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Conserved domains on  [gi|620695020|gb|KAK55059|]
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LysR substrate-binding domain protein [Bordetella bronchiseptica OSU054]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

LysR family transcriptional regulator similar to Pseudomonas aeruginosa HTH-type transcriptional regulator PtxR, which regulates the toxA (exotoxin) and regA genes; substrate binding domain-containing protein is a type 2 periplasmic binding protein (PBP2), similar to the regulatory domain of Vibrio vulnificus virulence gene regulator AphB that has been implicated in acid resistance and pathogenesis

Gene Ontology:  GO:0001216|GO:0032993|GO:0006355
PubMed:  19047729|8257110

Graphical summary

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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 ...
 153-351 9.56e-69

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: 214.61  E-value: 9.56e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLaSPEH----AERVfqtcDVSIEIGDLPDSTHIARLLGVLPAHLY 228
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVL-SDRLvdlvEEGF----DLAIRIGELPDSSLVARRLGPVRRVLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 229 ASPDYLARHGEPQHPDDLPRHECIQFRaGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNV 308
Cdd:cd08422   76 ASPAYLARHGTPQTPEDLARHRCLGYR-LPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALL-PDFLV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 620695020 309 REDIESGRLKRILPDWLAGPFPVYAVT-DTRMLPAKTRIFVEFL 351
Cdd:cd08422  154 AEDLASGRLVRVLPDWRPPPLPIYAVYpSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
65-124 1.88e-20

Bacterial regulatory helix-turn-helix protein, lysR family;


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 1.88e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020   65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQ 124
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 153-351 9.56e-69

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: 214.61  E-value: 9.56e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLaSPEH----AERVfqtcDVSIEIGDLPDSTHIARLLGVLPAHLY 228
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVL-SDRLvdlvEEGF----DLAIRIGELPDSSLVARRLGPVRRVLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 229 ASPDYLARHGEPQHPDDLPRHECIQFRaGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNV 308
Cdd:cd08422   76 ASPAYLARHGTPQTPEDLARHRCLGYR-LPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALL-PDFLV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 620695020 309 REDIESGRLKRILPDWLAGPFPVYAVT-DTRMLPAKTRIFVEFL 351
Cdd:cd08422  154 AEDLASGRLVRVLPDWRPPPLPIYAVYpSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
65-355 1.88e-56

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 185.07  E-value: 1.88e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEEL 144
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 145 QNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQT--CDVSIEIGDLPDSTHIARLLGV 222
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEgeLDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 223 LPAHLYASPDY-LARHGEPqhpddlprheciqfragtgrvtrwplnsgerhveitpgnrfsVNSVSMVRNLATLGAGIAI 301
Cdd:COG0583  163 ERLVLVASPDHpLARRAPL------------------------------------------VNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 620695020 302 LaPMGNVREDIESGRLKRILPDWLAGPFPVYAVT-DTRMLPAKTRIFVEFLMERL 355
Cdd:COG0583  201 L-PRFLAADELAAGRLVALPLPDPPPPRPLYLVWrRRRHLSPAVRAFLDFLREAL 254
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
62-353 1.99e-46

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 160.70  E-value: 1.99e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNRLQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAH 141
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 142 EELQNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEhAERVFQTCDVSIEIGDLPDSTHIARLLG 221
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPA-PDLIADGLDVVIRVGALQDSSLFSRRLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 222 VLPAHLYASPDYLARHGEPQHPDDLPRHECIQFR----------AGTGRVTRwplnsgerhveITPGNRFSVN-SVSMVR 290
Cdd:PRK10632 160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSvrpdnefeliAPEGISTR-----------LIPQGRFVTNdPQTLVR 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 620695020 291 NLATlGAGIAILaPMGNVREDIESGRLKRILPDWLAGPFPVYAV-TDTRMLPAKTRIFVEFLME 353
Cdd:PRK10632 229 WLTA-GAGIAYV-PLMWVIDEINRGELEILFPRYQSDPRPVYALyTEKDKLPLKVQVCINYLTD 290
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 152-356 5.79e-30

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: 113.92  E-value: 5.79e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  152 SGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQ--TCDVSIEIGDLPDSTHIARLLGVLPAHLYA 229
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLegELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  230 SPDYLARHGEPQHPDDLPRHECIQFRAGTGrvTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNVR 309
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSG--LRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALL-PRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 620695020  310 EDIESGRLKRILPDWLAGPFPVYAVTDT-RMLPAKTRIFVEFLMERLS 356
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKgRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
65-124 1.88e-20

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 1.88e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020   65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQ 124
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 68-140 2.87e-14

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 72.49  E-value: 2.87e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 620695020  68 MEL-----FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIA 140
Cdd:PRK09906   1 MELrhlryFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKA 78
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
75-147 1.67e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.57  E-value: 1.67e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 620695020    75 ARTLSFSRAAENLAIPKSTLSRQVAELERSvGL--RLLSRTTRR---VELTEAGQLYFERCQRIVAEARiaHEELQNL 147
Cdd:smart00347  22 EGPLSVSELAKRLGVSPSTVTRVLDRLEKK-GLvrREPSPEDRRsvlVSLTEEGRELIEQLLEARSETL--AELLAGL 96
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
78-149 4.05e-03

