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Conserved domains on  [gi|503743559|ref|WP_013977635|]
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LysR family transcriptional regulator [Clostridium sp. SY8519]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-187 2.28e-45

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.25  E-value: 2.28e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  81 HSRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWknkMEFEEP-VQE 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL---GPPPDPgLVA 157

                        170       180
                 ....*....|....*....|....*...
gi 503743559 160 QFVGCFPLMAVVGNNHPYAGMGKIAPEL 187
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLVNSL 185
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-299 9.34e-15

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: 71.55  E-value: 9.34e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   90 EGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTwknkmeFEEPVQEQFV----GCF 165
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR------RGPPDDPGLEarplGEE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  166 PLMAVVGNNHPYAGMGKIAPELLETQEVMMIEwkessDSYDSYYNLSSSWKQLGVEPASVVLFSkmeNLLTQLQIQES-- 243
Cdd:pfam03466  75 PLVLVAPPDHPLARGEPVSLEDLADEPLILLP-----PGSGLRDLLDRALRAAGLRPRVVLEVN---SLEALLQLVAAgl 146

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  244 -IALLPSYVAGNS--TGTIRFLELevePEKQPQMELVSVYH-EKQLNPAMIFLISALSDE 299
Cdd:pfam03466 147 gIALLPRSAVARElaDGRLVALPL---PEPPLPRELYLVWRkGRPLSPAVRAFIEFLREA 203
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-187 2.28e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.25  E-value: 2.28e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  81 HSRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWknkMEFEEP-VQE 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL---GPPPDPgLVA 157

                        170       180
                 ....*....|....*....|....*...
gi 503743559 160 QFVGCFPLMAVVGNNHPYAGMGKIAPEL 187
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLVNSL 185
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-296 2.37e-22

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 94.45  E-value: 2.37e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  81 HSRAVAFGNEgTIDIGFPSCVDSLVVMPRLQGFARRHPDihlniLLMDPVDLQHSLDNEMV---DLIVTWKNKMEFEEPV 157
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPD-----TLIELVSLITTQQEEKLrrgELDVGFMRHPVYSDEI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 158 QEQFVGCFPLMAVVGNNHPYAGMGKIAPELLETQEVMMIEWKESSdsydSYYNLSSSW-KQLGVEPASVVLFSKMENLLT 236
Cdd:PRK09906 155 DYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSG----SLAPIIKAWfAQHNSQPNIVQVATNILVTMN 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 237 QLQIQESIALLPSYVAGNSTGTIRFLELEVEpekQPQMELVSVYHEKQLNPAMIFLISAL 296
Cdd:PRK09906 231 LVGMGLGCTIIPGYMNNFNTGQVVFRPLAGN---VPSIALLMAWKKGEMKPALRDFIAIV 287
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-62 1.07e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.89  E-value: 1.07e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 503743559    7 RYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGR 62
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-299 9.34e-15

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: 71.55  E-value: 9.34e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   90 EGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTwknkmeFEEPVQEQFV----GCF 165
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR------RGPPDDPGLEarplGEE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  166 PLMAVVGNNHPYAGMGKIAPELLETQEVMMIEwkessDSYDSYYNLSSSWKQLGVEPASVVLFSkmeNLLTQLQIQES-- 243
Cdd:pfam03466  75 PLVLVAPPDHPLARGEPVSLEDLADEPLILLP-----PGSGLRDLLDRALRAAGLRPRVVLEVN---SLEALLQLVAAgl 146

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  244 -IALLPSYVAGNS--TGTIRFLELevePEKQPQMELVSVYH-EKQLNPAMIFLISALSDE 299
Cdd:pfam03466 147 gIALLPRSAVARElaDGRLVALPL---PEPPLPRELYLVWRkGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-296 2.07e-12

