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Conserved domains on  [gi|2067186253|dbj|GJA84187|]
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LysR family transcriptional regulator [Aeromonas caviae]

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];
1-289 2.28e-48

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.57  E-value: 2.28e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKL 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  81 KCEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFglITEEQERSGLCID 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI--RLGPPPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 161 VLNPIRTLMVVAPSHPLAGLKRVlqqdltdhtqvtlsyvdafsvksllpiggqhigLSSFELMRDAVLDGLGWAVLPSPL 240
Cdd:COG0583   159 PLGEERLVLVASPDHPLARRAPL---------------------------------VNSLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2067186253 241 IQSQLRLGELLTLKHKFSLQWRDYGVYLSENAHHGKVLAWLKKAIEAYL 289
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-289 2.28e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.57  E-value: 2.28e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKL 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  81 KCEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFglITEEQERSGLCID 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI--RLGPPPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 161 VLNPIRTLMVVAPSHPLAGLKRVlqqdltdhtqvtlsyvdafsvksllpiggqhigLSSFELMRDAVLDGLGWAVLPSPL 240
Cdd:COG0583   159 PLGEERLVLVASPDHPLARRAPL---------------------------------VNSLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2067186253 241 IQSQLRLGELLTLKHKFSLQWRDYGVYLSENAHHGKVLAWLKKAIEAYL 289
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-292 1.59e-23

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 97.57  E-value: 1.59e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   6 IQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKLKCEHH 85
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  86 ASGAEVALRVARDDAI--PEVVWReMLGALRRQFPGTSISLVLASPPEL-PALVEEGFvDAAFGLITEEQERSGLCIDVL 162
Cdd:PRK10094   87 NDGVERQVNIVINNLLynPQAVAQ-LLAWLNERYPFTQFHISRQIYMGVwDSLLYEGF-SLAIGVTGTEALANTFSLDPL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 163 NPIRTLMVVAPSHPLAGLKRVLQQDL--------TDHTQVTLSYVDAFsvksLLPigGQH-IGLSSFELMRDAVLDGLGW 233
Cdd:PRK10094  165 GSVQWRFVMAADHPLANVEEPLTEAQlrrfpavnIEDSARTLTKRVAW----RLP--GQKeIIVPDMETKIAAHLAGVGI 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2067186253 234 AVLPSPLIQSQLRLGELL--TLKHK-----FSLQWRdygvylseNAHHGKVLAWLKK-------AIEAYLEPF 292
Cdd:PRK10094  239 GFLPKSLCQSMIDNQQLVsrVIPTMrppspLSLAWR--------KFGSGKAVEDIVTlftqrrpEISGFLEIF 303
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-289 2.72e-19

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: 83.88  E-value: 2.72e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  93 LRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFglITEEQERSGLCIDVLNPIRTLMVVA 172
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI--RRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 173 PSHPLAGLKRVLQQDLTDHTQVTLSY--------VDAFSVKSLLPIGGQHIglSSFELMRDAVLDGLGWAVLPSPLIQSQ 244
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPgsglrdllDRALRAAGLRPRVVLEV--NSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2067186253 245 LRLGELLTLKHKFSLQWRDYGVYLSENAHHGKVLAWLKKAIEAYL 289
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 108-281 2.53e-13

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 67.24  E-value: 2.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQD 187
Cdd:cd05466    17 PLLAAFRQRYPGVELSLVEGGSSELLEALLEGELD--LAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLAD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 188 LTDHTQVTLSyvDAFSVKSLLPIGGQHIGL--------SSFELMRDAVLDGLGWAVLPSPLIQsQLRLGELLTLKHKFSL 259
Cdd:cd05466    95 LADEPLILFE--RGSGLRRLLDRAFAEAGFtpnialevDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLPLEDPP 171

                         170       180
                  ....*....|....*....|..
gi 2067186253 260 QWRDYGVYLSENAHHGKVLAWL 281
Cdd:cd05466   172 LSRTIGLVWRKGRYLSPAARAF 193
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-289 2.28e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.57  E-value: 2.28e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKL 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  81 KCEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFglITEEQERSGLCID 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI--RLGPPPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 161 VLNPIRTLMVVAPSHPLAGLKRVlqqdltdhtqvtlsyvdafsvksllpiggqhigLSSFELMRDAVLDGLGWAVLPSPL 240
Cdd:COG0583   159 PLGEERLVLVASPDHPLARRAPL---------------------------------VNSLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2067186253 241 IQSQLRLGELLTLKHKFSLQWRDYGVYLSENAHHGKVLAWLKKAIEAYL 289
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-292 1.59e-23