DNA-binding transcriptional regulator, MarR family [Transcription];


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 37.26  E-value: 4.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  78 LSFSRAAENLAIPKSTLSRQVAELERSvGL--RLLSRTTRR---VELTEAGQLYFERCQRIVAE------ARIAHEELQN 146
Cdd:COG1846   53 LTQSELAERLGLTKSTVSRLLDRLEEK-GLveREPDPEDRRavlVRLTEKGRALLEEARPALEAllaellAGLSEEELEA 131


                 ...
gi 620695020 147 LVE 149
Cdd:COG1846  132 LLR 134
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 153-351 9.56e-69

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: 214.61  E-value: 9.56e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLaSPEH----AERVfqtcDVSIEIGDLPDSTHIARLLGVLPAHLY 228
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVL-SDRLvdlvEEGF----DLAIRIGELPDSSLVARRLGPVRRVLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 229 ASPDYLARHGEPQHPDDLPRHECIQFRaGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNV 308
Cdd:cd08422   76 ASPAYLARHGTPQTPEDLARHRCLGYR-LPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALL-PDFLV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 620695020 309 REDIESGRLKRILPDWLAGPFPVYAVT-DTRMLPAKTRIFVEFL 351
Cdd:cd08422  154 AEDLASGRLVRVLPDWRPPPLPIYAVYpSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
65-355 1.88e-56

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 185.07  E-value: 1.88e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEEL 144
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 145 QNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQT--CDVSIEIGDLPDSTHIARLLGV 222
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEgeLDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 223 LPAHLYASPDY-LARHGEPqhpddlprheciqfragtgrvtrwplnsgerhveitpgnrfsVNSVSMVRNLATLGAGIAI 301
Cdd:COG0583  163 ERLVLVASPDHpLARRAPL------------------------------------------VNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 620695020 302 LaPMGNVREDIESGRLKRILPDWLAGPFPVYAVT-DTRMLPAKTRIFVEFLMERL 355
Cdd:COG0583  201 L-PRFLAADELAAGRLVALPLPDPPPPRPLYLVWrRRRHLSPAVRAFLDFLREAL 254
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-351 2.85e-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 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: 162.01  E-value: 2.85e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLaSPEHAERVFQTCDVSIEIGDLPDSTHIARLLGVLPAHLYASPD 232
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVL-SDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 233 YLARHGEPQHPDDLPRHECIQFRAGTGRvTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIaILAPMGNVREDI 312
Cdd:cd08477   80 YLARHGTPTTPEDLARHECLGFSYWRAR-NRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGI-VLQPEALLAEDL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 620695020 313 ESGRLKRILPDWLAGPFPVYAVT--DTRMLPaKTRIFVEFL 351
Cdd:cd08477  158 ASGRLVELLPDYLPPPRPMHLLYppDRRPTP-KLRSFIDFL 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
62-353 1.99e-46

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 160.70  E-value: 1.99e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNRLQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAH 141
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 142 EELQNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEhAERVFQTCDVSIEIGDLPDSTHIARLLG 221
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPA-PDLIADGLDVVIRVGALQDSSLFSRRLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 222 VLPAHLYASPDYLARHGEPQHPDDLPRHECIQFR----------AGTGRVTRwplnsgerhveITPGNRFSVN-SVSMVR 290
Cdd:PRK10632 160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSvrpdnefeliAPEGISTR-----------LIPQGRFVTNdPQTLVR 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 620695020 291 NLATlGAGIAILaPMGNVREDIESGRLKRILPDWLAGPFPVYAV-TDTRMLPAKTRIFVEFLME 353
Cdd:PRK10632 229 WLTA-GAGIAYV-PLMWVIDEINRGELEILFPRYQSDPRPVYALyTEKDKLPLKVQVCINYLTD 290
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-354 3.43e-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 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: 156.52  E-value: 3.43e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTfyLDLASPEH-AERVFQTCDVSIEIGDLPDSTHIARLLGVLPAHLYASP 231
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIE--LDLGVSDRpVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 232 DYLARHGEPQHPDDLPRHECIQFR-AGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILAPMGnVRE 310
Cdd:cd08472   79 AYLARHGTPRHPEDLERHRAVGYFsARTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFM-VRP 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 620695020 311 DIESGRLKRILPDWLAGPFPVYAVT-DTRMLPAKTRIFVEFLMER 354
Cdd:cd08472  158 HLASGRLVEVLPDWRPPPLPVSLLYpHRRHLSPRVRVFVDWVAEL 202
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-351 6.43e-44