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: 64.93  E-value: 2.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTwknkmeFEEPVQEQFVGCF----PL 167
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIV------ALPVDDPGLESEPlfeePL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 168 MAVVGNNHPYAGMGKIAPELLETQEVMMiewkeSSDSYDSYYNLSSSWKQLGVEPASVVlfsKMENLLTQLQIQES---I 244
Cdd:cd05466   75 VLVVPPDHPLAKRKSVTLADLADEPLIL-----FERGSGLRRLLDRAFAEAGFTPNIAL---EVDSLEAIKALVAAglgI 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503743559 245 ALLP-SYVAGNSTGTIRFLELEvepEKQPQMELVSVYH-EKQLNPAMIFLISAL 296
Cdd:cd05466  147 ALLPeSAVEELADGGLVVLPLE---DPPLSRTIGLVWRkGRYLSPAARAFLELL 197
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-252 2.46e-06

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 47.17  E-value: 2.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWKNKmeFEEPVQEQFVGCFPLMAVV 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPV--DEEEFDSQPLCNEPLVAVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 172 GNNHPYAGMGKIAPELLETQEVMMiewkessdsYDSYYNLS----SSWKQLGVEPASVVLFSKMENLLTQLQIQESIALL 247
Cdd:cd08438   79 PRGHPLAGRKTVSLADLADEPFIL---------FNEDFALHdriiDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALL 149


                 ....*
gi 503743559 248 PSYVA 252
Cdd:cd08438  150 PRSIA 154
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-187 2.28e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.25  E-value: 2.28e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  81 HSRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWknkMEFEEP-VQE 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL---GPPPDPgLVA 157

                        170       180
                 ....*....|....*....|....*...
gi 503743559 160 QFVGCFPLMAVVGNNHPYAGMGKIAPEL 187
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLVNSL 185
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-296 2.37e-22

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 94.45  E-value: 2.37e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  81 HSRAVAFGNEgTIDIGFPSCVDSLVVMPRLQGFARRHPDihlniLLMDPVDLQHSLDNEMV---DLIVTWKNKMEFEEPV 157
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPD-----TLIELVSLITTQQEEKLrrgELDVGFMRHPVYSDEI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 158 QEQFVGCFPLMAVVGNNHPYAGMGKIAPELLETQEVMMIEWKESSdsydSYYNLSSSW-KQLGVEPASVVLFSKMENLLT 236
Cdd:PRK09906 155 DYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSG----SLAPIIKAWfAQHNSQPNIVQVATNILVTMN 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 237 QLQIQESIALLPSYVAGNSTGTIRFLELEVEpekQPQMELVSVYHEKQLNPAMIFLISAL 296
Cdd:PRK09906 231 LVGMGLGCTIIPGYMNNFNTGQVVFRPLAGN---VPSIALLMAWKKGEMKPALRDFIAIV 287
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-191 9.21e-22

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 92.71  E-value: 9.21e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVq 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGR- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  81 hsRA---VAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWknkmefeEPV 157
Cdd:PRK11242  80 --RAihdVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAF-------APV 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 503743559 158 QEQFVGCFPLMA-----VVGNNHPYAGMGK-IAPELLETQ 191
Cdd:PRK11242 151 HSPEIEAQPLFTetlalVVGRHHPLAARRKaLTLDELADE 190
PRK09986 PRK09986
LysR family transcriptional regulator;
1-296 5.38e-21

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 90.55  E-value: 5.38e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  81 HSRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDlIVTWKN-KMEFEEPVQE 159
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELD-AGIWRMaDLEPNPGFTS 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 160 QFVGCFPLMAVVGNNHPYAGMGKIAPELLETQEVMMIewkeSSDSYDSYYNLSSSWKQLGVEPASVVLFSKMENLLTQLQ 239
Cdd:PRK09986 166 RRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITL----PFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVS 241

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 503743559 240 IQESIALLPSYVAGNSTGTIRFLELevepEKQPQMELVSVYHEKQLNPAMIFLISAL 296
Cdd:PRK09986 242 MGIGITLLPDSYAQIPWPGVVFRPL----KERIPADLYAVYHPDQVTPALNKLLAAL 294
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-62 1.07e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.89  E-value: 1.07e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 503743559    7 RYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGR 62
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-120 2.45e-18

