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Conserved domains on  [gi|1755689953|gb|QEY61954|]
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LysR family transcriptional regulator [Pseudomonas lalkuanensis]

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];
7-290 1.20e-50

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.12  E-value: 1.20e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   7 TLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEEL 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  87 AHHMEQGWEAEVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQ--GYLGAGLC 164
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPdpGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 165 SVEFVAVAHPDHPLhrlqrqinfqdlesqlqvvirdtgrtqprnvgwlgAEQRWTVGSLSTAANFVSSGLGFAWLPRHLI 244
Cdd:COG0583   162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1755689953 245 ERELKDGQLKPLPLEQGGSRHPsFYLYSNKDKALGPASQILVELIK 290
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-290 1.20e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.12  E-value: 1.20e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   7 TLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEEL 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  87 AHHMEQGWEAEVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQ--GYLGAGLC 164
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPdpGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 165 SVEFVAVAHPDHPLhrlqrqinfqdlesqlqvvirdtgrtqprnvgwlgAEQRWTVGSLSTAANFVSSGLGFAWLPRHLI 244
Cdd:COG0583   162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1755689953 245 ERELKDGQLKPLPLEQGGSRHPsFYLYSNKDKALGPASQILVELIK 290
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-260 5.63e-30

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 115.04  E-value: 5.63e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  14 LQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKqasQLEELAHHMEQ- 92
Cdd:PRK11074   10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK---KMQETRRQCQQv 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  93 --GWEAEVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI---TGLDIQG-YLGAGLCSV 166
Cdd:PRK11074   87 anGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIgatRAIPVGGrFAFRDMGML 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 167 EFVAVAHPDHPLHRLQRQINFQDLESQLQVVIRDTGRTQPRNVGWLGAEQ-RWTVGSLSTAANFVSSGLGFAWLPRHLIE 245
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQrRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                         250
                  ....*....|....*
gi 1755689953 246 RELKDGQLKPLPLEQ 260
Cdd:PRK11074  247 PLINSGKLVELTLEN 261
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-290 1.56e-26

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: 103.52  E-value: 1.56e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  97 EVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQ--GYLGAGLCSVEFVAVAHP 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDdpGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 175 DHPLHRlQRQINFQDLESQLQVVIRDTGRTQPRNVGWLGA-----EQRWTVGSLSTAANFVSSGLGFAWLPRHLIERELK 249
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1755689953 250 DGQLKPLPLEQGGSRHPsFYLYSNKDKALGPASQILVELIK 290
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 97-259 1.11e-25

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 100.81  E-value: 1.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  97 EVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI--TG-LDIQGYLGAGLCSVEFVAVAH 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIgaTGeLPPGGVKTRPLGEVEFVFAVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 174 PDHPLHRLQRQINFQDLESQLQVVIRDTGRTQP-RNVGWLGAEQRWTVGSLSTAANFVSSGLGFAWLPRHLIERELKDGQ 252
Cdd:cd08431    81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160


                  ....*..
gi 1755689953 253 LKPLPLE 259
Cdd:cd08431   161 LVEKALE 167
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-290 1.20e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.12  E-value: 1.20e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   7 TLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEEL 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  87 AHHMEQGWEAEVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQ--GYLGAGLC 164
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPdpGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 165 SVEFVAVAHPDHPLhrlqrqinfqdlesqlqvvirdtgrtqprnvgwlgAEQRWTVGSLSTAANFVSSGLGFAWLPRHLI 244
Cdd:COG0583   162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1755689953 245 ERELKDGQLKPLPLEQGGSRHPsFYLYSNKDKALGPASQILVELIK 290
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-260 5.63e-30

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 115.04  E-value: 5.63e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  14 LQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKqasQLEELAHHMEQ- 92
Cdd:PRK11074   10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK---KMQETRRQCQQv 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  93 --GWEAEVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI---TGLDIQG-YLGAGLCSV 166
Cdd:PRK11074   87 anGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIgatRAIPVGGrFAFRDMGML 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 167 EFVAVAHPDHPLHRLQRQINFQDLESQLQVVIRDTGRTQPRNVGWLGAEQ-RWTVGSLSTAANFVSSGLGFAWLPRHLIE 245
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQrRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                         250
                  ....*....|....*
gi 1755689953 246 RELKDGQLKPLPLEQ 260
Cdd:PRK11074  247 PLINSGKLVELTLEN 261
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-290 1.56e-26