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: 150.44  E-value: 6.43e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLAS--PEHAERVFqtcDVSIEIGDLPDSTHIARLLgvLPAH--LY 228
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDrpVDLVEEGF---DLDIRVGDLPDSSLIARKL--APNRriLC 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 229 ASPDYLARHGEPQHPDDLPRHECIQFRAGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIaILAPMGNV 308
Cdd:cd08479   76 ASPAYLERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGI-ILRSEWDV 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 620695020 309 REDIESGRLKRILPDWLAGPFPVYAVTDTRM-LPAKTRIFVEFL 351
Cdd:cd08479  155 APYLRSGRLVRVLPDWQLPDADIWAVYPSRLsRSARVRVFVDFL 198
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 151-351 4.46e-42

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: 146.07  E-value: 4.46e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 151 PSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTfyLDLASPEH-----AERvfqtCDVSIEIGDLPDSTHIA-RLLGVLP 224
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIR--LELVVDDGlvdivAEG----FDAGIRLGESVEKDMVAvPLGPPLR 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 225 AHLYASPDYLARHGEPQHPDDLPRHECIQFR-AGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILa 303
Cdd:cd08474   75 MAVVASPAYLARHGTPEHPRDLLNHRCIRYRfPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYL- 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 620695020 304 PMGNVREDIESGRLKRILPDWLAGPFPVYAV-TDTRMLPAKTRIFVEFL 351
Cdd:cd08474  154 FEDLVAEHLASGRLVRVLEDWSPPFPGGYLYyPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-351 1.73e-39

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: 138.92  E-value: 1.73e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPAdfGTDFLSEAFTEFSRRYPEVTFYLDLaSPEHAERVFQTCDVSIEIGDLPDSTHIARLLGVLPAHLYASPD 232
Cdd:cd08476    1 GRLRVSLPL--VGGLLLPVLAAFMQRYPEIELDLDF-SDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 233 YLARHGEPQHPDDLPRHECIQFR-AGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNVRED 311
Cdd:cd08476   78 YLARHGTPETPADLAEHACLRYRfPTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACL-PDFSVREA 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 620695020 312 IESGRLKRILPDWLAGPFPVYAVTDT-RMLPAKTRIFVEFL 351
Cdd:cd08476  157 LADGRLVTVLDDYVEERGQFRLLWPSsRHLSPKLRVFVDFM 197
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-355 7.86e-38

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: 134.58  E-value: 7.86e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLAspehaERVFQTC----DVSIEIGDLPDSTHIARLLGVLPAHLY 228
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLL-----DRVVNLLeegvDVAVRIGHLPDSSLVATRVGSVRRVVC 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 229 ASPDYLARHGEPQHPDDLPRHECIQFrAGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNV 308
Cdd:cd08471   76 ASPAYLARHGTPKHPDDLADHDCIAF-TGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRV-LSYQV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 620695020 309 REDIESGRLKRILPDWLAGPFPVYAVTDT-RMLPAKTRIFVEFLMERL 355
Cdd:cd08471  154 AEELAAGRLQRVLEDFEPPPLPVHLVHPEgRLAPAKVRAFVDFAVPRL 201
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 62-353 2.03e-36

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 133.96  E-value: 2.03e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNRLQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAH 141
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 142 EELQNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDlASPEHAERVFQTCDVSIEIGDLP--DSTHIARL 219
Cdd:PRK14997  81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLE-ATNRRVDVVGEGVDVAIRVRPRPfeDSDLVMRV 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 220 LGVLPAHLYASPDYLARHGEPQHPDDLPRHECIQFRAGTgRVTRWPL---NSGERHVEITPgnRFSVNSVSMVRNLATLG 296
Cdd:PRK14997 160 LADRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGK-HIHRWELygpQGARAEVHFTP--RMITTDMLALREAAMAG 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 620695020 297 AGIAILaPMGNVREDIESGRLKRILPDWLAGPFPVYAVTDTR--MLPAkTRIFVEFLME 353
Cdd:PRK14997 237 VGLVQL-PVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRrgLLPS-VRALVDFLTE 293
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-351 2.46e-34

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: 125.53  E-value: 2.46e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTfyLDLA-SPEHAERVFQTCDVSIEIGDLPDSTHIARLLGVLPAHLYASP 231
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEIL--VDLSlTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 232 DYLARHGEPQHPDDLPRHECIQF---RAGTGrvtrWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILAPMgNV 308
Cdd:cd08480   79 SYLARHGTPLTPQDLARHNCLGFnfrRALPD----WPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALF-HV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 620695020 309 REDIESGRLKRILPDWLAGPF-PVYAV-TDTRMLPAKTRIFVEFL 351
Cdd:cd08480  154 ADDIAAGRLVPVLEEYNPGDRePIHAVyVGGGRLPARVRAFLDFL 198
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-351 5.04e-34