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 97.57  E-value: 1.59e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   6 IQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKLKCEHH 85
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  86 ASGAEVALRVARDDAI--PEVVWReMLGALRRQFPGTSISLVLASPPEL-PALVEEGFvDAAFGLITEEQERSGLCIDVL 162
Cdd:PRK10094   87 NDGVERQVNIVINNLLynPQAVAQ-LLAWLNERYPFTQFHISRQIYMGVwDSLLYEGF-SLAIGVTGTEALANTFSLDPL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 163 NPIRTLMVVAPSHPLAGLKRVLQQDL--------TDHTQVTLSYVDAFsvksLLPigGQH-IGLSSFELMRDAVLDGLGW 233
Cdd:PRK10094  165 GSVQWRFVMAADHPLANVEEPLTEAQlrrfpavnIEDSARTLTKRVAW----RLP--GQKeIIVPDMETKIAAHLAGVGI 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2067186253 234 AVLPSPLIQSQLRLGELL--TLKHK-----FSLQWRdygvylseNAHHGKVLAWLKK-------AIEAYLEPF 292
Cdd:PRK10094  239 GFLPKSLCQSMIDNQQLVsrVIPTMrppspLSLAWR--------KFGSGKAVEDIVTlftqrrpEISGFLEIF 303
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-209 2.09e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 86.20  E-value: 2.09e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSG-SIANAARRLGKSRSAVSSAIATLEVELGVELFER-GTNQSRLTEIGEQVLDDCRRLLQAANSL 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  79 KLKCEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSglc 158
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEAD--IGIATESLADD--- 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2067186253 159 idvlNPIRTL--------MVVAPSHPLAGLKRVLQQDLTDHTQVTL-------SYVD-AFSVKSLLP 209
Cdd:PRK12682  156 ----PDLATLpcydwqhaVIVPPDHPLAQEERITLEDLAEYPLITYhpgftgrSRIDrAFAAAGLQP 218
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-289 2.72e-19

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: 83.88  E-value: 2.72e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  93 LRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFglITEEQERSGLCIDVLNPIRTLMVVA 172
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI--RRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 173 PSHPLAGLKRVLQQDLTDHTQVTLSY--------VDAFSVKSLLPIGGQHIglSSFELMRDAVLDGLGWAVLPSPLIQSQ 244
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPgsglrdllDRALRAAGLRPRVVLEV--NSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2067186253 245 LRLGELLTLKHKFSLQWRDYGVYLSENAHHGKVLAWLKKAIEAYL 289
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.11e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.11e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   3 LNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-254 2.84e-16

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 77.04  E-value: 2.84e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   3 LNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAAnslkLKC 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQA----VEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  83 EHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLIteeqerSGLC---- 158
Cdd:PRK10837   81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVD--IGLI------EGPChspe 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 159 IDVLNPIRTLMVV--APSHPLAGLKRVLQQ------DLTDHTQVTLSYVDaFSVKSLLPigGQHIG--LSSFELMRDAVL 228
Cdd:PRK10837  153 LISEPWLEDELVVfaAPDSPLARGPVTLEQlaaapwILRERGSGTREIVD-YLLLSHLP--RFELAmeLGNSEAIKHAVR 229

                         250       260
                  ....*....|....*....|....*.
gi 2067186253 229 DGLGWAVLPSPLIQSQLRLGELLTLK 254
Cdd:PRK10837  230 HGLGISCLSRRVIADQLQAGTLVEVA 255
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-208 7.30e-15

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 73.47  E-value: 7.30e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSG-SIANAARRLGKSRSAVSSAIATLEVELGVELFER-GTNQSRLTEIGEQVLDDCRRLLQAANSL 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  79 KLKCEHHASGAEVALRVARDD-----AIPEVVwremlGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITE--E 151
Cdd:PRK12684   81 KRVGKEFAAQDQGNLTIATTHtqaryALPAAI-----KEFKKRYPKVRLSILQGSPTQIAEMVLHGQAD--LAIATEaiA 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2067186253 152 QERSGLCIDVLNPIRTLmVVAPSHPLAGLKRVLQQDLTDHTQVTlsYVDAFSVKSLL 208
Cdd:PRK12684  154 DYKELVSLPCYQWNHCV-VVPPDHPLLERKPLTLEDLAQYPLIT--YDFAFAGRSKI 207
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-195 8.57e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 73.15  E-value: 8.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSG-SIANAARRLGKSRSAVSSAIATLEVELGVELFER-GTNQSRLTEIGEQVLDDCRRLLQAANSL 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  79 KLKCEHHASGAEVALRVARDD-----AIPEVVwremlGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQE 153
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVATTHtqaryALPKVV-----RQFKEVFPKVHLALRQGSPQEIAEMLLNGEAD--IGIATEALD 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2067186253 154 RS-GLcidVLNPIRT---LMVVAPSHPLAGLKRVLQQDLTDHTQVT 195
Cdd:PRK12683  154 REpDL---VSFPYYSwhhVVVVPKGHPLTGRENLTLEAIAEYPIIT 196
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-217 1.13e-14

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 73.01  E-value: 1.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSG-SIANAARRLGKSRSAVSSAIATLEVELGVELFER-GTNQSRLTEIGEQVLDDCRRLLQAANSL 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARsGKHLTQVTPAGEEIIRIAREILSKVESI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  79 KLKCEHHASGAEVALRVARDD-----AIPEVVWRemlgaLRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQE 153
Cdd:PRK12681   81 KSVAGEHTWPDKGSLYIATTHtqaryALPPVIKG-----FIERYPRVSLHMHQGSPTQIAEAAAKGNAD--FAIATEALH 153

