MULTISPECIES: LysR family transcriptional regulator [Pseudomonas]
Protein Classification
LysR family transcriptional regulator( domain architecture ID 13300132)
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 | ||||
| PBP2_CrgA_like | cd08422 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ... |
92-288 | 5.54e-93 | ||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176114 [Multi-domain] Cd Length: 197 Bit Score: 273.55 E-value: 5.54e-93
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| PRK11242 super family | cl32664 | DNA-binding transcriptional regulator CynR; Provisional |
18-125 | 1.04e-17 | ||||
DNA-binding transcriptional regulator CynR; Provisional The actual alignment was detected with superfamily member PRK11242: Pssm-ID: 183051 [Multi-domain] Cd Length: 296 Bit Score: 81.54 E-value: 1.04e-17
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| Name | Accession | Description | Interval | E-value | |||||
| PBP2_CrgA_like | cd08422 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ... |
92-288 | 5.54e-93 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176114 [Multi-domain] Cd Length: 197 Bit Score: 273.55 E-value: 5.54e-93
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| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
1-293 | 1.56e-64 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 203.56 E-value: 1.56e-64
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| PRK14997 | PRK14997 | LysR family transcriptional regulator; Provisional |
10-293 | 7.27e-50 | |||||
LysR family transcriptional regulator; Provisional Pssm-ID: 184959 [Multi-domain] Cd Length: 301 Bit Score: 167.09 E-value: 7.27e-50
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
91-293 | 6.63e-38 | |||||
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: 133.18 E-value: 6.63e-38
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| LysR_Sec_metab | NF040786 | selenium metabolism-associated LysR family transcriptional regulator; LysR family ... |
9-288 | 1.38e-23 | |||||
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: 97.69 E-value: 1.38e-23
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| PRK11242 | PRK11242 | DNA-binding transcriptional regulator CynR; Provisional |
18-125 | 1.04e-17 | |||||
DNA-binding transcriptional regulator CynR; Provisional Pssm-ID: 183051 [Multi-domain] Cd Length: 296 Bit Score: 81.54 E-value: 1.04e-17
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
7-62 | 3.57e-16 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 71.26 E-value: 3.57e-16
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| MarR | COG1846 | DNA-binding transcriptional regulator, MarR family [Transcription]; |
23-83 | 1.18e-03 | |||||
DNA-binding transcriptional regulator, MarR family [Transcription]; Pssm-ID: 441451 [Multi-domain] Cd Length: 142 Bit Score: 38.41 E-value: 1.18e-03
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| HTH_MARR | smart00347 | helix_turn_helix multiple antibiotic resistance protein; |
23-81 | 5.73e-03 | |||||
helix_turn_helix multiple antibiotic resistance protein; Pssm-ID: 197670 [Multi-domain] Cd Length: 101 Bit Score: 35.65 E-value: 5.73e-03
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| Name | Accession | Description | Interval | E-value | |||||
| PBP2_CrgA_like | cd08422 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ... |
92-288 | 5.54e-93 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176114 [Multi-domain] Cd Length: 197 Bit Score: 273.55 E-value: 5.54e-93
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| PBP2_CrgA_like_8 | cd08477 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-288 | 2.52e-69 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176166 Cd Length: 197 Bit Score: 213.63 E-value: 2.52e-69
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| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
1-293 | 1.56e-64 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 203.56 E-value: 1.56e-64
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| PBP2_CrgA_like_9 | cd08479 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-288 | 1.18e-62 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176168 [Multi-domain] Cd Length: 198 Bit Score: 196.66 E-value: 1.18e-62
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| PBP2_CrgA_like_3 | cd08472 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-290 | 5.24e-59 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176161 Cd Length: 202 Bit Score: 187.33 E-value: 5.24e-59
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| PBP2_CrgA_like_5 | cd08474 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
