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Conserved domains on  [gi|489003578|ref|WP_002914199|]
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MULTISPECIES: LysR family transcriptional regulator [Klebsiella]

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];
7-292 7.92e-57

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 183.91  E-value: 7.92e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELER 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  87 QSALLKGEHSGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIIS 166
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYL---LPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 167 EPLYREQHWLYCSDLHPmffsrqldkeqisqcplvtrsywntsdLRRRgfskgSATVETVDAQLLLILSGKYIGYLPEHY 246
Cdd:COG0583  158 RPLGEERLVLVASPDHP---------------------------LARR-----APLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489003578 247 AWPWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLLK 292
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-292 7.92e-57

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 183.91  E-value: 7.92e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELER 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  87 QSALLKGEHSGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIIS 166
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYL---LPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 167 EPLYREQHWLYCSDLHPmffsrqldkeqisqcplvtrsywntsdLRRRgfskgSATVETVDAQLLLILSGKYIGYLPEHY 246
Cdd:COG0583  158 RPLGEERLVLVASPDHP---------------------------LARR-----APLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489003578 247 AWPWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLLK 292
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-293 7.34e-31

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: 114.69  E-value: 7.34e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   96 SGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHW 175
Cdd:pfam03466   1 SGRLRIGAPPTLASYL---LPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  176 LYCSDLHPMFFSRQLDKEQISQCPLV-------TRSYWNtSDLRRRGFS-KGSATVETVDAQLLLILSGKYIGYLPEHYA 247
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLIllppgsgLRDLLD-RALRAAGLRpRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 489003578  248 WPWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLLKK 293
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 98-291 1.09e-22

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: 93.05  E-value: 1.09e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  98 TLCISTLDSIeteTALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLY 177
Cdd:cd05466    1 TLRIGASPSI---AAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 178 CSDLHPMFFSRQLDKEQISQCPLVTRSywNTSDLRRR--------GFS-KGSATVETVDAQLLLILSGKYIGYLPEHYAw 248
Cdd:cd05466   78 VPPDHPLAKRKSVTLADLADEPLILFE--RGSGLRRLldrafaeaGFTpNIALEVDSLEAIKALVAAGLGIALLPESAV- 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 489003578 249 PWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLL 291
Cdd:cd05466  155 EELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-202 3.82e-21

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 91.19  E-value: 3.82e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQ-VFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLG---FTlcQRGRGGFSLTEKGQQFLQQAIRVLSELN 82
Cdd:PRK12684   1 MNLHQLRfVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGveiFT--RHGKRLRGLTEPGRIILASVERILQEVE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  83 ELERQSALLKGEHSGTLCISTldsIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGS-YNSQV 161
Cdd:PRK12684  79 NLKRVGKEFAAQDQGNLTIAT---THTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATeAIADY 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 489003578 162 HNIISEPLYREQHWLYCSDLHPMFFSRQLDKEQISQCPLVT 202
Cdd:PRK12684 156 KELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLIT 196
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-292 7.92e-57

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 183.91  E-value: 7.92e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELER 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  87 QSALLKGEHSGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIIS 166
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYL---LPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 167 EPLYREQHWLYCSDLHPmffsrqldkeqisqcplvtrsywntsdLRRRgfskgSATVETVDAQLLLILSGKYIGYLPEHY 246
Cdd:COG0583  158 RPLGEERLVLVASPDHP---------------------------LARR-----APLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489003578 247 AWPWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLLK 292
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-293 7.34e-31

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: 114.69  E-value: 7.34e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   96 SGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHW 175
Cdd:pfam03466   1 SGRLRIGAPPTLASYL---LPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  176 LYCSDLHPMFFSRQLDKEQISQCPLV-------TRSYWNtSDLRRRGFS-KGSATVETVDAQLLLILSGKYIGYLPEHYA 247
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLIllppgsgLRDLLD-RALRAAGLRpRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 489003578  248 WPWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLLKK 293
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 98-291 1.09e-22

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: 93.05  E-value: 1.09e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  98 TLCISTLDSIeteTALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLY 177
Cdd:cd05466    1 TLRIGASPSI---AAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 178 CSDLHPMFFSRQLDKEQISQCPLVTRSywNTSDLRRR--------GFS-KGSATVETVDAQLLLILSGKYIGYLPEHYAw 248
Cdd:cd05466   78 VPPDHPLAKRKSVTLADLADEPLILFE--RGSGLRRLldrafaeaGFTpNIALEVDSLEAIKALVAAGLGIALLPESAV- 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 489003578 249 PWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLL 291
Cdd:cd05466  155 EELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-202 3.82e-21