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067186253 154 rsgLCID-VLNPI----RTLmVVAPSHPLAGLKRVLQQDLTDHTQVTlsYVDAFSVKSLLPIGGQHIGL 217
Cdd:PRK12681  154 ---LYDDlIMLPCyhwnRSV-VVPPDHPLAKKKKLTIEELAQYPLVT--YVFGFTGRSELDTAFNRAGL 216
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 108-281 2.53e-13

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 67.24  E-value: 2.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQD 187
Cdd:cd05466    17 PLLAAFRQRYPGVELSLVEGGSSELLEALLEGELD--LAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLAD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 188 LTDHTQVTLSyvDAFSVKSLLPIGGQHIGL--------SSFELMRDAVLDGLGWAVLPSPLIQsQLRLGELLTLKHKFSL 259
Cdd:cd05466    95 LADEPLILFE--RGSGLRRLLDRAFAEAGFtpnialevDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLPLEDPP 171

                         170       180
                  ....*....|....*....|..
gi 2067186253 260 QWRDYGVYLSENAHHGKVLAWL 281
Cdd:cd05466   172 LSRTIGLVWRKGRYLSPAARAF 193
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
2-134 1.31e-12

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 66.71  E-value: 1.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   2 KLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKLK 81
Cdd:PRK10632    3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQ 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2067186253  82 CEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASP-PELPA 134
Cdd:PRK10632   83 LYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPaPDLIA 136
PRK09986 PRK09986
LysR family transcriptional regulator;
3-201 3.90e-12

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 65.13  E-value: 3.90e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   3 LNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKLKC 82
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  83 EHHASGAEVALRVArddAIPEVVWREMLGALRR---QFPGTSISLVLASPPELPALVEEGFVDAAFGLITEEQERSGLCI 159
Cdd:PRK09986   89 EQIGRGEAGRIEIG---IVGTALWGRLRPAMRHflkENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTS 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2067186253 160 DVLNPIRTLMVVAPSHPLAGLKRVLQQDLTDHTQVTLSYVDA 201
Cdd:PRK09986  166 RRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHS 207
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
14-252 1.22e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 64.27  E-value: 1.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  14 DSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGE-------QVLDDCRRLLQAANS-----LKLK 81
Cdd:PRK15421   15 NCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEillqlanQVLPQISQALQACNEpqqtrLRIA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  82 CEHHASgaevalrvarddaipeVVW-REMLGALRRQFPGTSI---SLVLASPPelPALvEEGFVDAAfgLITEEQERSGL 157
Cdd:PRK15421   95 IECHSC----------------IQWlTPALENFHKNWPQVEMdfkSGVTFDPQ--PAL-QQGELDLV--MTSDILPRSGL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 158 CIDVLNPIRTLMVVAPSHPLAGLKRVLQQDLTDHT----QVTLSYVDAFsvKSLLPIGGQHIGLSSFE---LMRDAVLDG 230
Cdd:PRK15421  154 HYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETlliyPVQRSRLDVW--RHFLQPAGVSPSLKSVDntlLLIQMVAAR 231

                         250       260
                  ....*....|....*....|..
gi 2067186253 231 LGWAVLPSPLIQSQLRLGELLT 252
Cdd:PRK15421  232 MGIAALPHWVVESFERQGLVVT 253
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-271 1.65e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 63.50  E-value: 1.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   3 LNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLL-------QAA 75
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILalceetcRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  76 NSLKlkcehhaSGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAF--GLITEEQE 153
Cdd:CHL00180   87 EDLK-------NLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIvgGEVPTELK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 154 RSgLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQDLTDHTQVTL---SYVDAFSVKSLLPIGGQ------HIGLSSFELMR 224
Cdd:CHL00180  160 KI-LEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLdsnSTIRKVIDNILIQNGIDskrfkiEMELNSIEAIK 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2067186253 225 DAVLDGLGWAVLPSPLIQSQLRLG-------ELLTLKHKFSL--QWRDYGVYLSEN 271
Cdd:CHL00180  239 NAVQSGLGAAFVSVSAIEKELELGllhwikiENITIKRMLSIitNPNRYKSKASET 294
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 108-262 5.15e-11

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 60.58  E-value: 5.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQD 187
Cdd:cd08420    17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEID--LGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 188 LTDHTQV-------TLSYVDAFSVKSLLPIGGQHIG--LSSFELMRDAVLDGLGWAVLPSPLIQSQLRLGEL-------L 251
Cdd:cd08420    95 LAAEPWIlrepgsgTREVFERALAEAGLDGLDLNIVmeLGSTEAIKEAVEAGLGISILSRLAVRKELELGRLvalpvegL 174

                         170
                  ....*....|.
gi 2067186253 252 TLKHKFSLQWR 262
Cdd:cd08420   175 RLTRPFSLIYH 185
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-264 2.67e-10