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: 124.59  E-value: 5.04e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYP----EVTF---YLDLAspehAERVfqtcDVSIEIGDLPDSTH-IARLLGVLP 224
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPelelELSFsdrFVDLI----EEGI----DLAVRIGELADSTGlVARRLGTQR 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 225 AHLYASPDYLARHGEPQHPDDLPRHECIQFRAGtGRVTRWPLNS-GERHVEITPGNRFSVNSVSMVRNLATLGAGIAILa 303
Cdd:cd08475   73 MVLCASPAYLARHGTPRTLEDLAEHQCIAYGRG-GQPLPWRLADeQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQL- 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 620695020 304 PMGNVREDIESGRLKRILPDWLAGPFPVYAV-TDTRMLPAKTRIFVEFL 351
Cdd:cd08475  151 PTWLVADHLQRGELVEVLPELAPEGLPIHAVwPRTRHLPPKVRAAVDAL 199
PRK09801 PRK09801
LysR family transcriptional regulator;
68-351 3.10e-33

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 125.92  E-value: 3.10e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  68 MELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEELQNL 147
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 148 VETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASpEHAERVFQTCDVSIEIGD-LPDsTHIARLLGVLPAH 226
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFD-RQIDLVQDNIDLDIRINDeIPD-YYIAHLLTKNKRI 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 227 LYASPDYLARHGEPQHPDDLPRHECIQFRAGTGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIaILAPMG 306
Cdd:PRK09801 169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGI-MLRSEW 247

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 620695020 307 NVREDIESGRLKRILPDWL--AGPFPVYAVTDTRMLpaKTRIFVEFL 351
Cdd:PRK09801 248 DVLPFLESGKLVQVLPEYAqsANIWAVYREPLYRSM--KLRVCVEFL 292
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 153-355 4.80e-32

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: 119.34  E-value: 4.80e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 153 GPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLaSPEHAERVFQTCDVSIEIGDLPDSTHIARLLGVLPAHLYASPD 232
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIEL-TNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 233 YLARHGEPQHPDDLPRHECIQfragtGRVTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNVREDI 312
Cdd:cd08470   80 YLERHGTPHSLADLDRHNCLL-----GTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQL-PDYYVDEHL 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 620695020 313 ESGRLKRILPDWLAGPFPVYAV-TDTRMLPAKTRIFVEFLMERL 355
Cdd:cd08470  154 AAGRLVPVLEDYRPPDEGIWALyPHNRHLSPKVRLLVDYLADAL 197
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 151-351 9.05e-31

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: 116.12  E-value: 9.05e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 151 PSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYL-------DLAspehAERVfqtcDVSIEIGDLP--DSTHIARLLG 221
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLeatnrrvDLI----EEGI----DVALRVRFPPleDSSLVMRVLG 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 222 VLPAHLYASPDYLARHGEPQHPDDLPRHECIQFRAGTGRvTRWPL---NSGERHVEITPgnRFSVNSVSMVRNLATLGAG 298
Cdd:cd08473   73 QSRQRLVASPALLARLGRPRSPEDLAGLPTLSLGDVDGR-HSWRLegpDGESITVRHRP--RLVTDDLLTLRQAALAGVG 149

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 620695020 299 IAILaPMGNVREDIESGRLKRILPDWLAGPFPVYAVTDTR--MLPAkTRIFVEFL 351
Cdd:cd08473  150 IALL-PDHLCREALRAGRLVRVLPDWTPPRGIVHAVFPSRrgLLPA-VRALIDFL 202
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 151-351 1.66e-30

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: 115.51  E-value: 1.66e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 151 PSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTfyLDLASPEH-----AERVfqtcDVSIEIGDLPDSTHIARLLGVLPA 225
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIE--LELVSNEGiidliERKT----DVAIRIGELTDSTLHARPLGKSRL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 226 HLYASPDYLARHGEPQHPDDLPRHECIQFrAGTGRVTRWPL-NSGERHVEITPgnRFSVNSVSMVRNLATLGAGIAILAP 304
Cdd:cd08478   75 RILASPDYLARHGTPQSIEDLAQHQLLGF-TEPASLNTWPIkDADGNLLKIQP--TITASSGETLRQLALSGCGIACLSD 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 620695020 305 MgNVREDIESGRLKRIL-PDWLAGPFPVYAVT-DTRMLPAKTRIFVEFL 351
Cdd:cd08478  152 F-MTDKDIAEGRLIPLFaEQTSDVRQPINAVYyRNTALSLRIRCFIDFL 199
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 152-356 5.79e-30

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: 113.92  E-value: 5.79e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  152 SGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQ--TCDVSIEIGDLPDSTHIARLLGVLPAHLYA 229
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLegELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  230 SPDYLARHGEPQHPDDLPRHECIQFRAGTGrvTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILaPMGNVR 309
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSG--LRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALL-PRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 620695020  310 EDIESGRLKRILPDWLAGPFPVYAVTDT-RMLPAKTRIFVEFLMERLS 356
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKgRPLSPAVRAFIEFLREALA 205
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 75-353 1.14e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 93.75  E-value: 1.14e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  75 ARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEELQNLVETPSgp 154
Cdd:PRK11139  18 ARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAKGA-- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 155 LRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLdLASpeHAERVFQTCDVSIEI----GDLPdSTHIARLLG--VLPAhly 228
Cdd:PRK11139  96 LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRL-KAV--DRLEDFLRDDVDVAIrygrGNWP-GLRVEKLLDeyLLPV--- 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 229 ASPDYLARHGEPQHPDDLPRHECIQfraGTGRVT--RWPLNSGERHVEITPGNRFSvNSvSMVRNLATLGAGIAiLAPMG 306
Cdd:PRK11139 169 CSPALLNGGKPLKTPEDLARHTLLH---DDSREDwrAWFRAAGLDDLNVQQGPIFS-HS-SMALQAAIHGQGVA-LGNRV 242