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: 103.52  E-value: 1.56e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  97 EVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQ--GYLGAGLCSVEFVAVAHP 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDdpGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 175 DHPLHRlQRQINFQDLESQLQVVIRDTGRTQPRNVGWLGA-----EQRWTVGSLSTAANFVSSGLGFAWLPRHLIERELK 249
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1755689953 250 DGQLKPLPLEQGGSRHPsFYLYSNKDKALGPASQILVELIK 290
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 97-259 1.11e-25

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 100.81  E-value: 1.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  97 EVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI--TG-LDIQGYLGAGLCSVEFVAVAH 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIgaTGeLPPGGVKTRPLGEVEFVFAVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 174 PDHPLHRLQRQINFQDLESQLQVVIRDTGRTQP-RNVGWLGAEQRWTVGSLSTAANFVSSGLGFAWLPRHLIERELKDGQ 252
Cdd:cd08431    81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160


                  ....*..
gi 1755689953 253 LKPLPLE 259
Cdd:cd08431   161 LVEKALE 167
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-305 8.66e-24

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 98.73  E-value: 8.66e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  12 RTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEELAHHME 91
Cdd:PRK10094    8 RTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  92 QGWEAEVRLVVDAAYPNARLVRALSAFMPQSRG-CRVRLREEVLSGVEEVLLEGSADLAI--TGLD--IQGYLGAGLCSV 166
Cdd:PRK10094   88 DGVERQVNIVINNLLYNPQAVAQLLAWLNERYPfTQFHISRQIYMGVWDSLLYEGFSLAIgvTGTEalANTFSLDPLGSV 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 167 EFVAVAHPDHPLHRLQRQINFQDLESQLQVVIRDTGRTQPRNVGW-LGAEQRWTVGSLSTAANFVSSGLGFAWLPRHLIE 245
Cdd:PRK10094  168 QWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWrLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQ 247

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 246 RELKDGQLKPLPLEQGgsRHPSFYLYSNKDKALGPASQILVELIKTfdSAPLDAPFAAPL 305
Cdd:PRK10094  248 SMIDNQQLVSRVIPTM--RPPSPLSLAWRKFGSGKAVEDIVTLFTQ--RRPEISGFLEIF 303
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 97-289 2.91e-17

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: 78.41  E-value: 2.91e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  97 EVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQgylGAGLCSV-----EFVAV 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVD---DPGLESEplfeePLVLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 172 AHPDHPLHRlQRQINFQDLESQlQVVIRDTGRTQPRNVGWLGAEQRWT------VGSLSTAANFVSSGLGFAWLPRHLIE 245
Cdd:cd05466    78 VPPDHPLAK-RKSVTLADLADE-PLILFERGSGLRRLLDRAFAEAGFTpnialeVDSLEAIKALVAAGLGIALLPESAVE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1755689953 246 rELKDGQLKPLPLEQGGSRHPsFYLYSNKDKALGPASQILVELI 289
Cdd:cd05466   156 -ELADGGLVVLPLEDPPLSRT-IGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 2.27e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 2.27e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   8 LDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-259 1.18e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 75.83  E-value: 1.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   7 TLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQ---LVKQASQ- 82
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRilaLCEETCRa 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  83 LEELaHHMEQGweaevRLVVDA-----AYPNARLVRALSAFMPQSrgcRVRLREEVLSGVEEVLLEGSADLAITG----- 152
Cdd:CHL00180   86 LEDL-KNLQRG-----TLIIGAsqttgTYLMPRLIGLFRQRYPQI---NVQLQVHSTRRIAWNVANGQIDIAIVGgevpt 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 153 -----LDIQGYLgaglcSVEFVAVAHPDHPLHRLQR-------QINFQDLESQLQV--VIRDTGRTQPRNVGWLGAEQRw 218
Cdd:CHL00180  157 elkkiLEITPYV-----EDELALIIPKSHPFAKLKKiqkedlyRLNFITLDSNSTIrkVIDNILIQNGIDSKRFKIEME- 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1755689953 219 tVGSLSTAANFVSSGLGFAWLPRHLIERELKDGQLKPLPLE 259
Cdd:CHL00180  231 -LNSIEAIKNAVQSGLGAAFVSVSAIEKELELGLLHWIKIE 270
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 137-289 1.05e-13