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: 58.77  E-value: 2.67e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFgLITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQD 187
Cdd:cd08436    17 ELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAF-VGLPERRPPGLASRELAREPLVAVVAPDHPLAGRRRVALAD 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 188 LTDHTQVTLSY-------VD-AFSVKSLlpigGQHIGL--SSFELMRDAVLDGLGWAVLPSPLIQsqlRLGELLTLKHKF 257
Cdd:cd08436    96 LADEPFVDFPPgtgarrqVDrAFAAAGV----RRRVAFevSDVDLLLDLVARGLGVALLPASVAA---RLPGLAALPLEP 168


                  ....*..
gi 2067186253 258 SLQWRDY 264
Cdd:cd08436   169 APRRRLY 175
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-253 5.98e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 58.85  E-value: 5.98e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKL 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  81 KCEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGtsISLVLASPPELPALVEEGfVDAAFGLITEEQERSGLCID 160
Cdd:PRK14997   82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPD--VSLQLEATNRRVDVVGEG-VDVAIRVRPRPFEDSDLVMR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 161 VLNPIRTLMVVAPShplaglkrVLQQDLTDHTQVTLSYVDAFSVKSllpigGQHIglSSFEL------------------ 222
Cdd:PRK14997  159 VLADRGHRLFASPD--------LIARMGIPSAPAELSHWPGLSLAS-----GKHI--HRWELygpqgaraevhftprmit 223

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 2067186253 223 -----MRDAVLDGLGWAVLPSPLIQSQLRLGELLTL 253
Cdd:PRK14997  224 tdmlaLREAAMAGVGLVQLPVLMVKEQLAAGELVAV 259
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-187 1.64e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 57.64  E-value: 1.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  13 ADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKLKCEHHASGAEVA 92
Cdd:PRK11074   14 ARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQ 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  93 LRVARDDAIPEVVWREMLGALRRQFPgtSISLVLAspPEL-----PALVeEGFVDAAFGLITeeqersglCIDV------ 161
Cdd:PRK11074   94 LSIAVDNIVRPDRTRQLIVDFYRHFD--DVELIIR--QEVfngvwDALA-DGRVDIAIGATR--------AIPVggrfaf 160

                         170       180
                  ....*....|....*....|....*...
gi 2067186253 162 --LNPIRTLMVVAPSHPLAGLKRVLQQD 187
Cdd:PRK11074  161 rdMGMLSWACVVSSDHPLASMDGPLSDD 188
PRK10341 PRK10341
transcriptional regulator TdcA;
2-151 3.57e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 56.79  E-value: 3.57e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   2 KLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDdcrRLLQAANSLK-- 79
Cdd:PRK10341    8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS---RSESITREMKnm 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2067186253  80 ---LKCEHHASGAEVALrvARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLITEE 151
Cdd:PRK10341   85 vneINGMSSEAVVDVSF--GFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNE 157
PRK09791 PRK09791
LysR family transcriptional regulator;
1-99 1.63e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 54.77  E-value: 1.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLddcrrllqaanslkl 80
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFY--------------- 69

                          90
                  ....*....|....*....
gi 2067186253  81 kceHHASGAEVALRVARDD 99
Cdd:PRK09791   70 ---QHASLILEELRAAQED 85
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 112-202 2.90e-08

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: 52.56  E-value: 2.90e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 112 ALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQDLTDH 191
Cdd:cd08415    21 RFRARHPDVRISLHTLSSSTVVEAVLSGQAD--LGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPADLAGE 98

                          90
                  ....*....|.
gi 2067186253 192 TQVTLSYVDAF 202
Cdd:cd08415    99 PLISLGRGDPL 109
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 93-285 4.25e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 52.27  E-value: 4.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  93 LRVARDDAIPEVVWREMLGALRRQFPGTSISL---VLASPPElpALVEeGFVDAAFGlITEEQERSGLCIDVLNPIRTLM 169
Cdd:cd08431     2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLseeVLGGTWD--ALAS-GRADLVIG-ATGELPPGGVKTRPLGEVEFVF 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 170 VVAPSHPLAGLKRVLQ-QDLTDHtqvtLSYVDAFSVKSLLPI------GGQHIGLSSFELMRDAVLDGLGWAVLPSPLIQ 242
Cdd:cd08431    78 AVAPNHPLAKLDGPLDaSAIKQY----PAIVVADTSRNLPPRssglleGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAK 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2067186253 243 SQLRLGELLTLK-------HKFSLQWRdygvylseNAHHGKVLAWLKKAI 285
Cdd:cd08431   154 PELASGELVEKAledprppQELFLAWR--------KDQRGKALAWFVQRL 195
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 108-281 9.36e-08

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: 51.40  E-value: 9.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLITEEQERsglcIDVLnPIRT--LMVVAP-SHPLAGLKRVL 184
Cdd:cd08438    17 PLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEE----FDSQ-PLCNepLVAVLPrGHPLAGRKTVS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 185 QQDLTDHTQVTlsYVDAFSVKSLLPIGGQHIGL--------SSFELMRDAVLDGLGWAVLPSPLIQSQLRLGELLTLKHK 256
Cdd:cd08438    92 LADLADEPFIL--FNEDFALHDRIIDACQQAGFtpniaarsSQWDFIAELVAAGLGVALLPRSIAQRLDNAGVKVIPLTD 169