91-288 | 1.44e-58 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176163 [Multi-domain] Cd Length: 202 Bit Score: 186.13 E-value: 1.44e-58
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| PBP2_CrgA_like_1 | cd08470 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-292 | 7.89e-56 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176159 Cd Length: 197 Bit Score: 179.04 E-value: 7.89e-56
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| PBP2_CrgA_like_10 | cd08480 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-288 | 1.88e-55 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176169 Cd Length: 198 Bit Score: 178.30 E-value: 1.88e-55
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| PBP2_CrgA_like_7 | cd08476 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-288 | 2.96e-50 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176165 Cd Length: 197 Bit Score: 164.73 E-value: 2.96e-50
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| PBP2_CrgA_like_2 | cd08471 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-292 | 6.50e-50 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176160 Cd Length: 201 Bit Score: 164.24 E-value: 6.50e-50
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| PRK14997 | PRK14997 | LysR family transcriptional regulator; Provisional |
10-293 | 7.27e-50 | |||||
LysR family transcriptional regulator; Provisional Pssm-ID: 184959 [Multi-domain] Cd Length: 301 Bit Score: 167.09 E-value: 7.27e-50
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| PBP2_CrgA_like_6 | cd08475 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
92-288 | 4.12e-49 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176164 [Multi-domain] Cd Length: 199 Bit Score: 161.95 E-value: 4.12e-49
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| PBP2_CrgA_like_4 | cd08473 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
91-288 | 1.83e-48 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176162 [Multi-domain] Cd Length: 202 Bit Score: 160.41 E-value: 1.83e-48
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| PBP2_CrgA | cd08478 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ... |
91-288 | 1.07e-46 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176167 [Multi-domain] Cd Length: 199 Bit Score: 155.57 E-value: 1.07e-46
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| PRK09801 | PRK09801 | LysR family transcriptional regulator; |
7-288 | 6.58e-41 | |||||
LysR family transcriptional regulator; Pssm-ID: 182085 [Multi-domain] Cd Length: 310 Bit Score: 144.02 E-value: 6.58e-41
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
91-293 | 6.63e-38 | |||||
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: 133.18 E-value: 6.63e-38
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| PRK11139 | PRK11139 | DNA-binding transcriptional activator GcvA; Provisional |
19-257 | 2.32e-37 | |||||
DNA-binding transcriptional activator GcvA; Provisional Pssm-ID: 182990 [Multi-domain] Cd Length: 297 Bit Score: 134.59 E-value: 2.32e-37
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| PRK10632 | PRK10632 | HTH-type transcriptional activator AaeR; |
1-288 | 3.47e-37 | |||||
HTH-type transcriptional activator AaeR; Pssm-ID: 182601 [Multi-domain] Cd Length: 309 Bit Score: 134.50 E-value: 3.47e-37
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| PBP2_GcdR_TrpI_HvrB_AmpR_like | cd08432 | The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ... |
93-288 | 2.93e-27 | |||||
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain] Cd Length: 194 Bit Score: 104.97 E-value: 2.93e-27
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| LysR_Sec_metab | NF040786 | selenium metabolism-associated LysR family transcriptional regulator; LysR family ... |
9-288 | 1.38e-23 | |||||
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: 97.69 E-value: 1.38e-23
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| PBP2_LTTR_substrate | cd05466 | The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ... |
94-288 | 8.41e-20 | |||||
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: 84.96 E-value: 8.41e-20
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| PRK11242 | PRK11242 | DNA-binding transcriptional regulator CynR; Provisional |
18-125 | 1.04e-17 | |||||
DNA-binding transcriptional regulator CynR; Provisional Pssm-ID: 183051 [Multi-domain] Cd Length: 296 Bit Score: 81.54 E-value: 1.04e-17
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
7-62 | 3.57e-16 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 71.26 E-value: 3.57e-16