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: 68.67  E-value: 1.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 137 VEEVLLEGSADLAItgldIQG-YLGAGLCSVEF-----VAVAHPDHPLHRLQRqINFQDLEsQLQVVIRDTG----RTQP 206
Cdd:cd08420    41 IAERVLDGEIDLGL----VEGpVDHPDLIVEPFaedelVLVVPPDHPLAGRKE-VTAEELA-AEPWILREPGsgtrEVFE 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 207 RNVGWLGAEQ-----RWTVGSlsTAA--NFVSSGLGFAWLPRHLIERELKDGQLKPLPLEqGGSRHPSFYLYSNKDKALG 279
Cdd:cd08420   115 RALAEAGLDGldlniVMELGS--TEAikEAVEAGLGISILSRLAVRKELELGRLVALPVE-GLRLTRPFSLIYHKDKYLS 191

                         170
                  ....*....|
gi 1755689953 280 PASQILVELI 289
Cdd:cd08420   192 PAAEAFLEFL 201
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-193 1.43e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 66.90  E-value: 1.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  12 RTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEELAHHME 91
Cdd:PRK11242    7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  92 QGWEAEVRLVVD---AAYPNARLVRALSAFMPqsrGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQgylgaglcSVEF 168
Cdd:PRK11242   87 DLSRGSLRLAMTptfTAYLIGPLIDAFHARYP---GITLTIREMSQERIEALLADDELDVGIAFAPVH--------SPEI 155

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1755689953 169 VA----------VAHPDHPLHRLQRQINFQDLESQ 193
Cdd:PRK11242  156 EAqplftetlalVVGRHHPLAARRKALTLDELADE 190
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 111-289 2.08e-11

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: 61.91  E-value: 2.08e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 111 LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI----TGLDIQGYLGAGLCSVEFVAVAHPDHPLHRLQRqIN 186
Cdd:cd08435    15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrlaDDEQPPDLASEELADEPLVVVARPGHPLARRAR-LT 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 187 FQDLESQ--------------LQVVIRDTGRTQPRNVgwlgAEqrwtVGSLSTAANFVSSGLGFAWLPRHLIERELKDGQ 252
Cdd:cd08435    94 LADLADYpwvlpppgtplrqrLEQLFAAAGLPLPRNV----VE----TASISALLALLARSDMLAVLPRSVAEDELRAGV 165

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1755689953 253 LKPLPLEQGGSRhPSFYLYSNKDKALGPASQILVELI 289
Cdd:cd08435   166 LRELPLPLPTSR-RPIGITTRRGGPLSPAARALLDAL 201
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-256 2.39e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 63.25  E-value: 2.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   9 DQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLrIEGRKAVLTEAGEVLLRrsrqLVKQASQLE-ELA 87
Cdd:PRK03635    5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQRLLR----HARQVRLLEaELL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  88 HHMEQGWEAEVRLVVdAAypNAR-----LVRALSAFMPQSrgcRVRLreEVLsgVE------EVLLEGSADLAITGLD-- 154
Cdd:PRK03635   80 GELPALDGTPLTLSI-AV--NADslatwFLPALAPVLARS---GVLL--DLV--VEdqdhtaELLRRGEVVGAVTTEPqp 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 155 IQGYLGAGLCSVEFVAVAHPDHPLHRLQRQINFQDLES----------QLQV-VIRDTGRTQPrnvgwlGAEQRWTVGSl 223
Cdd:PRK03635  150 VQGCRVDPLGAMRYLAVASPAFAARYFPDGVTAEALAKapavvfnrkdDLQDrFLRQAFGLPP------GSVPCHYVPS- 222