                         170       180       190
                  ....*....|....*....|....*....|
gi 2067186253 257 FSLQWR-----DYGVYLSENAHhgkvlAWL 281
Cdd:cd08438   170 PDLRWQlaliwRKGRYLSHAAR-----AWL 194
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-209 1.29e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 52.12  E-value: 1.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSG-SIANAARRLGKSRSAVSSAIATLEVELGVELF-ERGTNQSRLTEIGEQVLDDCRRLLQAANSL 78
Cdd:PRK12679    1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  79 KLKCEHHASGAEVALRVARDD-----AIPEVVwremlGALRRQFPGTSISLVLASPPELPALVEEGFVDAAfglITEEQE 153
Cdd:PRK12679   81 RRLADLFTNDTSGVLTIATTHtqarySLPEVI-----KAFRELFPEVRLELIQGTPQEIATLLQNGEADIG---IASERL 152

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2067186253 154 RSGLCIDVLNPIR--TLMVVAPSHPLAGLKRVLQQDLTDHTQVTL-------SYVD-AFSVKSLLP 209
Cdd:PRK12679  153 SNDPQLVAFPWFRwhHSLLVPHDHPLTQITPLTLESIAKWPLITYrqgitgrSRIDdAFARKGLLA 218
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 109-253 4.22e-07

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 49.43  E-value: 4.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 109 MLGALRRQFPGTSISLVLASPPELPALVEEGFVD-AAFGLITEEQE-RSGLCIDvlNPIrtLMVVAPSHPLAGLKRVLQQ 186
Cdd:cd08419    17 LLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDlAIMGRPPEDLDlVAEPFLD--NPL--VVIAPPDHPLAGQKRIPLE 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2067186253 187 DLTDHTQV-------TLSYVDAFSVKSLLPIggqHIG--LSSFELMRDAVLDGLGWAVLPSPLIQSQLRLGELLTL 253
Cdd:cd08419    93 RLAREPFLlrepgsgTRLAMERFFAEHGVTL---RVRmeLGSNEAIKQAVMAGLGLSVLSLHTLALELATGRLAVL 165
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-194 4.67e-07

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 49.19  E-value: 4.67e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  92 ALRVARDDAIPEVvwremLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLITEEQERSGLCIDVLNPIRTLMVV 171
Cdd:cd08435     6 AVPAAAPVLLPPA-----IARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVA 80

                          90       100
                  ....*....|....*....|...
gi 2067186253 172 APSHPLAGLKRVLQQDLTDHTQV 194
Cdd:cd08435    81 RPGHPLARRARLTLADLADYPWV 103
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-197 5.32e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 49.95  E-value: 5.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLKL 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  81 KCEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLI---TEEQERSGL 157
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFApvhSPEIEAQPL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2067186253 158 CIDVLNpirtlMVVAPSHPLAGLKRVLQ-QDLTDHTQVTLS 197
Cdd:PRK11242  161 FTETLA-----LVVGRHHPLAARRKALTlDELADEPLVLLS 196
PRK12680 PRK12680
LysR family transcriptional regulator;
1-236 6.85e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 50.01  E-value: 6.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSG-SIANAARRLGKSRSAVSSAIATLEVELGVELFER-GTNQSRLTEIGEQVLDDCRRLLQAANSL 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRkGRSLESVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  79 KLKCEHHASGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLITEEQERSGLC 158
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 159 IDvLNPIRTLMVVAPSHPLAGLKRVLQ-QDLTDH--------TQVTLSYVDAFSVKSLLPiggqHIGLSSF--ELMRDAV 227
Cdd:PRK12680  161 VP-LYRWRRLVVVPRGHALDTPRRAPDmAALAEHplisyessTRPGSSLQRAFAQLGLEP----SIALTALdaDLIKTYV 235


                  ....*....
gi 2067186253 228 LDGLGWAVL 236
Cdd:PRK12680  236 RAGLGVGLL 244
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-65 8.01e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 49.62  E-value: 8.01e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067186253   2 KLNQIQL-----FVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVL 65
Cdd:PRK10086   10 LLNGWQLsklhtFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF 78
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-259 2.73e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 48.04  E-value: 2.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   5 QIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNqSRLTEIGEQVLDDCR--RLLQAANSLKLKC 82
Cdd:PRK13348    6 QLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRqvALLEADLLSTLPA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  83 EHHASgaeVALRVA-RDDAIpeVVWreMLGALRRQFPGTSISLVLASPPE---LPALvEEGFVDAAfgLITEEQERSGLC 158
Cdd:PRK13348   85 ERGSP---PTLAIAvNADSL--ATW--FLPALAAVLAGERILLELIVDDQdhtFALL-ERGEVVGC--VSTQPKPMRGCL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 159 IDVLNPIRTLMVVAPshplAGLKRVLQQDLTDHTqVTLSYVDAFSVKS-----------LLPIGG--QHIgLSSFELMRD 225
Cdd:PRK13348  155 AEPLGTMRYRCVASP----AFAARYFAQGLTRHS-ALKAPAVAFNRKDtlqdsfleqlfGLPVGAypRHY-VPSTHAHLA 228

