcriptional regulator; Provisional Pssm-ID: 182948 [Multi-domain] Cd Length: 300 Bit Score: 51.48 E-value: 2.06e-07
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| PRK03635 | PRK03635 | ArgP/LysG family DNA-binding transcriptional regulator; |
3-72 | 4.94e-07 | |||||
ArgP/LysG family DNA-binding transcriptional regulator; Pssm-ID: 235144 [Multi-domain] Cd Length: 294 Bit Score: 50.16 E-value: 4.94e-07
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| PBP2_LTTR_aromatics_like_1 | cd08447 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
101-277 | 5.27e-07 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176138 [Multi-domain] Cd Length: 198 Bit Score: 49.18 E-value: 5.27e-07
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| PBP2_OxyR | cd08411 | The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ... |
138-191 | 1.05e-06 | |||||
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: 48.29 E-value: 1.05e-06
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| PBP2_LTTR_aromatics_like_2 | cd08448 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
124-277 | 1.85e-06 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176139 [Multi-domain] Cd Length: 197 Bit Score: 47.65 E-value: 1.85e-06
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| PRK11716 | PRK11716 | HTH-type transcriptional activator IlvY; |
35-73 | 2.12e-06 | |||||
HTH-type transcriptional activator IlvY; Pssm-ID: 236961 [Multi-domain] Cd Length: 269 Bit Score: 48.28 E-value: 2.12e-06
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| PBP2_LTTR_like_6 | cd08423 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
124-270 | 4.54e-06 | |||||
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: 46.44 E-value: 4.54e-06
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| PBP2_PAO1_like | cd08412 | The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ... |
132-277 | 6.18e-06 | |||||
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: 46.00 E-value: 6.18e-06
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| PRK10086 | PRK10086 | DNA-binding transcriptional regulator DsdC; |
9-64 | 7.33e-06 | |||||
DNA-binding transcriptional regulator DsdC; Pssm-ID: 182231 [Multi-domain] Cd Length: 311 Bit Score: 46.92 E-value: 7.33e-06
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| PBP2_LysR_opines_like | cd08415 | The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ... |
137-276 | 1.10e-05 | |||||
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. 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: 176107 [Multi-domain] Cd Length: 196 Bit Score: 45.25 E-value: 1.10e-05
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| PRK12683 | PRK12683 | transcriptional regulator CysB-like protein; Reviewed |
8-193 | 1.51e-05 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 237172 [Multi-domain] Cd Length: 309 Bit Score: 45.80 E-value: 1.51e-05
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| PBP2_GltC_like | cd08434 | The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ... |
138-193 | 1.98e-05 | |||||
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: 44.45 E-value: 1.98e-05
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| PRK12684 | PRK12684 | CysB family HTH-type transcriptional regulator; |
8-71 | 4.91e-05 | |||||
CysB family HTH-type transcriptional regulator; Pssm-ID: 237173 [Multi-domain] Cd Length: 313 Bit Score: 44.20 E-value: 4.91e-05
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| PRK10082 | PRK10082 | hypochlorite stress DNA-binding transcriptional regulator HypT; |
1-72 | 6.74e-05 | |||||
hypochlorite stress DNA-binding transcriptional regulator HypT; Pssm-ID: 182228 [Multi-domain] Cd Length: 303 Bit Score: 43.89 E-value: 6.74e-05
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| PRK12682 | PRK12682 | transcriptional regulator CysB-like protein; Reviewed |
24-193 | 9.70e-05 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 183679 [Multi-domain] Cd Length: 309 Bit Score: 43.44 E-value: 9.70e-05
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| PBP2_HcaR | cd08450 | The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ... |
133-269 | 1.28e-04 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain] Cd Length: 196 Bit Score: 42.36 E-value: 1.28e-04
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| PRK15092 | PRK15092 | DNA-binding transcriptional repressor LrhA; Provisional |
9-72 | 1.40e-04 | |||||
DNA-binding transcriptional repressor LrhA; Provisional Pssm-ID: 237907 [Multi-domain] Cd Length: 310 Bit Score: 42.71 E-value: 1.40e-04
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| PRK12680 | PRK12680 | LysR family transcriptional regulator; |
8-73 | 2.05e-04 | |||||
LysR family transcriptional regulator; Pssm-ID: 183677 [Multi-domain] Cd Length: 327 Bit Score: 42.30 E-value: 2.05e-04
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| PBP2_BenM_CatM_CatR | cd08445 | The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ... |
124-260 | 3.35e-04 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136 Cd Length: 203 Bit Score: 41.06 E-value: 3.35e-04
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| PBP2_LTTR_like_4 | cd08440 | TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
137-193 | 6.30e-04 | |||||
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: 40.20 E-value: 6.30e-04
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| PRK09801 | PRK09801 | LysR family transcriptional regulator; |
7-64 | 1.44e-03 | |||||
LysR family transcriptional regulator; Pssm-ID: 182085 [Multi-domain] Cd Length: 310 Bit Score: 39.63 E-value: 1.44e-03
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| PRK14997 | PRK14997 | LysR family transcriptional regulator; Provisional |
1-64 | 1.53e-03 | |||||
LysR family transcriptional regulator; Provisional Pssm-ID: 184959 [Multi-domain] Cd Length: 301 Bit Score: 39.59 E-value: 1.53e-03
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| PBP2_LTTR_like_1 | cd08421 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
138-191 | 2.35e-03 | |||||
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: 176113 Cd Length: 198 Bit Score: 38.27 E-value: 2.35e-03
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| PBP2_IlvR | cd08453 | The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ... |
143-279 | 3.19e-03 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain] Cd Length: 200 Bit Score: 38.11 E-value: 3.19e-03
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| PRK10632 | PRK10632 | HTH-type transcriptional activator AaeR; |
12-64 | 3.46e-03 | |||||
HTH-type transcriptional activator AaeR; Pssm-ID: 182601 [Multi-domain] Cd Length: 309 Bit Score: 38.59 E-value: 3.46e-03
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| PRK15243 | PRK15243 | virulence genes transcriptional activator SpvR; |
1-73 | 6.42e-03 | |||||
virulence genes transcriptional activator SpvR; Pssm-ID: 185155 [Multi-domain] Cd Length: 297 Bit Score: 37.73 E-value: 6.42e-03
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