MULTISPECIES: LysR family transcriptional regulator [Acinetobacter]
Protein Classification
LysR family transcriptional regulator( domain architecture ID 11426483)
LysR family transcriptional regulator containing 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 (PBP2) fold proteins
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
4-286 | 1.56e-40 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; : Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 141.16 E-value: 1.56e-40
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| Name | Accession | Description | Interval | E-value | |||||
| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
4-286 | 1.56e-40 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 141.16 E-value: 1.56e-40
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| PBP2_CrgA_like | cd08422 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ... |
89-280 | 3.32e-24 | |||||
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: 96.74 E-value: 3.32e-24
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
88-285 | 3.51e-21 | |||||
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: 88.89 E-value: 3.51e-21
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| PRK09801 | PRK09801 | LysR family transcriptional regulator; |
8-184 | 1.36e-13 | |||||
LysR family transcriptional regulator; Pssm-ID: 182085 [Multi-domain] Cd Length: 310 Bit Score: 69.68 E-value: 1.36e-13
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| Name | Accession | Description | Interval | E-value | |||||
| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
4-286 | 1.56e-40 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 141.16 E-value: 1.56e-40
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| PBP2_CrgA_like | cd08422 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ... |
89-280 | 3.32e-24 | |||||
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: 96.74 E-value: 3.32e-24
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
88-285 | 3.51e-21 | |||||
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: 88.89 E-value: 3.51e-21
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| PRK09801 | PRK09801 | LysR family transcriptional regulator; |
8-184 | 1.36e-13 | |||||
LysR family transcriptional regulator; Pssm-ID: 182085 [Multi-domain] Cd Length: 310 Bit Score: 69.68 E-value: 1.36e-13
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| HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
5-63 | 1.37e-13 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 64.33 E-value: 1.37e-13
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| PBP2_LTTR_substrate | cd05466 | The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ... |
90-241 | 4.31e-13 | |||||
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: 66.47 E-value: 4.31e-13
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| PBP2_CrgA_like_8 | cd08477 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
89-280 | 2.38e-12 | |||||
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: 64.56 E-value: 2.38e-12
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| PBP2_CrgA_like_1 | cd08470 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
89-281 | 1.01e-11 | |||||
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: 62.71 E-value: 1.01e-11
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| PBP2_CrgA_like_9 | cd08479 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
89-185 | 3.77e-10 | |||||
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: 58.38 E-value: 3.77e-10
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| PRK15092 | PRK15092 | DNA-binding transcriptional repressor LrhA; Provisional |
1-163 | 2.90e-09 | |||||
DNA-binding transcriptional repressor LrhA; Provisional Pssm-ID: 237907 [Multi-domain] Cd Length: 310 Bit Score: 56.96 E-value: 2.90e-09
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| PBP2_CrgA_like_6 | cd08475 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
89-280 | 6.68e-09 | |||||
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: 54.48 E-value: 6.68e-09
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| PBP2_CrgA | cd08478 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ... |
88-280 | 9.79e-09 | |||||
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: 54.27 E-value: 9.79e-09
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| PBP2_CrgA_like_3 | cd08472 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
89-189 | 1.22e-08 | |||||
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: 54.06 E-value: 1.22e-08
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| PRK10086 | PRK10086 | DNA-binding transcriptional regulator DsdC; |
8-122 | 1.48e-08 | |||||
DNA-binding transcriptional regulator DsdC; Pssm-ID: 182231 [Multi-domain] Cd Length: 311 Bit Score: 54.62 E-value: 1.48e-08
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| PRK09986 | PRK09986 | LysR family transcriptional regulator; |
2-235 | 2.39e-07 | |||||
LysR family transcriptional regulator; Pssm-ID: 182183 [Multi-domain] Cd Length: 294 Bit Score: 51.26 E-value: 2.39e-07
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| PRK10082 | PRK10082 | hypochlorite stress DNA-binding transcriptional regulator HypT; |
11-237 | 3.74e-07 | |||||
hypochlorite stress DNA-binding transcriptional regulator HypT; Pssm-ID: 182228 [Multi-domain] Cd Length: 303 Bit Score: 50.44 E-value: 3.74e-07