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 91.19  E-value: 3.82e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQ-VFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLG---FTlcQRGRGGFSLTEKGQQFLQQAIRVLSELN 82
Cdd:PRK12684   1 MNLHQLRfVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGveiFT--RHGKRLRGLTEPGRIILASVERILQEVE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  83 ELERQSALLKGEHSGTLCISTldsIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGS-YNSQV 161
Cdd:PRK12684  79 NLKRVGKEFAAQDQGNLTIAT---THTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATeAIADY 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 489003578 162 HNIISEPLYREQHWLYCSDLHPMFFSRQLDKEQISQCPLVT 202
Cdd:PRK12684 156 KELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLIT 196
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 7-202 3.05e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 88.56  E-value: 3.05e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQ-VFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQR-GRGGFSLTEKGQQFLQQAIRVLSELNEL 84
Cdd:PRK12683   1 MNFQQLRiIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  85 ERQSALLKGEHSGTLCISTldsIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYN-SQVHN 163
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVAT---THTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAlDREPD 157

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489003578 164 IISEPLYREQHWLYCSDLHPMFFSRQLDKEQISQCPLVT 202
Cdd:PRK12683 158 LVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIIT 196
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-202 2.24e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 86.20  E-value: 2.24e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQ-VFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQR-GRGGFSLTEKGQQFLQQAIRVLSELNEL 84
Cdd:PRK12682   1 MNLQQLRfVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKGLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  85 ERQSALLKGEHSGTLCISTldsIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYN-SQVHN 163
Cdd:PRK12682  81 KRIGDDFSNQDSGTLTIAT---THTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESlADDPD 157

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489003578 164 IISEPLYREQHWLYCSDLHPMFFSRQLDKEQISQCPLVT 202
Cdd:PRK12682 158 LATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLIT 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 1.99e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.43  E-value: 1.99e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578    9 IRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQ 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-274 6.94e-18

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 81.91  E-value: 6.94e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  12 LQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELERQSALL 91
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  92 KGEHSGTLCIsTLDSIETETALSLPVV--LRSFSDkfphvhIKLIIRtpAEQLNGV----LNNHIDLAIGSynSQVHNII 165
Cdd:PRK11074  87 ANGWRGQLSI-AVDNIVRPDRTRQLIVdfYRHFDD------VELIIR--QEVFNGVwdalADGRVDIAIGA--TRAIPVG 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 166 SEPLYREQ---HWLY-CSDLHPM-FFSRQLDKEQISQCPLVTRSywNTS-DLRRRgfskgsaTVETVDAQLLLIL----- 234
Cdd:PRK11074 156 GRFAFRDMgmlSWACvVSSDHPLaSMDGPLSDDELRPYPSLCLE--DTSrTLPKR-------ITWLLDNQRRLVVpdwes 226

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 489003578 235 ------SGKYIGYLPEHYAWPWIKENRLRVL-LPNEFgfqsPFSAIC 274
Cdd:PRK11074 227 ainclsAGLCVGMVPTHFAKPLINSGKLVELtLENPF----PDSPCC 269
cbl PRK12679
HTH-type transcriptional regulator Cbl;
7-202 8.71e-18

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 81.78  E-value: 8.71e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLE-SYSRAQQELGISVSAISNAMSQLEGQLGFTL-CQRGRGGFSLTEKGQQFLQQAIRVLSELNEL 84
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  85 ERQSALLKGEHSGTLCISTldsIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSynSQVHN- 163
Cdd:PRK12679  81 RRLADLFTNDTSGVLTIAT---THTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAS--ERLSNd 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 489003578 164 --IISEPLYREQHWLYCSDLHPMFFSRQLDKEQISQCPLVT 202
Cdd:PRK12679 156 pqLVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLIT 196
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
12-182 4.42e-17

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 80.05  E-value: 4.42e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  12 LQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNE--LERQSA 89
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQeiLDIKNQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  90 llkgEHSGTLCISTLDSIeTETALsLPvVLRSFSDKFPhvHIKLIIRTPAEQLNgvLNNH-IDLAI-----GSYNSQVHN 163
Cdd:PRK10086  99 ----ELSGTLTVYSRPSI-AQCWL-VP-RLADFTRRYP--SISLTILTGNENVN--FQRAgIDLAIyfddaPSAQLTHHF 167

                        170       180       190
                 ....*....|....*....|....*....|....
gi 489003578 164 IISE-------PLYREQHWLY--------CSDLH 182
Cdd:PRK10086 168 LMDEeilpvcsPEYAERHALTgnpdnlrhCTLLH 201
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-154 1.06e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 75.83  E-value: 1.06e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   4 DASLNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNE 83
Cdd:CHL00180   2 DLPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEE 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489003578  84 LERQSALLKGEHSGTLCISTldSIETETALSlPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI 154
Cdd:CHL00180  82 TCRALEDLKNLQRGTLIIGA--SQTTGTYLM-PRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI 149
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 12-179 7.15e-15