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 83.19  E-value: 2.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 503743559  81 HSRAVAFGNEGTIDIGF-PSCVDSLVVMPRLQGFARRHPDI 120
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLaPGTAASSLTMPLLQAVRAEFPGI 121
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-125 1.20e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 75.81  E-value: 1.20e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   9 FVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRavafG 88
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIK----N 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 503743559  89 NE--GTIDI-GFPSCVDSLVVmPRLQGFARRHPDIHLNIL 125
Cdd:PRK10086  98 QElsGTLTVySRPSIAQCWLV-PRLADFTRRYPSISLTIL 136
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-299 9.34e-15

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: 71.55  E-value: 9.34e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   90 EGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTwknkmeFEEPVQEQFV----GCF 165
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR------RGPPDDPGLEarplGEE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  166 PLMAVVGNNHPYAGMGKIAPELLETQEVMMIEwkessDSYDSYYNLSSSWKQLGVEPASVVLFSkmeNLLTQLQIQES-- 243
Cdd:pfam03466  75 PLVLVAPPDHPLARGEPVSLEDLADEPLILLP-----PGSGLRDLLDRALRAAGLRPRVVLEVN---SLEALLQLVAAgl 146

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  244 -IALLPSYVAGNS--TGTIRFLELevePEKQPQMELVSVYH-EKQLNPAMIFLISALSDE 299
Cdd:pfam03466 147 gIALLPRSAVARElaDGRLVALPL---PEPPLPRELYLVWRkGRPLSPAVRAFIEFLREA 203
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 7-132 1.85e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.18  E-value: 1.85e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   7 RYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQhsRAVA 86
Cdd:PRK11139  12 RAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATR--KLRA 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503743559  87 FGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNI--------LLMDPVDL 132
Cdd:PRK11139  90 RSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLkavdrledFLRDDVDV 143
rbcR CHL00180
LysR transcriptional regulator; Provisional
 11-188 8.42e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 67.35  E-value: 8.42e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  11 VAAEcQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRAVAFGNE 90
Cdd:CHL00180  16 IATE-GSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  91 GTIDIGfPSCVDSLVVMPRLQG-FARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVT-------WKNKMEFEEPVQEQfv 162
Cdd:CHL00180  95 GTLIIG-ASQTTGTYLMPRLIGlFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggevpteLKKILEITPYVEDE-- 171

                        170       180
                 ....*....|....*....|....*.
gi 503743559 163 gcfpLMAVVGNNHPYAGMGKIAPELL 188
Cdd:CHL00180 172 ----LALIIPKSHPFAKLKKIQKEDL 193
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-296 2.07e-12

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: 64.93  E-value: 2.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTwknkmeFEEPVQEQFVGCF----PL 167
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIV------ALPVDDPGLESEPlfeePL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 168 MAVVGNNHPYAGMGKIAPELLETQEVMMiewkeSSDSYDSYYNLSSSWKQLGVEPASVVlfsKMENLLTQLQIQES---I 244
Cdd:cd05466   75 VLVVPPDHPLAKRKSVTLADLADEPLIL-----FERGSGLRRLLDRAFAEAGFTPNIAL---EVDSLEAIKALVAAglgI 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503743559 245 ALLP-SYVAGNSTGTIRFLELEvepEKQPQMELVSVYH-EKQLNPAMIFLISAL 296
Cdd:cd05466  147 ALLPeSAVEELADGGLVVLPLE---DPPLSRTIGLVWRkGRYLSPAARAFLELL 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
15-251 3.27e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 63.11  E-value: 3.27e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  15 CQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGrdfyrhtKIMLSRFDKAV-QHSRAVAFGNEGT- 92
Cdd:PRK15421  16 CGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQG-------EILLQLANQVLpQISQALQACNEPQq 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  93 ----IDIGFPSCVDSLVvmPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTW----KNKMEFeEPVQEqfvgc 164
Cdd:PRK15421  89 trlrIAIECHSCIQWLT--PALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSdilpRSGLHY-SPMFD----- 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 165 FPLMAVVGNNHPYAGMGKIAPELLETQEVMMiewkessdsYDSYYNLSSSWKQLgVEPASVV-LFSKMENLLTQLQI--- 240
Cdd:PRK15421 161 YEVRLVLAPDHPLAAKTRITPEDLASETLLI---------YPVQRSRLDVWRHF-LQPAGVSpSLKSVDNTLLLIQMvaa 230