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| PRK09906 | PRK09906 | DNA-binding transcriptional regulator HcaR; Provisional |
7-142 | 1.24e-15 | |||||
DNA-binding transcriptional regulator HcaR; Provisional Pssm-ID: 182137 [Multi-domain] Cd Length: 296 Bit Score: 75.58 E-value: 1.24e-15
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| PBP2_HvrB | cd08483 | The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ... |
94-288 | 5.12e-15 | |||||
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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: 176172 [Multi-domain] Cd Length: 190 Bit Score: 71.99 E-value: 5.12e-15
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| PBP2_GcdR_like | cd08481 | The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ... |
111-288 | 5.54e-15 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain] Cd Length: 194 Bit Score: 71.94 E-value: 5.54e-15
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| PRK10086 | PRK10086 | DNA-binding transcriptional regulator DsdC; |
7-293 | 1.81e-14 | |||||
DNA-binding transcriptional regulator DsdC; Pssm-ID: 182231 [Multi-domain] Cd Length: 311 Bit Score: 72.34 E-value: 1.81e-14
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| rbcR | CHL00180 | LysR transcriptional regulator; Provisional |
16-136 | 2.29e-13 | |||||
LysR transcriptional regulator; Provisional Pssm-ID: 177082 [Multi-domain] Cd Length: 305 Bit Score: 69.28 E-value: 2.29e-13
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| PRK11716 | PRK11716 | HTH-type transcriptional activator IlvY; |
26-150 | 3.09e-13 | |||||
HTH-type transcriptional activator IlvY; Pssm-ID: 236961 [Multi-domain] Cd Length: 269 Bit Score: 68.31 E-value: 3.09e-13
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| PRK09791 | PRK09791 | LysR family transcriptional regulator; |
7-126 | 1.44e-12 | |||||
LysR family transcriptional regulator; Pssm-ID: 182077 [Multi-domain] Cd Length: 302 Bit Score: 66.71 E-value: 1.44e-12
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| PRK10094 | PRK10094 | HTH-type transcriptional activator AllS; |
5-254 | 2.22e-12 | |||||
HTH-type transcriptional activator AllS; Pssm-ID: 182237 [Multi-domain] Cd Length: 308 Bit Score: 66.37 E-value: 2.22e-12
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| PRK10082 | PRK10082 | hypochlorite stress DNA-binding transcriptional regulator HypT; |
19-254 | 2.33e-11 | |||||
hypochlorite stress DNA-binding transcriptional regulator HypT; Pssm-ID: 182228 [Multi-domain] Cd Length: 303 Bit Score: 63.15 E-value: 2.33e-11
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| PRK09986 | PRK09986 | LysR family transcriptional regulator; |
3-241 | 1.29e-10 | |||||
LysR family transcriptional regulator; Pssm-ID: 182183 [Multi-domain] Cd Length: 294 Bit Score: 60.89 E-value: 1.29e-10
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| PRK15092 | PRK15092 | DNA-binding transcriptional repressor LrhA; Provisional |
7-112 | 2.80e-10 | |||||
DNA-binding transcriptional repressor LrhA; Provisional Pssm-ID: 237907 [Multi-domain] Cd Length: 310 Bit Score: 60.04 E-value: 2.80e-10
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| PRK15421 | PRK15421 | HTH-type transcriptional regulator MetR; |
19-254 | 4.15e-09 | |||||
HTH-type transcriptional regulator MetR; Pssm-ID: 185319 [Multi-domain] Cd Length: 317 Bit Score: 56.56 E-value: 4.15e-09
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| PBP2_TrpI | cd08482 | The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ... |
106-254 | 5.00e-09 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI 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: 176171 [Multi-domain] Cd Length: 195 Bit Score: 55.10 E-value: 5.00e-09
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| PRK13348 | PRK13348 | HTH-type transcriptional regulator ArgP; |
6-84 | 7.51e-09 | |||||
HTH-type transcriptional regulator ArgP; Pssm-ID: 237357 [Multi-domain] Cd Length: 294 Bit Score: 55.75 E-value: 7.51e-09
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| PRK11151 | PRK11151 | DNA-binding transcriptional regulator OxyR; Provisional |
19-125 | 1.51e-08 | |||||
DNA-binding transcriptional regulator OxyR; Provisional Pssm-ID: 182999 [Multi-domain] Cd Length: 305 Bit Score: 54.65 E-value: 1.51e-08
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| PRK11074 | PRK11074 | putative DNA-binding transcriptional regulator; Provisional |
13-141 | 1.78e-07 | |||||
putative DNA-binding transcriptional regulator; Provisional Pssm-ID: 182948 [Multi-domain] Cd Length: 300 Bit Score: 51.48 E-value: 1.78e-07
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| cysB | PRK12681 | HTH-type transcriptional regulator CysB; |