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 73.34  E-value: 7.15e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  12 LQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQR-GRgGFSLTEKGQQFLQQAIRVLSELNELERQsaL 90
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRrNR-SLLLTEEGQRYFLDIREIFDQLAEATRK--L 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  91 LKGEHSGTLCISTLDSIeteTALSLPVVLRSFSDKFPHVHIKLiirTPAEQLNGVLNNHIDLAI--GSYNSQvhNIISEP 168
Cdd:PRK11139  88 RARSAKGALTVSLLPSF---AIQWLVPRLSSFNEAHPDIDVRL---KAVDRLEDFLRDDVDVAIryGRGNWP--GLRVEK 159

                        170
                 ....*....|.
gi 489003578 169 LYREQHWLYCS 179
Cdd:PRK11139 160 LLDEYLLPVCS 170
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-231 1.69e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 69.33  E-value: 1.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   1 MHhdasLNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSE 80
Cdd:PRK10837   1 MH----ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  81 LNELERqsaLLKGEhSGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDlaIGSYNSQ 160
Cdd:PRK10837  77 AVEIEQ---LFRED-NGALRIYASSTIGNYI---LPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVD--IGLIEGP 147

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489003578 161 VHN--IISEPLYREQHWLYCSDLHPMfFSRQLDKEQISQCPLVTRsywntsdlrrrgfSKGSATVETVDAQLL 231
Cdd:PRK10837 148 CHSpeLISEPWLEDELVVFAAPDSPL-ARGPVTLEQLAAAPWILR-------------ERGSGTREIVDYLLL 206
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-291 3.97e-12

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: 64.08  E-value: 3.97e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLYCSDLHPMFFSRQLDKEQ 194
Cdd:cd08440   15 LPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 195 ISQCPLVTRSYwnTSDLRRrgfskgsaTVETVDAQLLLILSGKY-----------------IGYLPEhYAWPWIKENRLR 257
Cdd:cd08440   95 LAGYPLIALGR--GSGVRA--------LIDRALAAAGLTLRPAYevshmstalgmvaaglgVAVLPA-LALPLADHPGLV 163

                        170       180       190
                 ....*....|....*....|....*....|....
gi 489003578 258 VLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLL 291
Cdd:cd08440  164 ARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
33-154 5.83e-12

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 64.45  E-value: 5.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  33 ISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELN----ELERQSALLKGEhsgtlcISTLDSIe 108
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQqlrhTLDQQGPSLSGE------LSLFCSV- 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 489003578 109 teTA-LS-LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI 154
Cdd:PRK11716  76 --TAaYShLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAI 121
PRK12680 PRK12680
LysR family transcriptional regulator;
27-249 9.88e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 64.64  E-value: 9.88e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  27 AQQELGISVSA---------ISNAMSQLEGQLGFTL-CQRGRGGFSLTEKGQQFLQQAIRVLSELNELERQSALLKGEHS 96
Cdd:PRK12680  13 ADAELNITLAAarvhatqpgLSKQLKQLEDELGFLLfVRKGRSLESVTPAGVEVIERARAVLSEANNIRTYAANQRRESQ 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  97 GTLcisTLDSIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSY-NSQVHNIISEPLYREQHW 175
Cdd:PRK12680  93 GQL---TLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTaGGEPSAGIAVPLYRWRRL 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 176 LYCSDLHPM-FFSRQLDKEQISQCPLVT--RSYWNTSDLRRRGFSKG---SATVETVDAQLL--LILSGKYIGYLPEH-- 245
Cdd:PRK12680 170 VVVPRGHALdTPRRAPDMAALAEHPLISyeSSTRPGSSLQRAFAQLGlepSIALTALDADLIktYVRAGLGVGLLAEMav 249

                        250
                 ....*....|.
gi 489003578 246 -------YAWP 249
Cdd:PRK12680 250 nandedlRAWP 260
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 115-291 5.46e-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: 5.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI--GSYNSQvhNIISEPLYREQHWLYCSDLHPMFFSRQLDK 192
Cdd:cd08420   15 LPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLveGPVDHP--DLIVEPFAEDELVLVVPPDHPLAGRKEVTA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 193 EQISQCPLVTRsywntsdlrrrgfSKGSATVETVDAQLL-----------------------LILSGKYIGYLPEHYAWP 249
Cdd:cd08420   93 EELAAEPWILR-------------EPGSGTREVFERALAeagldgldlnivmelgsteaikeAVEAGLGISILSRLAVRK 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 489003578 250 WIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLL 291
Cdd:cd08420  160 ELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 115-291 6.57e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 60.36  E-value: 6.57e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSY--NSQVHNIISEPLYREQHWLYCSDLHPMFFSRQLDK 192
Cdd:cd08449   15 LGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFadTLNDPPLASELLWREPMVVALPEEHPLAGRKSLTL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 193 EQISQCPLVTRSYWNTSDLR-------RRGFSKgSATVETVDAQLL--LILSGKYIGYLPEHYA---WPWIKENRLRvll 260
Cdd:cd08449   95 ADLRDEPFVFLRLANSRFADflincclQAGFTP-QITQEVVEPQTLmaLVAAGFGVALVPESYArlpWPGVRFIPLK--- 170