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1755689953 224 STA-ANFVSSGLGFAWLPRHLIERELKDGQLKPL 256
Cdd:PRK03635  223 SEAfVRAALAGLGWGMIPELQIEPELASGELVDL 256
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-256 1.91e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 60.37  E-value: 1.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   7 TLD--QWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLrIEGRKAVLTEAGEVLLRrsrqLVKQASQLE 84
Cdd:PRK13348    1 MLDykQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLR----HLRQVALLE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  85 -ELAHHMEQGWEAEVRLV--VDAAYPNARLVRALSAFMPQSRgCRVRLREEVLSGVEEVLLEGSADLAITGLD--IQG-- 157
Cdd:PRK13348   76 aDLLSTLPAERGSPPTLAiaVNADSLATWFLPALAAVLAGER-ILLELIVDDQDHTFALLERGEVVGCVSTQPkpMRGcl 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 158 --YLGA----GLCSVEFVAVAHPDH-PLHRLQ--------RQINFQD--LESQLQVVIRDTGRTQ-PRNVGWLGAeqrwt 219
Cdd:PRK13348  155 aePLGTmryrCVASPAFAARYFAQGlTRHSALkapavafnRKDTLQDsfLEQLFGLPVGAYPRHYvPSTHAHLAA----- 229

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1755689953 220 vgslstaanfVSSGLGFAWLPRHLIERELKDGQLKPL 256
Cdd:PRK13348  230 ----------IRHGLGYGMVPELLIGPLLAAGRLVDL 256
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 126-289 3.80e-10

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: 58.31  E-value: 3.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 126 RVRLREEVLSGVEEVLLEGSADLAIT-------GLDIQGylgagLCSVEFVAVAHPDHPLHRlQRQINFQDL-------- 190
Cdd:cd08440    30 RVRLRDVSAEQVIEAVRSGEVDFGIGsepeadpDLEFEP-----LLRDPFVLVCPKDHPLAR-RRSVTWAELagyplial 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 191 --ESQLQVVIRDTGRTQPRNVGWlgaeqRWTVGSLSTAANFVSSGLGFAWLPRHLIERELKDG-QLKPLPlEQGGSRHps 267
Cdd:cd08440   104 grGSGVRALIDRALAAAGLTLRP-----AYEVSHMSTALGMVAAGLGVAVLPALALPLADHPGlVARPLT-EPVVTRT-- 175

                         170       180
                  ....*....|....*....|..
gi 1755689953 268 FYLYSNKDKALGPASQILVELI 289
Cdd:cd08440   176 VGLIRRRGRSLSPAAQAFLDLL 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-184 5.38e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 59.22  E-value: 5.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   8 LDQWRTLQAVVDHG-GFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAV-LTEAGEVLLRRSRQLVKQASQL-- 83
Cdd:PRK12684    3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLkr 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  84 --EELAHHmEQGweaevRLVVDAAYPNAR--LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQGYl 159
Cdd:PRK12684   83 vgKEFAAQ-DQG-----NLTIATTHTQARyaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADY- 155

                         170       180       190
                  ....*....|....*....|....*....|
gi 1755689953 160 gAGLCSVEF-----VAVAHPDHPLhrLQRQ 184
Cdd:PRK12684  156 -KELVSLPCyqwnhCVVVPPDHPL--LERK 182
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-193 1.09e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 58.49  E-value: 1.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   6 VTLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEE 85
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  86 LAHHMEQgweAEVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITG--LDIQGYLGAGL 163
Cdd:PRK15421   82 ACNEPQQ---TRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSdiLPRSGLHYSPM 158

                         170       180       190
                  ....*....|....*....|....*....|
gi 1755689953 164 CSVEFVAVAHPDHPLhRLQRQINFQDLESQ 193
Cdd:PRK15421  159 FDYEVRLVLAPDHPL-AAKTRITPEDLASE 187
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-78 3.43e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 56.96  E-value: 3.43e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1755689953   8 LDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVK 78
Cdd:PRK15092   13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR 83
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 113-289 4.13e-09

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


Pssm-ID: 176111  Cd Length: 197  Bit Score: 55.21  E-value: 4.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 113 RALSAFMPQSRGCRVRL----REEVLsgveEVLLEGSADLAITGldiQGYLGAGLCSVEF-----VAVAHPDHPLHRlQR 183
Cdd:cd08419    16 RLLGAFCRRHPGVEVSLrvgnREQVL----ERLADNEDDLAIMG---RPPEDLDLVAEPFldnplVVIAPPDHPLAG-QK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 184 QINFQDLESQlQVVIRDTGRTQPRNVGWLGAEQRWT------VGSLSTAANFVSSGLGFAWLPRHLIERELKDGQLKPL- 256
Cdd:cd08419    88 RIPLERLARE-PFLLREPGSGTRLAMERFFAEHGVTlrvrmeLGSNEAIKQAVMAGLGLSVLSLHTLALELATGRLAVLd 166