                        250
                 ....*....|.
gi 503743559 241 QESIALLPSYV 251
Cdd:PRK15421 231 RMGIAALPHWV 241
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-124 9.91e-11

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 61.54  E-value: 9.91e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQ 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 503743559  81 HSRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNI 124
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-197 6.95e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 58.89  E-value: 6.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRF----D 76
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVkvlkE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  77 KAVQHSRAVAfgneGTIDIGFPSCVDSLV---VMPRLQgfaRRHPDIHLNILLMDPVDLQHSLDNEMVDLIV--TWKNKM 151
Cdd:PRK11151  81 MASQQGETMS----GPLHIGLIPTVGPYLlphIIPMLH---QTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIlaLVKESE 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 503743559 152 EFEE-PVQEQfvgcfPLMAVVGNNHPYAGMGKIAPELLETQEVMMIE 197
Cdd:PRK11151 154 AFIEvPLFDE-----PMLLAVYEDHPWANRDRVPMSDLAGEKLLMLE 195
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
9-125 1.86e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.46  E-value: 1.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   9 FVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAvqHSRAVAFG 88
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDV--HEQLYAFN 87

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 503743559  89 NE--GTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNIL 125
Cdd:PRK10632  88 NTpiGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLV 126
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 18-124 2.88e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 56.87  E-value: 2.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  18 FTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRAVAFGNEGTIDIGf 97
Cdd:PRK11074  19 FSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQLSIA- 97

                         90       100       110
                 ....*....|....*....|....*....|.
gi 503743559  98 pscVDSLVVMPRLQG----FARRHPDIHLNI 124
Cdd:PRK11074  98 ---VDNIVRPDRTRQlivdFYRHFDDVELII 125
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-61 5.23e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 56.35  E-value: 5.23e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAG 61
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAG 62
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-124 8.74e-09

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 55.67  E-value: 8.74e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFV-VAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVT-LTPAGRDFYRHTKIMLSRfdka 78
Cdd:PRK12681   1 MKLQQLRYIVeVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSK---- 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 503743559  79 VQHSRAVA--FGNE--GTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNI 124
Cdd:PRK12681  77 VESIKSVAgeHTWPdkGSLYIATTHTQARYALPPVIKGFIERYPRVSLHM 126
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-146 1.05e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.42  E-value: 1.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLsRF-DKAv 79
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL-RFnDEA- 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503743559  80 qhSRAVAFGN-EGTIDIGFP-SCVDSLV---------VMPRLQGFARrhpdIHLNILLMDpvdlqhSLDNEMVDLIVT 146
Cdd:PRK15092  89 --CSSLMYSNlQGVLTIGASdDTADTILpfllnrvssVYPKLALDVR----VKRNAFMME------MLESQEVDLAVT 154
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-176 1.12e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 55.37  E-value: 1.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAEcQNF--TQAAEKCYISQTAMSQNMSKLEGTLGFELFRRE-KRHVTLTPAGRdfyrHTKIMLSRFDK 77
Cdd:PRK12684   1 MNLHQLRFVREAVR-QNFnlTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGR----IILASVERILQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  78 AVQHSRAVA--FGNE--GTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWKNKMEF 153
Cdd:PRK12684  76 EVENLKRVGkeFAAQdqGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADY 155