                         250       260       270
                  ....*....|....*....|....*....|....
gi 2067186253 226 AVLDGLGWAVLPSPLIQSQLRLGELLTLKHKFSL 259
Cdd:PRK13348  229 AIRHGLGYGMVPELLIGPLLAAGRLVDLAPGHPV 262
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 108-237 5.12e-06

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: 46.38  E-value: 5.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLiteeqeRSGLCIDV----LNPIRTLMVVAPSHPLAGLKRV 183
Cdd:cd08412    17 GLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTY------DLDLPEDIafepLARLPPYVWLPADHPLAGKDEV 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2067186253 184 LQQDLTDHTQVTL-------SYVDAFSVKSLLPIGGQHIglSSFELMRDAVLDGLGWAVLP 237
Cdd:cd08412    91 SLADLAAEPLILLdlphsreYFLSLFAAAGLTPRIAYRT--SSFEAVRSLVANGLGYSLLN 149
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-274 1.10e-05

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: 45.38  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  94 RVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGfvDAAFGLITEEQERSGLCIDVLNPIRTLMVVAP 173
Cdd:cd08426     3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSG--EADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 174 SHPLAGLKRVLQQDLTDHTQVTLSyvDAFSVKSLLPIGGQHIGL--------SSFELMRDAVLDGLGWAVLPSPLIQSQL 245
Cdd:cd08426    81 GHPLARQPSVTLAQLAGYPLALPP--PSFSLRQILDAAFARAGVqlepvlisNSIETLKQLVAAGGGISLLTELAVRREI 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2067186253 246 RLGEL--LTLKHKfSLQWRDYGVY------LSENAHH 274
Cdd:cd08426   159 RRGQLvaVPLADP-HMNHRQLELQtragrqLPAAASA 194
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 9-249 1.25e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 45.79  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   9 FVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFER-GTNQSrLTEIGEQVLDDCRRLLQ----AANSLKLkce 83
Cdd:PRK15092   19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARhGRNKL-LTEHGIQLLGYARKILRfndeACSSLMY--- 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  84 hhaSGAEVALRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAfglITEEQersglcidVLN 163
Cdd:PRK15092   95 ---SNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLA---VTTHR--------PSS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 164 PIRTLMVVAPSHPLAGLKRVLQQD------LTDHT----QVTLSYVDAFSVKSLLPIGGqhiglSSFELMRDAVLDGLGW 233
Cdd:PRK15092  161 FPALNLRTSPTLWYCAAEYVLQKGepiplvLLDEPspfrDMALATLNAAGIPWRIAYVA-----STLSAVRAAVKAGLGV 235

                         250
                  ....*....|....*..
gi 2067186253 234 AVLPSPLIQSQLR-LGE 249
Cdd:PRK15092  236 TARPVEMMSPDLRvLGE 252
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 109-253 1.81e-05

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: 44.74  E-value: 1.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 109 MLGALRRQFPGTSISLVLASppELPALVEEGFvDAAFGlITEEQErSGLcidV---LNPIRTLMVVAPS---------HP 176
Cdd:cd08422    19 LLAEFLARYPDVRLELVLSD--RLVDLVEEGF-DLAIR-IGELPD-SSL---VarrLGPVRRVLVASPAylarhgtpqTP 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 177 laglkrvlqQDLTDHTQVTLSYVDAFSVKSLLPIGGQH-------IGLSSFELMRDAVLDGLGWAVLPSPLIQSQLRLGE 249
Cdd:cd08422    91 ---------EDLARHRCLGYRLPGRPLRWRFRRGGGEVevrvrgrLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGR 161


                  ....
gi 2067186253 250 LLTL 253
Cdd:cd08422   162 LVRV 165
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-198 6.97e-05

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 42.90  E-value: 6.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQD 187
Cdd:cd08440    17 PVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVD--FGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAE 94

                          90
                  ....*....|.
gi 2067186253 188 LTDHTQVTLSY 198
Cdd:cd08440    95 LAGYPLIALGR 105
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
21-78 1.45e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 42.70  E-value: 1.45e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2067186253  21 AARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEqvlddcrRLLQAANSL 78
Cdd:PRK03601   21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGE-------RLLPYAETL 71
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 21-287 1.50e-04

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 42.52  E-value: 1.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  21 AARRLGKSR---------SAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQ--AANSLKLKcehhASGA 89
Cdd:PRK11139   17 AARHLSFTRaaeelfvtqAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDqlAEATRKLR----ARSA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  90 EVALRVArddAIPE-----VVWRemLGALRRQFPGtsISLVLASppelpALVEEGF----VDAAF--------GLITEEq 152
Cdd:PRK11139   93 KGALTVS---LLPSfaiqwLVPR--LSSFNEAHPD--IDVRLKA-----VDRLEDFlrddVDVAIrygrgnwpGLRVEK- 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 153 ersgLCIDVLNPirtlmVVAPSHpLAGLKRVLQ-QDLTDHT--QVT-----LSYVDAFSVKSLLPIGGQHIGLSSFELmr 224
Cdd:PRK11139  160 ----LLDEYLLP-----VCSPAL-LNGGKPLKTpEDLARHTllHDDsredwRAWFRAAGLDDLNVQQGPIFSHSSMAL-- 227