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1755689953 257 ----PLEqggsRHpsFYLYSNKDKALGPASQILVELI 289
Cdd:cd08419   167 vegfPIR----RQ--WYVVHRKGKRLSPAAQAFLDFL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
2-240 4.43e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 56.27  E-value: 4.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   2 KAPRVTLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQAS 81
Cdd:PRK09986    3 RLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  82 Q----LEELAHHmEQGwEAEVRLVVDAAYpnARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI---TGLD 154
Cdd:PRK09986   83 QslarVEQIGRG-EAG-RIEIGIVGTALW--GRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrmADLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 155 IQGYLGAGLCSVEFVAVAHP-DHPLHRLQRqINFQDLESQLQVVIRDTGRTQPRNVGWLGAEQRWT------VGSLSTAA 227
Cdd:PRK09986  159 PNPGFTSRRLHESAFAVAVPeEHPLASRSS-VPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSpqiirqVNEPQTVL 237

                         250
                  ....*....|...
gi 1755689953 228 NFVSSGLGFAWLP 240
Cdd:PRK09986  238 AMVSMGIGITLLP 250
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-240 4.67e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 56.32  E-value: 4.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  12 RTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEELAHHME 91
Cdd:PRK09906    7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  92 QGWE---------AEVRlVVDAAYPNARLvralsafmpQSRGCRVRLREEVLSGVEEVLLEGSADLAIT-------GLDI 155
Cdd:PRK09906   87 QEDRqltigfvpsAEVN-LLPKVLPMFRL---------RHPDTLIELVSLITTQQEEKLRRGELDVGFMrhpvysdEIDY 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 156 QGYLGAGLcsvefVAVAHPDHPLHRLQRqINFQDLESqLQVVIRD---TGRTQPRNVGWLGAEQR-----WTVGSLSTAA 227
Cdd:PRK09906  157 LELLDEPL-----VVVLPVDHPLAHEKE-ITAAQLDG-VNFISTDpaySGSLAPIIKAWFAQHNSqpnivQVATNILVTM 229

                         250
                  ....*....|...
gi 1755689953 228 NFVSSGLGFAWLP 240
Cdd:PRK09906  230 NLVGMGLGCTIIP 242
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-287 5.80e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 56.23  E-value: 5.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   5 RVTLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLE 84
Cdd:PRK10837    2 HITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  85 ELAhhmeQGWEAEVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLR----EEVLSGVEEV-----LLEGSADLaiTGLDI 155
Cdd:PRK10837   82 QLF----REDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSvgnsQDVINAVLDFrvdigLIEGPCHS--PELIS 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 156 QGYLgaglcSVEFVAVAHPDHPLhrLQRQINFQDLeSQLQVVIRDTGRTQPRNVGWL------GAEQRWTVGSLSTAANF 229
Cdd:PRK10837  156 EPWL-----EDELVVFAAPDSPL--ARGPVTLEQL-AAAPWILRERGSGTREIVDYLllshlpRFELAMELGNSEAIKHA 227

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1755689953 230 VSSGLGFAWLPRHLIERELKDGQLKPLPLEqGGSRHPSFYLYSNKDKALGPASQILVE 287
Cdd:PRK10837  228 VRHGLGISCLSRRVIADQLQAGTLVEVAVP-LPRLMRTLYRIHHRQKHLSNALQRFLS 284
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 25-182 1.59e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 51.97  E-value: 1.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  25 QAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAV-LTEAGEVLLRRSRQLVKQASQLEELAHHMEQGWEAevRLVVD 103
Cdd:PRK12683   21 EVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSG--HLTVA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 104 AAYPNAR--LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQGYlgAGLCSVEF-----VAVAHPDH 176
Cdd:PRK12683   99 TTHTQARyaLPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDRE--PDLVSFPYyswhhVVVVPKGH 176