                        170       180
                 ....*....|....*....|....*...
gi 503743559 154 EEPVqeqfvgCFPL-----MAVVGNNHP 176
Cdd:PRK12684 156 KELV------SLPCyqwnhCVVVPPDHP 177
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-188 1.53e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 55.00  E-value: 1.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQ-NFTQAAEKCYISQTAMSQNMSKLEGTLGFELF-RREKRHVTLTPAGRDFYRHTKIMLsrfdKA 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFiRHGKRLKGLTEPGKAVLDVIERIL----RE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  79 VQHSRAVA--FGN--EGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDL-IVTwknkmef 153
Cdd:PRK12682  77 VGNIKRIGddFSNqdSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIgIAT------- 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 503743559 154 EEPVQEQFVGCFP-----LMAVVGNNHPYAGMGKIAPELL 188
Cdd:PRK12682 150 ESLADDPDLATLPcydwqHAVIVPPDHPLAQEERITLEDL 189
PRK12680 PRK12680
LysR family transcriptional regulator;
1-227 3.47e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 53.86  E-value: 3.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQ-NFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHV-TLTPAGRDFYRHTKIMLSRFDKA 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  79 VQHSRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIhlnillmdPVDLQHSLDNEMVDLIVTWKNKMEF----- 153
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQV--------SVHLQQAAESAALDLLGQGDADIAIvstag 152

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503743559 154 EEPVQEQFVgcfPL-----MAVVGNNHPYAGMGKiAPELLETQEVMMIEWKESSDSYDSyynLSSSWKQLGVEPaSVVL 227
Cdd:PRK12680 153 GEPSAGIAV---PLyrwrrLVVVPRGHALDTPRR-APDMAALAEHPLISYESSTRPGSS---LQRAFAQLGLEP-SIAL 223
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-288 6.57e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 51.74  E-value: 6.57e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDL-IVTWKnkmEFEEPVQEQFVGCFPLMAV 170
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVgFVRPP---PDPPGLASRPLLREPLVVA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 171 VGNNHPYAGMGKIAPELLETQEVMMIEWKESSDSYDSYYNLSsswKQLGVEPASVVLFSKMENLLTQLQIQESIALLPSY 250
Cdd:cd08414   78 LPADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALC---RRAGFTPRIVQEASDLQTLLALVAAGLGVALVPAS 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 503743559 251 VAGNSTGTIRFLELEvepEKQPQMELVSVYHEKQLNPA 288
Cdd:cd08414  155 VARLQRPGVVYRPLA---DPPPRSELALAWRRDNASPA 189
PRK09791 PRK09791
LysR family transcriptional regulator;
7-226 8.17e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 52.84  E-value: 8.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   7 RYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRAVA 86
Cdd:PRK09791  11 RAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  87 FGNEGTIDIGFPSCVdSLVVMPR-LQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIV------TWKNKMEFEEPVQE 159
Cdd:PRK09791  91 GQLAGQINIGMGASI-ARSLMPAvISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyyqgPYDHEFTFEKLLEK 169

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503743559 160 QFVgcfplmAVVGNNHPYAGMGKIApelletqEVMMIEWKESSDSYDSYYNLSSSWKQLGVEPA-SVV 226
Cdd:PRK09791 170 QFA------VFCRPGHPAIGARSLK-------QLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQvGVV 224
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-122 9.30e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.35  E-value: 9.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   1 MDLQIYRYFVVAAECQ-NFTQAAEKCYISQTAMSQNMSKLEGTLGFELF-RREKRHVTLTPAGRDFYRHTKIMLSRFDKA 78
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFiRRGKRLTGLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 503743559  79 VQHSRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHL 122
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHL 124
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-143 7.66e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.43  E-value: 7.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  25 CYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRAVAFGNEGTIDIgFPSCVDSL 104
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSL-FCSVTAAY 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 503743559 105 VVMPR-LQGFARRHPDIHLNILLMDPVD-LQHSLDNEmVDL 143
Cdd:PRK11716  80 SHLPPiLDRFRAEHPLVEIKLTTGDAADaVEKVQSGE-ADL 119
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-137 9.60e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.20  E-value: 9.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   9 FVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREkRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRAvafG 88
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLSTLPA---E 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 503743559  89 NEGTIDIGFPSCVDSLVV--MPRLQGFARRHpdihlNILLMDPVDLQ-HSLD 137
Cdd:PRK13348  86 RGSPPTLAIAVNADSLATwfLPALAAVLAGE-----RILLELIVDDQdHTFA 132
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-83 1.65e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 48.90  E-value: 1.65e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503743559   9 FVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSR 83
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELR 93
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-252 2.46e-06