                        170       180       190
                 ....*....|....*....|....*....|...
gi 489003578 261 pnefgfQSPFSAIC--KRGRSNEPYLKAFRDLL 291
Cdd:cd08449  171 ------QAISADLYavYHPDSATPVIQAFLALL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-205 9.33e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.51  E-value: 9.33e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  10 RQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELERqsA 89
Cdd:PRK11242   4 RHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR--A 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  90 LlkgeH------SGTLCISTldsIETETA-LSLPVVLRsFSDKFPhvHIKLIIR-TPAEQLN-GVLNNHIDLAIGSYNSQ 160
Cdd:PRK11242  82 I----HdvadlsRGSLRLAM---TPTFTAyLIGPLIDA-FHARYP--GITLTIReMSQERIEaLLADDELDVGIAFAPVH 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489003578 161 VHNIISEPLYREQHWLYCSDLHPMFFSRQ-LDKEQISQCPLV-------TRSY 205
Cdd:PRK11242 152 SPEIEAQPLFTETLALVVGRHHPLAARRKaLTLDELADEPLVllsaefaTREQ 204
PRK10341 PRK10341
transcriptional regulator TdcA;
10-259 1.30e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 61.03  E-value: 1.30e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  10 RQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQqaiRVLSELNELERQSA 89
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS---RSESITREMKNMVN 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  90 LLKGEHSGTLCISTLDSIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIG--SYNSQVHNIISE 167
Cdd:PRK10341  87 EINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGtlSNEMKLQDLHVE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 168 PLYREQHWLYCSDLHPMFFSRQLDKEQISQ--CPLVTRSYWN--TSDLRRRGFSKGSAT-VETVDAQLLLILSGKYIGYL 242
Cdd:PRK10341 167 PLFESEFVLVASKSRTCTGTTTLESLKNEQwvLPQTNMGYYSelLTTLQRNGISIENIVkTDSVVTIYNLVLNADFLTVI 246

                        250
                 ....*....|....*..
gi 489003578 243 PEHYAWPWiKENRLRVL 259
Cdd:PRK10341 247 PCDMTSPF-GSNQFITI 262
PRK09791 PRK09791
LysR family transcriptional regulator;
5-191 2.73e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 60.16  E-value: 2.73e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   5 ASLNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNEL 84
Cdd:PRK09791   3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  85 ERQSALLKGEHSGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSY--NSQVH 162
Cdd:PRK09791  83 QEDIRQRQGQLAGQINIGMGASIARSL---MPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYyqGPYDH 159

                        170       180
                 ....*....|....*....|....*....
gi 489003578 163 NIISEPLYREQHWLYCSDLHPMFFSRQLD 191
Cdd:PRK09791 160 EFTFEKLLEKQFAVFCRPGHPAIGARSLK 188
PRK09986 PRK09986
LysR family transcriptional regulator;
7-252 2.29e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 57.43  E-value: 2.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNE-LE 85
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQsLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  86 RQSALLKGEHsGTLCISTLDsieteTAL--SLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI--GSYNSQV 161
Cdd:PRK09986  87 RVEQIGRGEA-GRIEIGIVG-----TALwgRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 162 HNIISEPLYREQHWLYCSDLHPMFFSRQLDKEQISQCPLVTRSYwNTSDLRRR--------GFSKgSATVETVDAQ--LL 231
Cdd:PRK09986 161 PGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPF-VHSDWGKFlqrvcqqaGFSP-QIIRQVNEPQtvLA 238

                        250       260
                 ....*....|....*....|....
gi 489003578 232 LILSGKYIGYLPEHYA---WPWIK 252
Cdd:PRK09986 239 MVSMGIGITLLPDSYAqipWPGVV 262
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-109 7.57e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 55.75  E-value: 7.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRgGFSLTEKGQQFLQQAIRVlsELNELER 86
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLLRHLRQV--ALLEADL 78

                         90       100
                 ....*....|....*....|....*
gi 489003578  87 QSALLKGEHSG-TLCIS-TLDSIET 109
Cdd:PRK13348  79 LSTLPAERGSPpTLAIAvNADSLAT 103
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 103-202 8.98e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl 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.