                  ....*.
gi 1755689953 177 PLHRLQ 182
Cdd:PRK12683  177 PLTGRE 182
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 110-259 2.80e-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: 49.91  E-value: 2.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 110 RLVRALSAFMPqsrGCRVRLREEVLSGVEEVLLEGSADLAITGLDIqgyLGAGLCSV-----EFVAVAHPDHPlhRLQRQ 184
Cdd:cd08417    17 PLLARLRQEAP---GVRLRFVPLDRDDLEEALESGEIDLAIGVFPE---LPPGLRSQplfedRFVCVARKDHP--LAGGP 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 185 INFQDLESQLQVVIRDTGRTQPRNVGWLGAEQ-----RWTVGSLSTAANFVSSGLGFAWLPRHLIERELKDGQLK--PLP 257
Cdd:cd08417    89 LTLEDYLAAPHVLVSPRGRGHGLVDDALAELGlsrrvALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRvlPLP 168


                  ..
gi 1755689953 258 LE 259
Cdd:cd08417   169 FE 170
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-287 4.90e-07

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 49.44  E-value: 4.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  98 VRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI-------TGLDIQGYlgaglCSVEFVA 170
Cdd:cd08421     2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIvagnvdaAGLETRPY-----RTDRLVV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 171 VAHPDHPLHRlQRQINFQDL----------ESQLQVVIRD----TGRTQprNVgwlgaeqRWTVGSLSTAANFVSSGLGF 236
Cdd:cd08421    77 VVPRDHPLAG-RASVAFADTldhdfvglpaGSALHTFLREaaarLGRRL--RL-------RVQVSSFDAVCRMVAAGLGI 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1755689953 237 AWLPRHLIERELKDGQLKPLPLEQGGSRHPsFYLYSNKDKALGPASQILVE 287
Cdd:cd08421   147 GIVPESAARRYARALGLRVVPLDDAWARRR-LLLCVRSFDALPPAARALVD 196
PRK12680 PRK12680
LysR family transcriptional regulator;
6-257 4.92e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 50.39  E-value: 4.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   6 VTLDQWRTLQAVVDHG-GFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRK-AVLTEAGEVLLRRSRQLVKQASQL 83
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSlESVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  84 EELAHHmeQGWEAEVRLVVDAAYPNARLV--RALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGlDIQGYLGA 161
Cdd:PRK12680   81 RTYAAN--QRRESQGQLTLTTTHTQARFVlpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVS-TAGGEPSA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 162 GLCSVEF----VAVAHPDHPLHRLQRQINFQDLESQLQVVIRDTGRTQP---RNVGWLGAEQRWTVGSLST--AANFVSS 232
Cdd:PRK12680  158 GIAVPLYrwrrLVVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSslqRAFAQLGLEPSIALTALDAdlIKTYVRA 237

                         250       260
                  ....*....|....*....|....*
gi 1755689953 233 GLGFAWLPRHLIERELKDGQLKPLP 257
Cdd:PRK12680  238 GLGVGLLAEMAVNANDEDLRAWPAP 262
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
17-85 5.74e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 50.14  E-value: 5.74e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1755689953  17 VVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEE 85
Cdd:PRK10632   13 VVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHE 81
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 17-150 6.71e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 49.99  E-value: 6.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  17 VVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEELAHHMEQGWEA 96
Cdd:PRK14997   13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1755689953  97 EVRLVVDAAYPNARLVRALSAFMPQSRGcrVRLREEVLSGVEEVLLEGsADLAI 150
Cdd:PRK14997   93 IVKLTCPVTLLHVHIGPMLAKFMARYPD--VSLQLEATNRRVDVVGEG-VDVAI 143
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-289 7.11e-07

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 48.84  E-value: 7.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  97 EVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAIT--GLDIQGYLGAGLCSVEFVAVAHP 174
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAfsPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 175 DHPLHRlQRQINFQDL----------ESQLQVVIRDTGRTQPRNVgwlgaEQRWTVGSLSTAANFVSSGLGFAWLPRHLI 244
Cdd:cd08426    81 GHPLAR-QPSVTLAQLagyplalpppSFSLRQILDAAFARAGVQL-----EPVLISNSIETLKQLVAAGGGISLLTELAV 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1755689953 245 ERELKDGQLKPLPLEQGGSRHPSFYLYSNKDKALGPASQILVELI 289
Cdd:cd08426   155 RREIRRGQLVAVPLADPHMNHRQLELQTRAGRQLPAAASAFLQLL 199
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 14-87 7.62e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 49.64  E-value: 7.62e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1755689953  14 LQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEELA 87
Cdd:PRK11151    9 LVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 115-290 8.12e-07