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 225 DAVLDGLGWAVLPSPLIQSQLRLGELLTLkhkFSL----QWRDYGVYLSENAHHGKVLA---WLKKAIEA 287
Cdd:PRK11139  228 QAAIHGQGVALGNRVLAQPEIEAGRLVCP---FDTvlpsPNAFYLVCPDSQAELPKVAAfrqWLLAEAAQ 294
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
5-76 1.56e-04

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 40.58  E-value: 1.56e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2067186253   5 QIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFER---GTNQ--SRLTEIGEQVLDDCRRLLQAAN 76
Cdd:COG2005    23 RIELLEAIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERqtgGKGGggARLTPEGRRLLALYRRLEAEAQ 99
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-202 1.73e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 1.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   3 LNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCR-------RLLQAA 75
Cdd:PRK11013    6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQrsyygldRIVSAA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  76 NSLKLKceHHASGAEVALRVARDDAIPEVVWRemlgaLRRQFPGTSISLVlasPPELPaLVEEGFVDAAF--GLITEEQE 153
Cdd:PRK11013   86 ESLREF--RQGQLSIACLPVFSQSLLPGLCQP-----FLARYPDVSLNIV---PQESP-LLEEWLSAQRHdlGLTETLHT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2067186253 154 RSGLCIDVLNPIRTLMVVAPSHPLAGlKRVLQ-QDLTDHTQVTLSYVDAF 202
Cdd:PRK11013  155 PAGTERTELLTLDEVCVLPAGHPLAA-KKVLTpDDFAGENFISLSRTDSY 203
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 108-197 1.85e-04

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: 41.72  E-value: 1.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLITEEQERsglcIDVLnPIRT--LMVVAPS-HPLAGLKRVL 184
Cdd:cd08414    17 RLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPG----LASR-PLLRepLVVALPAdHPLAARESVS 91

                          90
                  ....*....|...
gi 2067186253 185 QQDLTDHTQVTLS 197
Cdd:cd08414    92 LADLADEPFVLFP 104
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 110-281 2.46e-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: 41.03  E-value: 2.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 110 LGALRRQFPGtsISLVLASPPELPALVEEGfVDAA--FGliteEQERSGLCIDVLNPIRTLMVVAPSHpLAGLKRVLQQD 187
Cdd:cd08432    19 LARFQARHPD--IDLRLSTSDRLVDFAREG-IDLAirYG----DGDWPGLEAERLMDEELVPVCSPAL-LAGLPLLSPAD 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 188 LTDHTQVTLSYVD------AFSVKSLLPIGGQHIGLSSFELMRDAVLDGLGWAVLPSPLIQSQLRLGELLTL-KHKFSLQ 260
Cdd:cd08432    91 LARHTLLHDATRPeawqwwLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLVRPfDLPLPSG 170

                         170       180
                  ....*....|....*....|....
gi 2067186253 261 WRDYGVYLSENAHHGKVLA---WL 281
Cdd:cd08432   171 GAYYLVYPPGRAESPAVAAfrdWL 194
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 100-209 2.98e-04

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 41.07  E-value: 2.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 100 AIPEVVwremlGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITE--EQERSGLCIdvlnPIRT---LMVVAPS 174
Cdd:cd08413    14 VLPPVI-----AAFRKRYPKVKLSLHQGTPSQIAEMVLKGEAD--IAIATEalDDHPDLVTL----PCYRwnhCVIVPPG 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2067186253 175 HPLAGLKRVLQQDLTDHTQVTL-------SYVD-AFSVKSLLP 209
Cdd:cd08413    83 HPLADLGPLTLEDLAQYPLITYdfgftgrSSIDrAFARAGLEP 125
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 110-251 3.21e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 40.85  E-value: 3.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 110 LGALRRQFPGTSISLVLASPPELPAlvEEGFvDAAFGLiTEEQERSGLCIDVLNPIRTLMVVAPSHPLA-GLKRVLQQDL 188
Cdd:cd08482    19 LPAFQAALPDIDLQLSASDGPVDSL--RDGI-DAAIRF-NDAPWPAGMQVIELFPERVGPVCSPSLAPTvPLRQAPAAAL 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067186253 189 TDHTQV-TLSYVDAF----SVKSLLPIGGQ-HIGLSSFELMRDAVLDGLGWAVLPSPLIQSQLRLGELL 251
Cdd:cd08482    95 LGAPLLhTRSRPQAWpdwaAAQGLAPEKLGtGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRLV 163
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-237 3.74e-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: 176113  Cd Length: 198  Bit Score: 40.58  E-value: 3.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSGLciDVLnPIRT---LMVVAPSHPLAGLKRVL 184
Cdd:cd08421    17 EDLASFLAAHPDVRIDLEERLSADIVRAVAEGRAD--LGIVAGNVDAAGL--ETR-PYRTdrlVVVVPRDHPLAGRASVA 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2067186253 185 QQDLTDHTQVTL---SYVDAFSVKSLLPIGGQH---IGLSSFELMRDAVLDGLGWAVLP 237
Cdd:cd08421    92 FADTLDHDFVGLpagSALHTFLREAAARLGRRLrlrVQVSSFDAVCRMVAAGLGIGIVP 150
PRK09801 PRK09801
LysR family transcriptional regulator;
6-83 5.97e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 40.79  E-value: 5.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   6 IQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGE-------QVLDDCRRLLQAANSL 78
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQrcyehalEILTQYQRLVDDVTQI 90