Pssm-ID: 176135  Cd Length: 198  Bit Score: 54.43  E-value: 8.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 103 TLDSIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVH-NIISEPLYREQHWLYCSDL 181
Cdd:cd08444    3 TIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHpELVSFPYYDWHHHIIVPVG 82

                         90       100
                 ....*....|....*....|.
gi 489003578 182 HPMFFSRQLDKEQISQCPLVT 202
Cdd:cd08444   83 HPLESITPLTIETIAKWPIIT 103
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 115-291 1.12e-08

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


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 54.05  E-value: 1.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLYCSDLHPMFFSRQLDKEQ 194
Cdd:cd08414   15 LPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHPLAARESVSLAD 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 195 ISQCPLVT-----RSYWN---TSDLRRRGFS-KGSATVETVDAQLLLILSGKYIGYLPE---HYAWPWIkenRLRVLLpn 262
Cdd:cd08414   95 LADEPFVLfprepGPGLYdqiLALCRRAGFTpRIVQEASDLQTLLALVAAGLGVALVPAsvaRLQRPGV---VYRPLA-- 169

                        170       180
                 ....*....|....*....|....*....
gi 489003578 263 EFGFQSPFSAICKRGRSNePYLKAFRDLL 291
Cdd:cd08414  170 DPPPRSELALAWRRDNAS-PALRAFLELA 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
9-104 1.57e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 54.77  E-value: 1.57e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   9 IRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELERQS 88
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90
                 ....*....|....*....
gi 489003578  89 ALLKGEHSGTL---CISTL 104
Cdd:PRK10632  84 YAFNNTPIGTLrigCSSTM 102
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 12-154 3.46e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 53.88  E-value: 3.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  12 LQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQR-GRGGfSLTEKGQQFLQQAIRVLsELNElERQSAL 90
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARhGRNK-LLTEHGIQLLGYARKIL-RFND-EACSSL 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489003578  91 LKGEHSGTLCISTLDsietETALS-LPVVLRSFSDKFPHVHIKLII-RTP--AEQLNgvlNNHIDLAI 154
Cdd:PRK15092  93 MYSNLQGVLTIGASD----DTADTiLPFLLNRVSSVYPKLALDVRVkRNAfmMEMLE---SQEVDLAV 153
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-169 5.60e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 53.23  E-value: 5.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNE--- 83
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKakl 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  84 LERQSAllkgEHSGTLCISTLDSIETETalsLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI---GSYNSQ 160
Cdd:PRK09906  81 RARKIV----QEDRQLTIGFVPSAEVNL---LPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFmrhPVYSDE 153

                        170
                 ....*....|.
gi 489003578 161 VHN--IISEPL 169
Cdd:PRK09906 154 IDYleLLDEPL 164
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 114-202 5.72e-08

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: 51.85  E-value: 5.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 114 SLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVH-NIISEPLYREQHWLYCSDLHPMFFSRQLDK 192
Cdd:cd08413   14 VLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHpDLVTLPCYRWNHCVIVPPGHPLADLGPLTL 93

                         90
                 ....*....|
gi 489003578 193 EQISQCPLVT 202
Cdd:cd08413   94 EDLAQYPLIT 103
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 98-261 1.37e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 51.06  E-value: 1.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  98 TLCISTLDSIEtetALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLY 177
Cdd:cd08417    1 TFRIAASDYLE---ALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 178 CSDLHPmFFSRQLDKEQISQCPLVTRSYWNTSD------LRRRGFS-KGSATVETVDAQLLLILSGKYIGYLPEHYAWPW 250
Cdd:cd08417   78 ARKDHP-LAGGPLTLEDYLAAPHVLVSPRGRGHglvddaLAELGLSrRVALTVPHFLAAPALVAGTDLIATVPRRLAEAL 156

                        170
                 ....*....|..
gi 489003578 251 IKENRLRVL-LP 261
Cdd:cd08417  157 AERLGLRVLpLP 168
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-256 1.96e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 51.35  E-value: 1.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  12 LQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNEL--ERQSA 89
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMpsELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  90 LLKGEHSGTLCISTLDSIETETALSLPVVLRSFSdkFPHVHIKLIIRTpaeqlnGV----LNNHIDLAIG--SYNSQVHN 163
Cdd:PRK10094  87 NDGVERQVNIVINNLLYNPQAVAQLLAWLNERYP--FTQFHISRQIYM------GVwdslLYEGFSLAIGvtGTEALANT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 164 IISEPLYREQHWLYCSDLHPMF-FSRQLDKEQISQCPLVtrsywNTSDLRRRgFSKGSA---------TVETVDAQLLLI 233
Cdd:PRK10094 159 FSLDPLGSVQWRFVMAADHPLAnVEEPLTEAQLRRFPAV-----NIEDSART-LTKRVAwrlpgqkeiIVPDMETKIAAH 232