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: 48.89  E-value: 8.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 115 LSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLDIQGYLG----AGLCSVEFVAVAHPDHPlhrLQRQINFQDL 190
Cdd:cd08418    19 INRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKelisEPLFESDFVVVARKDHP---LQGARSLEEL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 191 ESQLQVV----------IRDTGRTQPRNVgwlgaEQRWTVGSLSTAANFVSSGLGFAWLPRHLIERELKDGQLKPLPLEQ 260
Cdd:cd08418    96 LDASWVLpgtrmgyynnLLEALRRLGYNP-----RVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRLITIPVEE 170

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1755689953 261 ggsRHPS--FYLYSNKDKALGPASQILVELIK 290
Cdd:cd08418   171 ---PLPSadYYLIYRKKSRLTPLAEQLVELFR 199
PRK10341 PRK10341
transcriptional regulator TdcA;
15-294 2.77e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 47.93  E-value: 2.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  15 QAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRS----RQLVKQASQLEELAHhm 90
Cdd:PRK10341   16 QEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSesitREMKNMVNEINGMSS-- 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  91 eqgweaevRLVVDAAYPNARLV------RALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGLD----IQGYLG 160
Cdd:PRK10341   94 --------EAVVDVSFGFPSLIgftfmsDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSnemkLQDLHV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 161 AGLCSVEFVAVAHPDHPlhrLQRQINFQDLESQlQVVIRDTgrtqprNVGW----LGAEQRWTVG--------SLSTAAN 228
Cdd:PRK10341  166 EPLFESEFVLVASKSRT---CTGTTTLESLKNE-QWVLPQT------NMGYyselLTTLQRNGISienivktdSVVTIYN 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1755689953 229 FVSSGLGFAWLPRHLIeRELKDGQLKPLPLEQggsRHPS--FYLYSNKDKALGPASQILVELIKTFDS 294
Cdd:PRK10341  236 LVLNADFLTVIPCDMT-SPFGSNQFITIPIEE---TLPVaqYAAVWSKNYRIKKAASVLVELAKEYSS 299
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-289 9.64e-06

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: 45.28  E-value: 9.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 110 RLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGL---DIQGYLGAGLCSVEFVAVAHPDHPL-HRlqRQI 185
Cdd:cd08436    14 DLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLperRPPGLASRELAREPLVAVVAPDHPLaGR--RRV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 186 NFQDL--------------ESQLQVVIRDTGrtqprnvgwLGAEQRWTVGSLSTAANFVSSGLGFAWLPRHLIERelkDG 251
Cdd:cd08436    92 ALADLadepfvdfppgtgaRRQVDRAFAAAG---------VRRRVAFEVSDVDLLLDLVARGLGVALLPASVAAR---LP 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1755689953 252 QLKPLPLEQGGSRHpsFYLYSNKDKAlGPASQILVELI 289
Cdd:cd08436   160 GLAALPLEPAPRRR--LYLAWSAPPP-SPAARAFLELL 194
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-190 4.12e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 44.60  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   8 LDQWRTLQAVVDHG-GFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAV-LTEAGEVLLRRSRQLVKQASQLEE 85
Cdd:PRK12682    3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  86 LAhhmEQGWEAEV-RLVVDAAYPNARLV--RALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAIT--GLDIQGYLG 160
Cdd:PRK12682   83 IG---DDFSNQDSgTLTIATTHTQARYVlpRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAteSLADDPDLA 159