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 620695020 307 NVREDIESGRLKRILPDWLAGPFPVYAVTDTRML-PAKTRIFVEFLME 353
Cdd:PRK11139 243 LAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAeLPKVAAFRQWLLA 290
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
65-124 1.88e-20

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 1.88e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020   65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQ 124
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
65-353 2.24e-17

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 81.59  E-value: 2.24e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQR----IVAEAR-I 139
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSsldtLNQEILdI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 140 AHEELqnlvetpSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLdLASPEHAErvFQT--CDVSIEIGDLP-DSTHI 216
Cdd:PRK10086  96 KNQEL-------SGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTI-LTGNENVN--FQRagIDLAIYFDDAPsAQLTH 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 217 ARLLG--VLPAhlyASPDYLARHGEPQHPDDLPRHECIQFRAGtgrvtrWPLNSGERHVEiTPGNRFSVN----SVSMV- 289
Cdd:PRK10086 166 HFLMDeeILPV---CSPEYAERHALTGNPDNLRHCTLLHDRQA------WSNDSGTDEWH-SWAQHFGVNllppSSGIGf 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 620695020 290 --RNLATLGA----GIAilapMGN---VREDIESGRLkrILPdwlAGPFPV------YAVTDTRMLPAKTRIFVEFLME 353
Cdd:PRK10086 236 drSDLAVIAAmnhiGVA----MGRkrlVQKRLASGEL--VAP---FGDMEVkchqhyYVTTLPGRQWPKIEAFIDWLKE 305
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 71-183 6.02e-16

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 77.30  E-value: 6.02e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  71 FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFE---RCQRIVAEARIAHEELQNL 147
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRyarRALQDLEAGRRAIHDVADL 88

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 620695020 148 vetPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVT 183
Cdd:PRK11242  89 ---SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGIT 121
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 154-351 9.45e-15

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: 71.84  E-value: 9.45e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 154 PLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDlASPEHAErvFQTCDVSIEI----GDLPDsTHIARLLG--VLPAhl 227
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLS-TSDRLVD--FAREGIDLAIrygdGDWPG-LEAERLMDeeLVPV-- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 228 yASPDYLARHGEPQhPDDLPRHECIQFRAGTGRVTRWPLNSGERHVEITPGNRFsvNSVSMVRNLATLGAGIAiLAPMGN 307
Cdd:cd08432   75 -CSPALLAGLPLLS-PADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRF--DDSSLALQAAVAGLGVA-LAPRAL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 620695020 308 VREDIESGRLKRILPDWLAGPFPVYAVT-DTRMLPAKTRIFVEFL 351
Cdd:cd08432  150 VADDLAAGRLVRPFDLPLPSGGAYYLVYpPGRAESPAVAAFRDWL 194
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 68-140 2.87e-14

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 72.49  E-value: 2.87e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 620695020  68 MEL-----FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIA 140
Cdd:PRK09906   1 MELrhlryFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKA 78
rbcR CHL00180
LysR transcriptional regulator; Provisional
 65-320 3.58e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 72.36  E-value: 3.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVA---EARIAH 141
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 142 EELQNLvetPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEH-AERVFQ-TCDVSIEIGDLPdsTHIARL 219
Cdd:CHL00180  87 EDLKNL---QRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRiAWNVANgQIDIAIVGGEVP--TELKKI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 220 LGVLPahlYASpDYLARHGEPQHP---------DDLPRHECIQFRAgtgrvtrwplNSGERHV--------EITPgNRFS 282
Cdd:CHL00180 162 LEITP---YVE-DELALIIPKSHPfaklkkiqkEDLYRLNFITLDS----------NSTIRKVidniliqnGIDS-KRFK 226

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 620695020 283 V----NSVSMVRNLATLGAGIAILAPMGnVREDIESGRLKRI 320
Cdd:CHL00180 227 IemelNSIEAIKNAVQSGLGAAFVSVSA-IEKELELGLLHWI 267
PRK09791 PRK09791
LysR family transcriptional regulator;
64-182 4.86e-14

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 72.10  E-value: 4.86e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  64 RLQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEE 143
Cdd:PRK09791   6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 620695020 144 LQNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEV 182
Cdd:PRK09791  86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQV 124
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 62-186 6.71e-13

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 68.52  E-value: 6.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNrLQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAH 141
Cdd:PRK11151   1 MN-IRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLK 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 620695020 142 EELQNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYL 186
Cdd:PRK11151  80 EMASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYL 124
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
71-145 8.14e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 68.29  E-value: 8.14e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 620695020  71 FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEELQ 145
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 155-351 2.48e-11