                        250       260
                 ....*....|....*....|...
gi 489003578 234 LSGKYIGYLPEHYAWPWIKENRL 256
Cdd:PRK10094 233 LAGVGIGFLPKSLCQSMIDNQQL 255
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 114-291 3.88e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 49.59  E-value: 3.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 114 SLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLYCSDLHPMFFSRQLDKE 193
Cdd:cd08446   15 TVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVPKSHPLAARPAVSLA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 194 QISQCPLV------TRSYWN--TSDLRRRGFS-KGSATVETVDAQLLLILSGKYIGYLPE---HYAWPWIKENRLRVLLP 261
Cdd:cd08446   95 DLRNEPLIlfprggRPSFADevLGLFRRAGVEpRVAQEVEDVVAALALVAAGFGVCIVPEsvaALRWPGVVFRPLADAEA 174

                        170       180       190
                 ....*....|....*....|....*....|
gi 489003578 262 nefgfQSPFSAICKRGRSNePYLKAFRDLL 291
Cdd:cd08446  175 -----KVPLSCIYRKDDRS-PILRAFLDVV 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-183 4.19e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 50.45  E-value: 4.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNEleR 86
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ--A 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  87 QSAL------LKGEHSGTLCISTLDSietetALSLPVvLRSFSDKFPHVHIKLIiRTPAEQLNG-VLNNHIDLAIGSYNS 159
Cdd:PRK11233  79 QLAVhnvgqaLSGQVSIGLAPGTAAS-----SLTMPL-LQAVRAEFPGIVLYLH-ENSGATLNEkLMNGQLDMAVIYEHS 151

                        170       180
                 ....*....|....*....|....
gi 489003578 160 QVHNIISEPLYREQHWLYCSDLHP 183
Cdd:PRK11233 152 PVAGLSSQPLLKEDLFLVGTQDCP 175
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 115-292 1.17e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 48.12  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQV--HNIISEPLYREQHWLYCSDLHPMFFSRQLDK 192
Cdd:cd08418   15 MPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMylKELISEPLFESDFVVVARKDHPLQGARSLEE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 193 EQISQCPL-VTRS--YWNTSD-LRRRGFS-KGSATVETVDAQLLLILSGKYIGYLPEHYAWPWIKENRLRVLLPNEFGFQ 267
Cdd:cd08418   95 LLDASWVLpGTRMgyYNNLLEaLRRLGYNpRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRLITIPVEEPLPS 174

                        170       180
                 ....*....|....*....|....*
gi 489003578 268 SPFSAICKRGRSNEPYLKAFRDLLK 292
Cdd:cd08418  175 ADYYLIYRKKSRLTPLAEQLVELFR 199
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 115-291 2.73e-06

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: 47.27  E-value: 2.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGS-YNSQVHN-IISEPLYREQHWLYCSDLHPMFFSRQLDK 192
Cdd:cd08435   15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRlADDEQPPdLASEELADEPLVVVARPGHPLARRARLTL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 193 EQISQCPLV-------TRSyWNTSDLRRRGFSKGSATVET--VDAQLLLILSGKYIGYLPEHYAWPWIKENRLRVlLPNE 263
Cdd:cd08435   95 ADLADYPWVlpppgtpLRQ-RLEQLFAAAGLPLPRNVVETasISALLALLARSDMLAVLPRSVAEDELRAGVLRE-LPLP 172

                        170       180
                 ....*....|....*....|....*....
gi 489003578 264 FGF-QSPFSAICKRGRSNEPYLKAFRDLL 291
Cdd:cd08435  173 LPTsRRPIGITTRRGGPLSPAARALLDAL 201
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
7-92 7.15e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 46.69  E-value: 7.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRgGFSLTEKGQQFLQQAIRV-------LS 79
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRLLRHARQVrlleaelLG 80

                         90
                 ....*....|...
gi 489003578  80 ELNELERQSALLK 92
Cdd:PRK03635  81 ELPALDGTPLTLS 93
PRK09801 PRK09801
LysR family transcriptional regulator;
10-261 1.54e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 45.80  E-value: 1.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  10 RQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELERQSA 89
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  90 LLKGEHSGTLCIS-TLDSIETETALSLPVVLRSFSDKfpHVHIKLIIRtpaeQLNGVLNNhIDLAIgSYNSQVHNIISEP 168
Cdd:PRK09801  89 QIKTRPEGMIRIGcSFGFGRSHIAPAITELMRNYPEL--QVHFELFDR----QIDLVQDN-IDLDI-RINDEIPDYYIAH 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 169 LYREQHWLYCSDlhPMFFSRQLDKEQISQCP----LVTRS------YWNTSDLRRRGFSKGSATVETVDAQLLL--ILSG 236
Cdd:PRK09801 161 LLTKNKRILCAA--PEYLQKYPQPQSLQELSrhdcLVTKErdmthgIWELGNGQEKKSVKVSGHLSSNSGEIVLqwALEG 238