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| PRK10341 | PRK10341 | transcriptional regulator TdcA; |
7-116 | 6.72e-07 | |||||
transcriptional regulator TdcA; Pssm-ID: 182391 [Multi-domain] Cd Length: 312 Bit Score: 49.86 E-value: 6.72e-07
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| PBP2_CrgA_like_10 | cd08480 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
89-250 | 1.13e-06 | |||||
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: 48.10 E-value: 1.13e-06
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| PRK11139 | PRK11139 | DNA-binding transcriptional activator GcvA; Provisional |
15-184 | 3.56e-06 | |||||
DNA-binding transcriptional activator GcvA; Provisional Pssm-ID: 182990 [Multi-domain] Cd Length: 297 Bit Score: 47.53 E-value: 3.56e-06
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| PBP2_LTTR_like_5 | cd08426 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
90-237 | 4.25e-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: 176117 [Multi-domain] Cd Length: 199 Bit Score: 46.53 E-value: 4.25e-06
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| PBP2_CrgA_like_7 | cd08476 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
89-262 | 6.05e-06 | |||||
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: 46.08 E-value: 6.05e-06
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| PBP2_CrgA_like_4 | cd08473 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
88-251 | 1.08e-05 | |||||
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: 45.24 E-value: 1.08e-05
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| PRK11716 | PRK11716 | HTH-type transcriptional activator IlvY; |
32-122 | 1.67e-05 | |||||
HTH-type transcriptional activator IlvY; Pssm-ID: 236961 [Multi-domain] Cd Length: 269 Bit Score: 45.19 E-value: 1.67e-05
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| PRK03601 | PRK03601 | HTH-type transcriptional regulator HdfR; |
3-248 | 4.37e-05 | |||||
HTH-type transcriptional regulator HdfR; Pssm-ID: 235137 [Multi-domain] Cd Length: 275 Bit Score: 44.24 E-value: 4.37e-05
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| PRK14997 | PRK14997 | LysR family transcriptional regulator; Provisional |
2-250 | 7.42e-05 | |||||
LysR family transcriptional regulator; Provisional Pssm-ID: 184959 [Multi-domain] Cd Length: 301 Bit Score: 43.44 E-value: 7.42e-05
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| PRK10632 | PRK10632 | HTH-type transcriptional activator AaeR; |
19-235 | 7.92e-05 | |||||
HTH-type transcriptional activator AaeR; Pssm-ID: 182601 [Multi-domain] Cd Length: 309 Bit Score: 43.60 E-value: 7.92e-05
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| PBP2_LTTR_like_4 | cd08440 | TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
90-237 | 8.17e-05 | |||||
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: 42.51 E-value: 8.17e-05
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| PRK11013 | PRK11013 | DNA-binding transcriptional regulator LysR; Provisional |
1-124 | 8.97e-05 | |||||
DNA-binding transcriptional regulator LysR; Provisional Pssm-ID: 236819 [Multi-domain] Cd Length: 309 Bit Score: 43.44 E-value: 8.97e-05
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| PBP2_LrhA_like | cd08439 | The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ... |
90-235 | 1.74e-04 | |||||
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130 Cd Length: 185 Bit Score: 41.55 E-value: 1.74e-04
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| rbcR | CHL00180 | LysR transcriptional regulator; Provisional |
6-234 | 3.75e-04 | |||||
LysR transcriptional regulator; Provisional Pssm-ID: 177082 [Multi-domain] Cd Length: 305 Bit Score: 41.54 E-value: 3.75e-04
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| PRK09791 | PRK09791 | LysR family transcriptional regulator; |
8-116 | 1.27e-03 | |||||
LysR family transcriptional regulator; Pssm-ID: 182077 [Multi-domain] Cd Length: 302 Bit Score: 39.75 E-value: 1.27e-03
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| PRK10094 | PRK10094 | HTH-type transcriptional activator AllS; |
4-72 | 1.31e-03 | |||||
HTH-type transcriptional activator AllS; Pssm-ID: 182237 [Multi-domain] Cd Length: 308 Bit Score: 39.79 E-value: 1.31e-03
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| PBP2_CidR | cd08438 | The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ... |
90-235 | 1.69e-03 | |||||
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: 38.69 E-value: 1.69e-03
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| PBP2_GltC_like | cd08434 | The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ... |
91-235 | 1.71e-03 | |||||
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: 38.67 E-value: 1.71e-03
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| PRK11242 | PRK11242 | DNA-binding transcriptional regulator CynR; Provisional |
7-122 | 2.22e-03 | |||||
DNA-binding transcriptional regulator CynR; Provisional Pssm-ID: 183051 [Multi-domain] Cd Length: 296 Bit Score: 38.78 E-value: 2.22e-03
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| PRK13348 | PRK13348 | HTH-type transcriptional regulator ArgP; |
4-73 | 2.37e-03 | |||||
HTH-type transcriptional regulator ArgP; Pssm-ID: 237357 [Multi-domain] Cd Length: 294 Bit Score: 38.80 E-value: 2.37e-03
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