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: 62.23  E-value: 2.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 155 LRVNMPADFGTDFLSEAFTEFSRRYPEVTFYL-DLASPEHAERVFQ-TCDVSIEIGDLPDSTHIARLLGVLPAHLYASPD 232
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLvEGGSSELLEALLEgELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 233 YLARHGEPQHPDDLPRHECIQFRAGTGRvTRWPLNSGERHvEITPGNRFSVNSVSMVRNLATLGAGIAILAPMgnVREDI 312
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSGL-RRLLDRAFAEA-GFTPNIALEVDSLEAIKALVAAGLGIALLPES--AVEEL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 620695020 313 ESGRLKRILPDWLAGPFPVYAVTDT-RMLPAKTRIFVEFL 351
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTIGLVWRKgRYLSPAARAFLELL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
62-191 5.18e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 59.74  E-value: 5.18e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNRLQGMEL-----FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAE 136
Cdd:PRK09986   1 MERLYRIDLkllryFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDN 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 620695020 137 ARIAHEELQNLVETPSGPLRVNMpadFGTDF---LSEAFTEFSRRYPEVTFYLDLASP 191
Cdd:PRK09986  81 AEQSLARVEQIGRGEAGRIEIGI---VGTALwgrLRPAMRHFLKENPNVEWLLRELSP 135
PRK10341 PRK10341
transcriptional regulator TdcA;
66-182 1.58e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 58.34  E-value: 1.58e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  66 QGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEELQ 145
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 620695020 146 NLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEV 182
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKA 126
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 62-186 2.43e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.77  E-value: 2.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNrLQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAH 141
Cdd:PRK11233   1 MN-FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQ 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 620695020 142 EELQNLVETPSGPLRVNM-PADFGTDFLSEAFTEFSRRYPEVTFYL 186
Cdd:PRK11233  80 LAVHNVGQALSGQVSIGLaPGTAASSLTMPLLQAVRAEFPGIVLYL 125
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
92-302 1.58e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 55.21  E-value: 1.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  92 STLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEELQNLVETPSGPLRVnmpadFGT-----D 166
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSL-----FCSvtaayS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 167 FLSEAFTEFSRRYPEVTFYLDLASPEHA-ERVfQTCDVSIEIGDLPDS-------THIARLLGVLPAHLYASP-DYLARH 237
Cdd:PRK11716  81 HLPPILDRFRAEHPLVEIKLTTGDAADAvEKV-QSGEADLAIAAKPETlpasvafSPIDEIPLVLIAPALPCPvRQQLSQ 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 620695020 238 GEP---QHPDDLPRHeciqfraGTGR--VTRWplnsgERHVEITPgNRFSVNS-----VSMVRnlatLGAGIAIL 302
Cdd:PRK11716 160 EKPdwsRIPFILPEH-------GPARrrIDLW-----FRRHKIKP-NIYATVSgheaiVSMVA----LGCGVGLL 217
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 156-351 4.77e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 52.70  E-value: 4.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 156 RVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQTCDVSIEIGDLPDSTHIARLLGVLPAHLYA--SPDY 233
Cdd:cd08426    3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAvvPPGH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 234 -LARHGEPQhPDDLPRHECIQFRAGTGrvTRWPLNSGERHVEITPGNRFSVNSVSMVRNLATLGAGIAILAPMGnVREDI 312
Cdd:cd08426   83 pLARQPSVT-LAQLAGYPLALPPPSFS--LRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELA-VRREI 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 620695020 313 ESGRLKrILPdwLAGPFPVYA-----VTDTRMLPAKTRIFVEFL 351
Cdd:cd08426  159 RRGQLV-AVP--LADPHMNHRqlelqTRAGRQLPAAASAFLQLL 199
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
71-349 5.01e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 53.90  E-value: 5.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  71 FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAHEELQNLVET 150
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 151 PSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQT-CDVSIEIGDLPDS--THIaRLLGVLPAHL 227
Cdd:PRK10082  99 AQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGQSdCIFSFHDEDLLEApfDHI-RLFESQLFPV 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 228 YASPDylarHGEPQHPDDLPRHECIQFRAGT--GRVTRWPLNsgeRHVEITpGNRFSVNSVS-MVRNLATLGAGIAILaP 304
Cdd:PRK10082 178 CASDE----HGEALFNLAQPHFPLLNYSRNSymGRLINRTLT---RHSELS-FSTFFVSSMSeLLKQVALDGCGIAWL-P 248

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 620695020 305 MGNVREDIESGRLKRILPDWLAGPFPVYAV-TDTRMLPAKTRIFVE 349
Cdd:PRK10082 249 EYAIQQEIRSGQLVVLNRDELVIPIQAYAYrMNTRMNPVAERFWRE 294
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
66-157 1.07e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 52.67  E-value: 1.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  66 QGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRtTRRVELTEAGQlyfERCQRIVAEARIAHEELQ 145
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQ---RLLRHLRQVALLEADLLS 80