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 47.17  E-value: 2.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWKNKmeFEEPVQEQFVGCFPLMAVV 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPV--DEEEFDSQPLCNEPLVAVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 172 GNNHPYAGMGKIAPELLETQEVMMiewkessdsYDSYYNLS----SSWKQLGVEPASVVLFSKMENLLTQLQIQESIALL 247
Cdd:cd08438   79 PRGHPLAGRKTVSLADLADEPFIL---------FNEDFALHdriiDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALL 149


                 ....*
gi 503743559 248 PSYVA 252
Cdd:cd08438  150 PRSIA 154
PRK09801 PRK09801
LysR family transcriptional regulator;
2-142 2.82e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.11  E-value: 2.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559   2 DLQIyryFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQH 81
Cdd:PRK09801  10 DLQV---LVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDD 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503743559  82 SRAVAFGNEGTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNI--------LLMDPVDLQHSLDNEMVD 142
Cdd:PRK09801  87 VTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFelfdrqidLVQDNIDLDIRINDEIPD 155
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-61 6.66e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 46.55  E-value: 6.66e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503743559   1 MDLQIYRYFVVAAECQNFTQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAG 61
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 106-197 1.92e-05

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 44.44  E-value: 1.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 106 VMPRLQgfaRRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTwknKMEFEEP-VQEQFVGCFPLMAVVGNNHPYAGMGKIA 184
Cdd:cd08411   19 LLPALR---QAYPKLRLYLREDQTERLLEKLRSGELDAALL---ALPVDEPgLEEEPLFDEPFLLAVPKDHPLAKRKSVT 92

                         90
                 ....*....|...
gi 503743559 185 PELLETQEVMMIE 197
Cdd:cd08411   93 PEDLAGERLLLLE 105
PRK10341 PRK10341
transcriptional regulator TdcA;
21-124 6.19e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 44.08  E-value: 6.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  21 AAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRAVAFGNEGTIDIGFPSC 100
Cdd:PRK10341  27 AAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVVDVSFGFPSL 106

                         90       100
                 ....*....|....*....|....
gi 503743559 101 VDSLVVMPRLQGFARRHPDIHLNI 124
Cdd:PRK10341 107 IGFTFMSDMINKFKEVFPKAQVSM 130
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-296 8.97e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 42.64  E-value: 8.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWKNKMEFEEPVQEQFVGCFPLMAVV 171
Cdd:cd08449    1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPPLASELLWREPMVVAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 172 GNNHPYAGMGKIAPELLETQEVMMIEwKESSDSYDSYYNL------SSSWKQLGVEPASVvlfskMENLLTQLQiqesIA 245
Cdd:cd08449   81 PEEHPLAGRKSLTLADLRDEPFVFLR-LANSRFADFLINCclqagfTPQITQEVVEPQTL-----MALVAAGFG----VA 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 503743559 246 LLPSYVAGNSTGTIRFLELevepeKQ-PQMELVSVYHEKQLNPAMIFLISAL 296
Cdd:cd08449  151 LVPESYARLPWPGVRFIPL-----KQaISADLYAVYHPDSATPVIQAFLALL 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-144 1.42e-04

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: 42.06  E-value: 1.42e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503743559  91 GTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNIllmdpvdlqhSLDNEMVDLI 144
Cdd:cd08474    3 GTLRINAPRVAARLLLAPLLARFLARYPDIRLEL----------VVDDGLVDIV 46
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-144 1.89e-04

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: 41.66  E-value: 1.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503743559  91 GTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNIllmdpvdlqhSLDNEMVDLI 144
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLEL----------VLSDRLVDLV 44
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 19-122 1.95e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 42.37  E-value: 1.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  19 TQAAEKCYISQTAMSQNMSKLEGTLGFELFRREKRHVTLTPAGRDFYRHTKIMLSRFDKAVQHSRavafGNEGTIDIGFP 98
Cdd:PRK10837  21 TQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLFR----EDNGALRIYAS 96

