MULTISPECIES: LysR substrate-binding domain-containing protein [unclassified Vibrio]
Protein Classification
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 ... |
207-369 | 1.90e-78 | ||||
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: 240.03 E-value: 1.90e-78
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| transpos_IS3 super family | cl41295 | IS3 family transposase; |
12-207 | 1.96e-53 | ||||
IS3 family transposase; The actual alignment was detected with superfamily member NF033516: Pssm-ID: 468052 [Multi-domain] Cd Length: 369 Bit Score: 181.22 E-value: 1.96e-53
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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 ... |
207-369 | 1.90e-78 | ||||
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: 240.03 E-value: 1.90e-78
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| transpos_IS3 | NF033516 | IS3 family transposase; |
12-207 | 1.96e-53 | ||||
IS3 family transposase; Pssm-ID: 468052 [Multi-domain] Cd Length: 369 Bit Score: 181.22 E-value: 1.96e-53
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
205-373 | 1.04e-33 | ||||
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: 124.32 E-value: 1.04e-33
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| InsE | COG2963 | Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons]; |
1-92 | 3.24e-28 | ||||
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442203 [Multi-domain] Cd Length: 93 Bit Score: 106.16 E-value: 3.24e-28
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| PRK10632 | PRK10632 | HTH-type transcriptional activator AaeR; |
214-371 | 7.78e-25 | ||||
HTH-type transcriptional activator AaeR; Pssm-ID: 182601 [Multi-domain] Cd Length: 309 Bit Score: 102.92 E-value: 7.78e-25
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| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
205-375 | 7.27e-24 | ||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 99.17 E-value: 7.27e-24
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| PHA02517 | PHA02517 | putative transposase OrfB; Reviewed |
121-207 | 3.13e-14 | ||||
putative transposase OrfB; Reviewed Pssm-ID: 222853 [Multi-domain] Cd Length: 277 Bit Score: 72.20 E-value: 3.13e-14
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| HTH_Tnp_1 | pfam01527 | Transposase; Transposase proteins are necessary for efficient DNA transposition. This family ... |
3-78 | 1.13e-13 | ||||
Transposase; Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family. Pssm-ID: 426308 [Multi-domain] Cd Length: 75 Bit Score: 65.45 E-value: 1.13e-13
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| transpos_IS630 | NF033545 | IS630 family transposase; |
14-141 | 4.50e-04 | ||||
IS630 family transposase; Pssm-ID: 468076 [Multi-domain] Cd Length: 298 Bit Score: 41.86 E-value: 4.50e-04
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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 ... |
207-369 | 1.90e-78 | ||||
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: 240.03 E-value: 1.90e-78
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| PBP2_CrgA_like_8 | cd08477 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
207-369 | 5.01e-54 | ||||
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: 177.04 E-value: 5.01e-54
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| PBP2_CrgA_like_3 | cd08472 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
210-371 | 9.64e-54 | ||||
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: 176.55 E-value: 9.64e-54
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| transpos_IS3 | NF033516 | IS3 family transposase; |
12-207 | 1.96e-53 | ||||
IS3 family transposase; Pssm-ID: 468052 [Multi-domain] Cd Length: 369 Bit Score: 181.22 E-value: 1.96e-53
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| PBP2_CrgA_like_1 | cd08470 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
198-373 | 2.34e-52 | ||||
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: 172.88 E-value: 2.34e-52
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| PBP2_CrgA_like_5 | cd08474 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
208-369 | 2.18e-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 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: 162.63 E-value: 2.18e-48
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| PBP2_CrgA_like_2 | cd08471 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
210-373 | 7.93e-47 | ||||
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: 158.46 E-value: 7.93e-47
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| PBP2_CrgA_like_6 | cd08475 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
210-367 | 1.75e-46 | ||||
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: 157.72 E-value: 1.75e-46
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| PBP2_CrgA_like_9 | cd08479 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
205-369 | 2.69e-46 | ||||
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: 156.99 E-value: 2.69e-46
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| PBP2_CrgA_like_10 | cd08480 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
210-369 | 4.58e-41 | ||||
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: 143.63 E-value: 4.58e-41
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| PBP2_CrgA_like_7 | cd08476 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
209-369 | 8.86e-40 | ||||
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: 140.07 E-value: 8.86e-40
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| LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
205-373 | 1.04e-33 | ||||
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: 124.32 E-value: 1.04e-33
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| PBP2_CrgA_like_4 | cd08473 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
210-368 | 8.71e-30 | ||||