                         90
                 ....*....|..
gi 620695020 146 NLVETPSGPLRV 157
Cdd:PRK13348  81 TLPAERGSPPTL 92
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 65-181 1.13e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 52.77  E-value: 1.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEAriahEEL 144
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQA----VEI 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 620695020 145 QNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPE 181
Cdd:PRK10837  81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQ 117
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 62-328 3.14e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 51.58  E-value: 3.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNrLQGMELFVEVAR-TLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVE-LTEAGQLYFERCQRIVAEAri 139
Cdd:PRK12683   1 MN-FQQLRIIREAVRqNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDA-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 140 ahEELQNLVET----PSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQTCDVSIEI-----GDL 210
Cdd:PRK12683  78 --ENLRRLAEQfadrDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIatealDRE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 211 PDsthiarlLGVLPAH-----LYASPDYLARHGEPQHPDDLPRHECIQFRAG-TGRvTRwpLNSGERHVEITPGNRFSVN 284
Cdd:PRK12683 156 PD-------LVSFPYYswhhvVVVPKGHPLTGRENLTLEAIAEYPIITYDQGfTGR-SR--IDQAFAEAGLVPDIVLTAL 225

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 620695020 285 SVSMVRNLATLGAGIAILAPMG-NVREDIesgRLKRILPDWLAGP 328
Cdd:PRK12683 226 DADVIKTYVELGMGVGIVAAMAyDPQRDT---GLVALDTDHLFEA 267
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 62-356 1.23e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 49.60  E-value: 1.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNrLQGMELFVEVAR-TLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVE-LTEAGQLYFERCQRIVAEA-- 137
Cdd:PRK12682   1 MN-LQQLRFVREAVRrNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVgn 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 138 --RIAHEELQNlvetPSGPLRV---NMPADFgtdFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQ--TCDVSIEIGDL 210
Cdd:PRK12682  80 ikRIGDDFSNQ----DSGTLTIattHTQARY---VLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVIsgEADIGIATESL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 211 PDSTHiarlLGVLPAH-----LYASPDYLARHGEPQHPDDLPRHECIQFRAG-TGRVTrwpLNSGERHVEITPGNRFSVN 284
Cdd:PRK12682 153 ADDPD----LATLPCYdwqhaVIVPPDHPLAQEERITLEDLAEYPLITYHPGfTGRSR---IDRAFAAAGLQPDIVLEAI 225

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 620695020 285 SVSMVRNLATLGAGIAILAPMGnvREDIESGRLKRILPDWLAGPFPVY-AVTDTRMLPAKTRIFVEFLMERLS 356
Cdd:PRK12682 226 DSDVIKTYVRLGLGVGIVAEMA--YRPDRDGDLVALPAGHLFGPNTAWvALKRGAYLRNYVYKFIELCAPHLS 296
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 66-138 1.49e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.17  E-value: 1.49e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 620695020  66 QGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYfercqriVAEAR 138
Cdd:PRK11074   5 YSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWF-------VKEAR 70
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
69-323 2.97e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 48.23  E-value: 2.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  69 ELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRtTRRVELTEAGQL---YFERCQRIVAEARiahEELQ 145
Cdd:PRK03635   8 EALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRllrHARQVRLLEAELL---GELP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 146 NLVETPSgPLRVNMPAD-FGTDFLsEAFTEFSRRYPeVTFYLDLASPEH----------------AERVFQTCDVsieig 208
Cdd:PRK03635  84 ALDGTPL-TLSIAVNADsLATWFL-PALAPVLARSG-VLLDLVVEDQDHtaellrrgevvgavttEPQPVQGCRV----- 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 209 dlpdsthiaRLLGVLPAHLYASPDYLARH-GEPQHPDDLPRHECIQF-----------RAGTGRvtrwPLNSGERHVeit 276
Cdd:PRK03635 156 ---------DPLGAMRYLAVASPAFAARYfPDGVTAEALAKAPAVVFnrkddlqdrflRQAFGL----PPGSVPCHY--- 219

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 620695020 277 pgnrfsVNSVSMVRNLATLGAGIAiLAPMGNVREDIESGRLKRILPD 323
Cdd:PRK03635 220 ------VPSSEAFVRAALAGLGWG-MIPELQIEPELASGELVDLTPG 259
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
62-191 1.46e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 46.51  E-value: 1.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNrLQGMELFVEVART-LSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRR-VELTEAGQLYFERCQRIVAEA-- 137
Cdd:PRK12684   1 MN-LHQLRFVREAVRQnFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRlRGLTEPGRIILASVERILQEVen 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 620695020 138 --RI----AHEELQNLV-ETPSGPLRVNMPAdfgtdflseAFTEFSRRYPEVTFYLDLASP 191
Cdd:PRK12684  80 lkRVgkefAAQDQGNLTiATTHTQARYALPA---------AIKEFKKRYPKVRLSILQGSP 131
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 65-182 1.66e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.14  E-value: 1.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  65 LQGMELFVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQ-------RIVAEA 137
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQrsyygldRIVSAA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 620695020 138 riaheelQNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEV 182
Cdd:PRK11013  86 -------ESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDV 123
cbl PRK12679
HTH-type transcriptional regulator Cbl;
62-320 2.50e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 45.57  E-value: 2.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  62 MNrLQGMELFVEVART-LSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRR-VELTEAGQLYFERCQRIVAEARI 139
Cdd:PRK12679   1 MN-FQQLKIIREAARQdYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 140 AHEELQNLVETPSGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQTCDVSIEIGdlpdsthiARL 219
Cdd:PRK12679  80 VRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIA--------SER 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 220 LGVLPAhLYASPDY------LARHGEP---QHP---DDLPRHECIQFRAG-TGRvTRwpLNSGERHVEITPGNRFSVNSV 286
Cdd:PRK12679 152 LSNDPQ-LVAFPWFrwhhslLVPHDHPltqITPltlESIAKWPLITYRQGiTGR-SR--IDDAFARKGLLADIVLSAQDS 227