                         90       100
                 ....*....|....*....|....
gi 503743559  99 SCVDSLVVMPRLQGFARRHPDIHL 122
Cdd:PRK10837  97 STIGNYILPAMIARYRRDYPQLPL 120
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-222 2.63e-04

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 41.38  E-value: 2.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGfpsCVDSL--VVMPRL-QGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTWknKMEFEEPVQEQFVGCFPLM 168
Cdd:cd08412    1 TLRIG---CFSTLapYYLPGLlRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTY--DLDLPEDIAFEPLARLPPY 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503743559 169 AVVGNNHPYAGMGKIAPELLETQEVMMIEWKESSDSYDSYynlsssWKQLGVEP 222
Cdd:cd08412   76 VWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFLSL------FAAAGLTP 123
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-62 3.46e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 41.72  E-value: 3.46e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503743559   1 MDLQIYRYFVVAAECQ-NFTQAAEKCYISQTAMSQNMSKLEGTLGFELF-RREKRHVTLTPAGR 62
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGK 64
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 107-134 4.45e-04

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: 40.64  E-value: 4.45e-04
                         10        20
                 ....*....|....*....|....*....
gi 503743559 107 MPRLQGFARRHPDIHLNIL-LMDPVDLQH 134
Cdd:cd08432   16 IPRLARFQARHPDIDLRLStSDRLVDFAR 44
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-188 6.43e-04

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 39.89  E-value: 6.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  92 TIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDL-IVTWKNkmEFEEPVQEQFVGCFPLMAV 170
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLaFVGLPE--RRPPGLASRELAREPLVAV 78

                         90
                 ....*....|....*...
gi 503743559 171 VGNNHPYAGMGKIAPELL 188
Cdd:cd08436   79 VAPDHPLAGRRRVALADL 96
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 93-299 7.87e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 40.03  E-value: 7.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  93 IDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDL-IVTWKNKMEFEEPVQEqfvgcfPLMA-- 169
Cdd:cd08418    2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFaIGTLPDEMYLKELISE------PLFEsd 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559 170 ---VVGNNHPYAGMGKIaPELLETQEVMmiewKESSDSYdsYYNLSSSWKQLGVEPASVVLFSKMENLLTQLQIQESIAL 246
Cdd:cd08418   76 fvvVARKDHPLQGARSL-EELLDASWVL----PGTRMGY--YNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTI 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503743559 247 LPSYVAGNSTGTIRFLELEVEpEKQPQMELVSVYHEK-QLNPAMIFLISALSDE 299
Cdd:cd08418  149 LSRDMGRGPLDSFRLITIPVE-EPLPSADYYLIYRKKsRLTPLAEQLVELFRRY 201
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-132 1.08e-03

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: 39.42  E-value: 1.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 503743559  91 GTIDIGFPSCVDSLVVMPRLQGFARRHPDIHLNILLMD-PVDL 132
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDrPVDL 43
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 107-137 1.96e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 38.43  E-value: 1.96e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 503743559 107 MPRLQGFARRHPDIHLNILL-MDPVDLQH-SLD 137
Cdd:cd08481   16 IPRLPDFLARHPDITVNLVTrDEPFDFSQgSFD 48
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 98-189 5.36e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 37.16  E-value: 5.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503743559  98 PSCvdSLVVMPR-LQGFARRHPDIHLNILLMDPVDLQHSLDNEMVDLIVTwknKMEFEEP-VQEQFVGCFPLMAVVGNNH 175
Cdd:cd08415    8 PAL--ALSLLPRaIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLA---SLPLDHPgLESEPLASGRAVCVLPPGH 82

                         90
                 ....*....|....
gi 503743559 176 PYAGMGKIAPELLE 189
Cdd:cd08415   83 PLARKDVVTPADLA 96
 
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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