                        250       260
                 ....*....|....*....|....*
gi 489003578 237 KYIGYLPEHYAWPWIKENRLRVLLP 261
Cdd:PRK09801 239 KGIMLRSEWDVLPFLESGKLVQVLP 263
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 104-291 2.85e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 44.14  E-value: 2.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 104 LDSIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI--GSYNsqvH-NIISEPLYREQHWLYCSD 180
Cdd:cd08442    4 LGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFvaGPVE---HpRLEQEPVFQEELVLVSPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 181 LHPMFFsrqlDKEQISQCPLVTR----SY------WntsdLRRRGFSKGSA-TVETVDAQLLLILSGKYIGYLPEHYAWP 249
Cdd:cd08442   81 GHPPVS----RAEDLAGSTLLAFragcSYrrrledW----LAEEGVSPGKImEFGSYHAILGCVAAGMGIALLPRSVLDS 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 489003578 250 WIKENRLRVL-LPNEFGfQSPFSAICKRGrSNEPYLKAFRDLL 291
Cdd:cd08442  153 LQGRGSVSIHpLPEPFA-DVTTWLVWRKD-SFTAALQAFLDLL 193
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 15-154 3.36e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 44.60  E-value: 3.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  15 FEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELERQSALLKGE 94
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489003578  95 HSGTLcistldsietetALSLPVVLRsfsdkfpHVHI-----KLIIRTPAEQLN--------GVLNNHIDLAI 154
Cdd:PRK14997  90 PRGIV------------KLTCPVTLL-------HVHIgpmlaKFMARYPDVSLQleatnrrvDVVGEGVDVAI 143
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 7-183 4.13e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 44.25  E-value: 4.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSELNELER 86
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  87 QSALLKGEHSGTLCISTldsIETETALSLPVVLRSFSDKFPHVHIKLiIRTPAEQLNGVLNN-HIDLAIGSYNSQVHNII 165
Cdd:PRK11151  81 MASQQGETMSGPLHIGL---IPTVGPYLLPHIIPMLHQTFPKLEMYL-HEAQTHQLLAQLDSgKLDCAILALVKESEAFI 156

                        170
                 ....*....|....*...
gi 489003578 166 SEPLYREQHWLYCSDLHP 183
Cdd:PRK11151 157 EVPLFDEPMLLAVYEDHP 174
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 115-196 7.28e-05

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 42.90  E-value: 7.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLYCSDLHPMFFSRQLDKEQ 194
Cdd:cd08411   16 LPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPED 95


                 ..
gi 489003578 195 IS 196
Cdd:cd08411   96 LA 97
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-287 7.76e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 43.47  E-value: 7.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQAIRVLSEL----- 81
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIsqalq 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  82 --NELERQSALLKGE-HSgtlCISTLDSietetalslpvVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYN 158
Cdd:PRK15421  82 acNEPQQTRLRIAIEcHS---CIQWLTP-----------ALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDI 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 159 SQVHNIISEPLYREQHWLYCSDLHPMFFSRQLDKEQISQCPL----VTRSYWntsDLRRRGFSKG--SATVETVDAQLLL 232
Cdd:PRK15421 148 LPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLliypVQRSRL---DVWRHFLQPAgvSPSLKSVDNTLLL 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489003578 233 I--LSGKY-IGYLPEhyawpWIKEN--RLRVLLPNEF--GFQSPFSAICKRGRSNEPYLKAF 287
Cdd:PRK15421 225 IqmVAARMgIAALPH-----WVVESfeRQGLVVTKTLgeGLWSRLYAAVRDGEQRQPVTEAF 281
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 218-291 8.89e-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: 42.43  E-value: 8.89e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489003578 218 KGSATVETVDAQLLLILSGKYIGYLPEHYAWPWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLL 291
Cdd:cd08422  124 RGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
cysB PRK12681
HTH-type transcriptional regulator CysB;
27-202 1.05e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 43.35  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  27 AQQELGISVSA---------ISNAMSQLEGQLGFTLCQR-GRGGFSLTEKGQQFLQQAIRVLSELNELERQSALLKGEHS 96
Cdd:PRK12681  13 VNHNLNVSATAeglytsqpgISKQVRMLEDELGIQIFARsGKHLTQVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDK 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  97 GTLCISTLDsieTETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGS-----YNsqvhNIISEPLYr 171
Cdd:PRK12681  93 GSLYIATTH---TQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATealhlYD----DLIMLPCY- 164

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 489003578 172 eqHWLYC----SDlHPMFFSRQLDKEQISQCPLVT 202
Cdd:PRK12681 165 --HWNRSvvvpPD-HPLAKKKKLTIEELAQYPLVT 196
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 115-154 1.45e-04

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 42.18  E-value: 1.45e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI 154
Cdd:cd08430   15 LPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAI 54
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 115-173 1.89e-04