                        250       260       270
                 ....*....|....*....|....*....|....
gi 620695020 287 SMVRNLATLGAGIAILAPMGNvrEDIESGRLKRI 320
Cdd:PRK12679 228 DVIKTYVALGLGIGLVAEQSS--GEQEESNLIRL 259
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 71-240 2.66e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 45.40  E-value: 2.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  71 FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAG-QL--YFERCQRIVAEA--RIAHEELQ 145
Cdd:PRK15092  19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGiQLlgYARKILRFNDEAcsSLMYSNLQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 146 nlvetpsGPLRVNMPADFGTDFLSEAFTEFSRRYPEVTfyLDLA---SPEHAERVFQ-TCDVSIEIGDLPDSTHIarLLG 221
Cdd:PRK15092  99 -------GVLTIGASDDTADTILPFLLNRVSSVYPKLA--LDVRvkrNAFMMEMLESqEVDLAVTTHRPSSFPAL--NLR 167

                        170
                 ....*....|....*....
gi 620695020 222 VLPAHLYASPDYLARHGEP 240
Cdd:PRK15092 168 TSPTLWYCAAEYVLQKGEP 186
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
71-124 3.55e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 45.01  E-value: 3.55e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 620695020  71 FVEVARTLSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQ 124
Cdd:PRK03601   9 FLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGE 62
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
79-182 6.02e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 44.62  E-value: 6.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  79 SFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVELTEAGQLYFERCQRIVAEARIAheeLQNLVETPSGPLRVN 158
Cdd:PRK15421  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA---LQACNEPQQTRLRIA 94

                         90       100
                 ....*....|....*....|....
gi 620695020 159 MPADFGTDFLSEAFTEFSRRYPEV 182
Cdd:PRK15421  95 IECHSCIQWLTPALENFHKNWPQV 118
PRK12680 PRK12680
LysR family transcriptional regulator;
78-305 1.15e-03

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 40.38  E-value: 1.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  78 LSFSRAAENLAIPKSTLSRQVAELERSVGLRLLSRTTRRVE-LTEAGQLYFERCQRIVAEARIAHEELQNLVETPSGPLR 156
Cdd:PRK12680  17 LNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLT 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 157 VNMPADFGTDFLSEAFTEFSRRYPEVTFYLDLASPEHAERVFQTCDVSIEI----GDLPdSTHIA------RLLGVLPA- 225
Cdd:PRK12680  97 LTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvstaGGEP-SAGIAvplyrwRRLVVVPRg 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020 226 ----HLYASPDYLArhgepqhpddLPRHECIQFRAGTGrvtrwPLNSGER---HVEITPGNRFSVNSVSMVRNLATLGAG 298
Cdd:PRK12680 176 haldTPRRAPDMAA----------LAEHPLISYESSTR-----PGSSLQRafaQLGLEPSIALTALDADLIKTYVRAGLG 240


                 ....*..
gi 620695020 299 IAILAPM 305
Cdd:PRK12680 241 VGLLAEM 247
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
75-147 1.67e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.57  E-value: 1.67e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 620695020    75 ARTLSFSRAAENLAIPKSTLSRQVAELERSvGL--RLLSRTTRR---VELTEAGQLYFERCQRIVAEARiaHEELQNL 147
Cdd:smart00347  22 EGPLSVSELAKRLGVSPSTVTRVLDRLEKK-GLvrREPSPEDRRsvlVSLTEEGRELIEQLLEARSETL--AELLAGL 96
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
78-149 4.05e-03

DNA-binding transcriptional regulator, MarR family [Transcription];


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 37.26  E-value: 4.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 620695020  78 LSFSRAAENLAIPKSTLSRQVAELERSvGL--RLLSRTTRR---VELTEAGQLYFERCQRIVAE------ARIAHEELQN 146
Cdd:COG1846   53 LTQSELAERLGLTKSTVSRLLDRLEEK-GLveREPDPEDRRavlVRLTEKGRALLEEARPALEAllaellAGLSEEELEA 131


                 ...
gi 620695020 147 LVE 149
Cdd:COG1846  132 LLR 134
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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