21-125 | 5.24e-07 | |||||
HTH-type transcriptional regulator CysB; Pssm-ID: 183678 [Multi-domain] Cd Length: 324 Bit Score: 50.28 E-value: 5.24e-07
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| PBP2_LTTR_beta_lactamase | cd08484 | The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ... |
93-254 | 5.93e-07 | |||||
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. 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: 176173 [Multi-domain] Cd Length: 189 Bit Score: 48.91 E-value: 5.93e-07
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| PRK03635 | PRK03635 | ArgP/LysG family DNA-binding transcriptional regulator; |
8-257 | 6.66e-07 | |||||
ArgP/LysG family DNA-binding transcriptional regulator; Pssm-ID: 235144 [Multi-domain] Cd Length: 294 Bit Score: 49.77 E-value: 6.66e-07
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| PBP2_AmpR | cd08488 | The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ... |
93-254 | 4.30e-06 | |||||
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. 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: 176177 [Multi-domain] Cd Length: 191 Bit Score: 46.37 E-value: 4.30e-06
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| PRK12680 | PRK12680 | LysR family transcriptional regulator; |
21-294 | 2.20e-05 | |||||
LysR family transcriptional regulator; Pssm-ID: 183677 [Multi-domain] Cd Length: 327 Bit Score: 45.38 E-value: 2.20e-05
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| PBP2_CbbR_RubisCO_like | cd08419 | The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ... |
109-288 | 5.17e-05 | |||||
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111 Cd Length: 197 Bit Score: 43.26 E-value: 5.17e-05
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| PRK12683 | PRK12683 | transcriptional regulator CysB-like protein; Reviewed |
22-135 | 6.08e-05 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 237172 [Multi-domain] Cd Length: 309 Bit Score: 43.88 E-value: 6.08e-05
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| PBP2_CysL_like | cd08420 | C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ... |
94-288 | 1.07e-04 | |||||
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: 42.48 E-value: 1.07e-04
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| PRK12684 | PRK12684 | CysB family HTH-type transcriptional regulator; |
10-125 | 2.17e-04 | |||||
CysB family HTH-type transcriptional regulator; Pssm-ID: 237173 [Multi-domain] Cd Length: 313 Bit Score: 42.27 E-value: 2.17e-04
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| PBP2_BlaA | cd08487 | The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ... |
93-254 | 2.45e-04 | |||||
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. 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: 176176 [Multi-domain] Cd Length: 189 Bit Score: 41.38 E-value: 2.45e-04
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| PRK12682 | PRK12682 | transcriptional regulator CysB-like protein; Reviewed |
21-134 | 5.18e-04 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 183679 [Multi-domain] Cd Length: 309 Bit Score: 41.13 E-value: 5.18e-04
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| cbl | PRK12679 | HTH-type transcriptional regulator Cbl; |
30-155 | 7.30e-04 | |||||
HTH-type transcriptional regulator Cbl; Pssm-ID: 183676 [Multi-domain] Cd Length: 316 Bit Score: 40.56 E-value: 7.30e-04
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| MarR | COG1846 | DNA-binding transcriptional regulator, MarR family [Transcription]; |
23-83 | 1.18e-03 | |||||
DNA-binding transcriptional regulator, MarR family [Transcription]; Pssm-ID: 441451 [Multi-domain] Cd Length: 142 Bit Score: 38.41 E-value: 1.18e-03
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| PRK10837 | PRK10837 | putative DNA-binding transcriptional regulator; Provisional |
22-131 | 2.92e-03 | |||||
putative DNA-binding transcriptional regulator; Provisional Pssm-ID: 182768 [Multi-domain] Cd Length: 290 Bit Score: 38.52 E-value: 2.92e-03
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| HTH_MARR | smart00347 | helix_turn_helix multiple antibiotic resistance protein; |
23-81 | 5.73e-03 | |||||
helix_turn_helix multiple antibiotic resistance protein; Pssm-ID: 197670 [Multi-domain] Cd Length: 101 Bit Score: 35.65 E-value: 5.73e-03
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| PBP2_LTTR_like_4 | cd08440 | TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
94-288 | 8.22e-03 | |||||
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: 36.73 E-value: 8.22e-03
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