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: 41.75  E-value: 1.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQ 173
Cdd:cd08434   15 VPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEE 73
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 103-202 2.06e-04

The C-terminal substrate domain of LysR-type transcriptional regulator CysB 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.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 41.39  E-value: 2.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 103 TLDSIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVH-NIISEPLYREQHWLYCSDL 181
Cdd:cd08443    3 YVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYdDLITLPCYHWNRCVVVKRD 82

                         90       100
                 ....*....|....*....|.
gi 489003578 182 HPMFFSRQLDKEQISQCPLVT 202
Cdd:cd08443   83 HPLADKQSISIEELATYPIVT 103
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
16-96 2.12e-04

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 40.19  E-value: 2.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578  16 EAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQR-----GRGGFSLTEKGQQFLQQAIRVLSELNE-----LE 85
Cdd:COG2005   28 EAIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERqtggkGGGGARLTPEGRRLLALYRRLEAEAQRalaalFE 107

                         90
                 ....*....|.
gi 489003578  86 RQSALLKGEHS 96
Cdd:COG2005  108 ELFALLRSKTS 118
leuO PRK09508
leucine transcriptional activator; Reviewed
 7-133 2.21e-04

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 42.32  E-value: 2.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   7 LNIrqLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQR-GRgGFSLTEKGQQF---LQQAIRVLSelN 82
Cdd:PRK09508  24 LNL--LTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRyGR-GIQPTARARQLfgpVRQALQLVQ--N 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489003578  83 ELErqSALLKGEHSG---TLCI-STLDSIETetalslPVVLRSFSDKFPHVHIKL 133
Cdd:PRK09508  99 ELP--GSGFEPESSErvfNLCIcSPLDIRLT------SQIYNRIEQIAPNIHVVF 145
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 115-171 1.49e-03

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


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 39.08  E-value: 1.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489003578 115 LPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYR 171
Cdd:cd08415   15 LPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLAS 71
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 115-208 1.96e-03

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 38.64  E-value: 1.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 115 LPVVLRSFSDKFPHVHIKLI-IRTPaEQLNGVLNNHIDLAIGSYNSQVHNIISEPLYREQHWLYCSDLHPMFFSRQLDKE 193
Cdd:cd08452   15 LPPIVREYRKKFPSVKVELReLSSP-DQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIE 93

                         90
                 ....*....|....*..
gi 489003578 194 QISQCPLVT--RSYWNT 208
Cdd:cd08452   94 DLRDEPIITvaREAWPT 110
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-247 2.27e-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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 38.35  E-value: 2.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 103 TLDSIETETALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAI-GSYNSQVHNIISEPLYREQHWLYCSDL 181
Cdd:cd08436    3 AIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFvGLPERRPPGLASRELAREPLVAVVAPD 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489003578 182 HPMFFSRQLDKEQISQCPLVTRSY-WNTSDL-----RRRGFSKGSATvETVDAQLLLIL--SGKYIGYLPEHYA 247
Cdd:cd08436   83 HPLAGRRRVALADLADEPFVDFPPgTGARRQvdrafAAAGVRRRVAF-EVSDVDLLLDLvaRGLGVALLPASVA 155
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-134 4.43e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.05  E-value: 4.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578   5 ASLNIRQLQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTekgqqflQQAIRVLSELNE- 83
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPT-------VQGLRLFEEVQRs 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489003578  84 ---LER----QSALLKGEHsGTLCISTL----DSIetetalsLPVVLRSFSDKFPHVHIKLI 134
Cdd:PRK11013  75 yygLDRivsaAESLREFRQ-GQLSIACLpvfsQSL-------LPGLCQPFLARYPDVSLNIV 128
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 220-291 4.69e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 37.61  E-value: 4.69e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489003578 220 SATVETVDAQLLLILSGKYIGYLPEHYAWPWIKENRLRVLLPNEFGFQSPFSAICKRGRSNEPYLKAFRDLL 291
Cdd:cd08476  126 ALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
12-74 7.70e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 37.30  E-value: 7.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489003578  12 LQVFEAVARLESYSRAQQELGISVSAISNAMSQLEGQLGFTLCQRGRGGFSLTEKGQQFLQQA 74
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 100-201 8.33e-03

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: 36.75  E-value: 8.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489003578 100 CISTLdsieteTALSLPVVLRSFSDKFPHVHIKLIIRTPAEQLNGVLNNHIDLAIgSYNSQV-HNIISEPLYREQHWLYC 178
Cdd:cd08412    6 CFSTL------APYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLAL-TYDLDLpEDIAFEPLARLPPYVWL 78

                         90       100
                 ....*....|....*....|...
gi 489003578 179 SDLHPMFFSRQLDKEQISQCPLV 201
Cdd:cd08412   79 PADHPLAGKDEVSLADLAAEPLI 101
 
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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