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: 113.80 E-value: 8.71e-30
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| PBP2_CrgA | cd08478 | The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ... |
210-369 | 7.10e-29 | ||||
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: 111.28 E-value: 7.10e-29
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| InsE | COG2963 | Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons]; |
1-92 | 3.24e-28 | ||||
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442203 [Multi-domain] Cd Length: 93 Bit Score: 106.16 E-value: 3.24e-28
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| PRK10632 | PRK10632 | HTH-type transcriptional activator AaeR; |
214-371 | 7.78e-25 | ||||
HTH-type transcriptional activator AaeR; Pssm-ID: 182601 [Multi-domain] Cd Length: 309 Bit Score: 102.92 E-value: 7.78e-25
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| LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
205-375 | 7.27e-24 | ||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 99.17 E-value: 7.27e-24
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| PRK09801 | PRK09801 | LysR family transcriptional regulator; |
210-369 | 1.61e-17 | ||||
LysR family transcriptional regulator; Pssm-ID: 182085 [Multi-domain] Cd Length: 310 Bit Score: 82.39 E-value: 1.61e-17
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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, ... |
210-369 | 6.36e-17 | ||||
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: 78.39 E-value: 6.36e-17
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| PBP2_LTTR_substrate | cd05466 | The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ... |
205-369 | 1.50e-15 | ||||
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: 74.56 E-value: 1.50e-15
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| PRK14997 | PRK14997 | LysR family transcriptional regulator; Provisional |
213-372 | 4.75e-15 | ||||
LysR family transcriptional regulator; Provisional Pssm-ID: 184959 [Multi-domain] Cd Length: 301 Bit Score: 75.03 E-value: 4.75e-15
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| PHA02517 | PHA02517 | putative transposase OrfB; Reviewed |
121-207 | 3.13e-14 | ||||
putative transposase OrfB; Reviewed Pssm-ID: 222853 [Multi-domain] Cd Length: 277 Bit Score: 72.20 E-value: 3.13e-14
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| HTH_Tnp_1 | pfam01527 | Transposase; Transposase proteins are necessary for efficient DNA transposition. This family ... |
3-78 | 1.13e-13 | ||||
Transposase; Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family. Pssm-ID: 426308 [Multi-domain] Cd Length: 75 Bit Score: 65.45 E-value: 1.13e-13
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| Tra5 | COG2801 | Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; |
63-207 | 1.35e-08 | ||||
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442053 [Multi-domain] Cd Length: 309 Bit Score: 55.54 E-value: 1.35e-08
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| PBP2_GcdR_like | cd08481 | The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ... |
210-369 | 1.28e-05 | ||||
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: 45.36 E-value: 1.28e-05
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| Csa3 | COG3415 | CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ... |
61-206 | 1.30e-05 | ||||
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system Pssm-ID: 442641 [Multi-domain] Cd Length: 325 Bit Score: 46.77 E-value: 1.30e-05
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| PBP2_LTTR_beta_lactamase | cd08484 | The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ... |
212-336 | 3.26e-05 | ||||
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: 44.28 E-value: 3.26e-05
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| PRK11139 | PRK11139 | DNA-binding transcriptional activator GcvA; Provisional |
210-372 | 4.27e-05 | ||||
DNA-binding transcriptional activator GcvA; Provisional Pssm-ID: 182990 [Multi-domain] Cd Length: 297 Bit Score: 44.83 E-value: 4.27e-05
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| transpos_IS630 | NF033545 | IS630 family transposase; |
14-141 | 4.50e-04 | ||||
IS630 family transposase; Pssm-ID: 468076 [Multi-domain] Cd Length: 298 Bit Score: 41.86 E-value: 4.50e-04
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| HTH_28 | pfam13518 | Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ... |
13-59 | 5.86e-04 | ||||
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding. Pssm-ID: 463908 [Multi-domain] Cd Length: 52 Bit Score: 37.57 E-value: 5.86e-04
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| PBP2_HvrB | cd08483 | The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ... |
212-335 | 6.00e-04 | ||||
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: 40.41 E-value: 6.00e-04
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| HTH_21 | pfam13276 | HTH-like domain; This domain contains a predicted helix-turn-helix suggesting a DNA-binding ... |
144-202 | 8.70e-04 | ||||
HTH-like domain; This domain contains a predicted helix-turn-helix suggesting a DNA-binding function. Pssm-ID: 463824 [Multi-domain] Cd Length: 60 Bit Score: 37.16 E-value: 8.70e-04
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| PBP2_AmpR | cd08488 | The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ... |
213-336 | 1.75e-03 | ||||
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: 39.05 E-value: 1.75e-03
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| Csa3 | COG3415 | CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ... |
14-134 | 3.25e-03 | ||||
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system Pssm-ID: 442641 [Multi-domain] Cd Length: 325 Bit Score: 39.06 E-value: 3.25e-03
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