                  ....*
gi 2067186253  79 KLKCE 83
Cdd:PRK09801   91 KTRPE 95
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-192 1.03e-03

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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 39.50  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 109 MLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLITEEQERS---GLCIDVLNPIRTLMVVAPSHPLAGLKRVLQ 185
Cdd:cd08423    18 ALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPddpGLTRVPLLDDPLDLVLPADHPLAGREEVAL 97


                  ....*..
gi 2067186253 186 QDLTDHT 192
Cdd:cd08423    98 ADLADEP 104
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-79 1.53e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 39.42  E-value: 1.53e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2067186253  28 SRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQAANSLK 79
Cdd:PRK11716    4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLR 55
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-200 2.42e-03

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 38.17  E-value: 2.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  93 LRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDaaFGLITEEQERSGLCIDVLNPIRTLMVVA 172
Cdd:cd08456     2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCD--LGLVSTLHEPPGIERERLLRIDGVCVLP 79

                          90       100
                  ....*....|....*....|....*...
gi 2067186253 173 PSHPLAGLKRVLQQDLTDHTQVTLSYVD 200
Cdd:cd08456    80 PGHRLAVKKVLTPSDLEGEPFISLARTD 107
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-74 3.82e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 38.22  E-value: 3.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2067186253   5 QIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERgTNQSRLTEIGEQVLDDCR--RLLQA 74
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARqvRLLEA 76
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 108-237 4.20e-03

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 37.52  E-value: 4.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 108 EMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFglITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQD 187
Cdd:cd08434    17 DLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLAL--CSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVDLAE 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 188 LTDHTQVTLS--YVDAFSVKSLLpiggQHIGLS---SFELMRDAVLDGL-----GWAVLP 237
Cdd:cd08434    95 LADEPFVLLSpgFGLRPIVDELC----AAAGFTpkiAFEGEEDSTIAGLvaaglGVAILP 150
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 109-192 5.84e-03

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: 37.12  E-value: 5.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 109 MLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAfgLITEEQERSGLCIDVLNPIRTLMVVAPSHPLAGLKRVLQQDL 188
Cdd:cd08411    19 LLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAA--LLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDL 96


                  ....
gi 2067186253 189 TDHT 192
Cdd:cd08411    97 AGER 100
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-237 6.27e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 37.74  E-value: 6.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253   1 MKLNQIQLFVETADSGSIANAARRLGKSRSAVSSAIATLEVELGVELFERGTNQSRLTEIGEQVLDDCRRLLQaanslkl 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILR------- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  81 KCEH-----HASGAEVALRV---------ARDDAIPevvwreMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAfg 146
Cdd:PRK11233   74 QCEQaqlavHNVGQALSGQVsiglapgtaASSLTMP------LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMA-- 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 147 LITEEQERSGL-CIDVLNpiRTLMVVAP------SHPLAglkRVLQQDL---TDHTQVTLSYVDAFSVKSLLP-IGGQhi 215
Cdd:PRK11233  146 VIYEHSPVAGLsSQPLLK--EDLFLVGTqdcpgqSVDLA---AVAQMNLflpRDYSAVRLRVDEAFSLRRLTAkVIGE-- 218

                         250       260
                  ....*....|....*....|..
gi 2067186253 216 gLSSFELMRDAVLDGLGWAVLP 237
Cdd:PRK11233  219 -IESIATLTAAIASGMGVTVLP 239
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 93-198 8.99e-03

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, 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, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 36.70  E-value: 8.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253  93 LRVARDDAIPEVVWREMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFGLITEEqERSGLCIDvLNPIRTLMVVA 172
Cdd:cd08457     2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLE-ERQGFLIE-TRSLPAVVAVP 79

                          90       100
                  ....*....|....*....|....*.
gi 2067186253 173 PSHPLAGLKRVLQQDLTDHTQVTLSY 198
Cdd:cd08457    80 MGHPLAQLDVVSPQDLAGERIITLEN 105
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 103-188 9.63e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 36.59  E-value: 9.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067186253 103 EVVW-REMLGALRRQFPGTSISLVLASPPELPALVEEGFVDAAFglITEEQERSGLCIDVLNPiRTLMVVAPS-HPLAGL 180
Cdd:cd08450    11 EVQWlPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAF--MRPEIQSDGIDYQLLLK-EPLIVVLPAdHRLAGR 87


                  ....*...
gi 2067186253 181 KRVLQQDL 188
Cdd:cd08450    88 EKIPPQDL 95
 
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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