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1755689953 161 AGLC-SVEFVAVAHPDHPLhRLQRQINFQDL 190
Cdd:PRK12682  160 TLPCyDWQHAVIVPPDHPL-AQEERITLEDL 189
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 163-271 4.70e-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: 43.58  E-value: 4.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 163 LCSVEFVAVAHPD---------HP--LHRLQRqINFQDLESQLQVVIRDTGRTQPRNVgwlgaEQRWTVGSLSTAANFVS 231
Cdd:cd08422    67 LGPVRRVLVASPAylarhgtpqTPedLARHRC-LGYRLPGRPLRWRFRRGGGEVEVRV-----RGRLVVNDGEALRAAAL 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1755689953 232 SGLGFAWLPRHLIERELKDGQLKPLpLEQGGSRHPSFYLY 271
Cdd:cd08422   141 AGLGIALLPDFLVAEDLASGRLVRV-LPDWRPPPLPIYAV 179
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-153 4.77e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 44.04  E-value: 4.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  31 HRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQLEELAHHMEQGWEAEVRLV--VDAAYpn 108
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFcsVTAAY-- 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1755689953 109 ARLVRALSAFMPQSRGCRVRLR--------EEVLSgveevlleGSADLAITGL 153
Cdd:PRK11716   80 SHLPPILDRFRAEHPLVEIKLTtgdaadavEKVQS--------GEADLAIAAK 124
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 110-241 6.09e-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: 43.28  E-value: 6.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 110 RLVRALSAFMPQSRgcrVRLREEVLSGVEEVLLEGSADLAITGL--DIQGYLGAGLCSVEFVAVAHPDHPLhRLQRQINF 187
Cdd:cd08411    18 RLLPALRQAYPKLR---LYLREDQTERLLEKLRSGELDAALLALpvDEPGLEEEPLFDEPFLLAVPKDHPL-AKRKSVTP 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 188 QDLESQlQVVIRDTG---RTQPRNV-GWLGAEQRWTV--GSLSTAANFVSSGLGFAWLPR 241
Cdd:cd08411    94 EDLAGE-RLLLLEEGhclRDQALELcRLAGAREQTDFeaTSLETLRQMVAAGLGITLLPE 152
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 224-289 6.22e-05

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 43.05  E-value: 6.22e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1755689953 224 STAANFVSSGLGFAWLPRHLIERELKDGQLKP---LPLEQGGsrhpSFYLYSNKDKALGPASQILVELI 289
Cdd:cd08481   130 SMLAQAAVAGLGVALLPRFLIEEELARGRLVVpfnLPLTSDK----AYYLVYPEDKAESPPVQAFRDWL 194
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 111-260 2.46e-04

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


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 41.39  E-value: 2.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 111 LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAITGL--DIQGYLGAGLCSVEFVAVAHPDHPLhRLQRQINFQ 188
Cdd:cd08438    15 FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLpvDEEEFDSQPLCNEPLVAVLPRGHPL-AGRKTVSLA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 189 DL----------ESQLQVVIRDTGRTQ---PRNVGwlgaeqrwTVGSLSTAANFVSSGLGFAWLPRhLIERELKDGQLKP 255
Cdd:cd08438    94 DLadepfilfneDFALHDRIIDACQQAgftPNIAA--------RSSQWDFIAELVAAGLGVALLPR-SIAQRLDNAGVKV 164


                  ....*
gi 1755689953 256 LPLEQ 260
Cdd:cd08438   165 IPLTD 169
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
13-88 3.53e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 41.53  E-value: 3.53e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1755689953  13 TLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEvllrrsRQLVKQASQLEELAH 88
Cdd:PRK10086   21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK------RVFWALKSSLDTLNQ 90
PRK09791 PRK09791
LysR family transcriptional regulator;
6-290 5.91e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 40.90  E-value: 5.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   6 VTLDQWRTLQAVVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLvkqasqLEE 85
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLI------LEE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  86 LAHHME-----QGWEA-EVRLVVDAAYPNARLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAI-----TGLD 154
Cdd:PRK09791   79 LRAAQEdirqrQGQLAgQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyyqGPYD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 155 IQgYLGAGLCSVEFVAVAHPDHPLHRLQRQINFQDLE-----------SQLQVVIRDTGRTQPRNVgwlGAEQRWTVGSL 223
Cdd:PRK09791  159 HE-FTFEKLLEKQFAVFCRPGHPAIGARSLKQLLDYSwtmptphgsyyKQLSELLDDQAQTPQVGV---VCETFSACISL 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1755689953 224 STAANFVSSglgfawLPRHLIERELKDGQLKPLPLEQGGSRhPSFYLYSNKDKALGPASQILVELIK 290
Cdd:PRK09791  235 VAKSDFLSI------LPEEMGCDPLHGQGLVMLPVSEILPK-ATYYLIQRRDTRQTPLTASLITLFR 294
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 17-82 6.29e-04

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 40.82  E-value: 6.29e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1755689953  17 VVDHGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSRQLVKQASQ 82
Cdd:PRK11233   12 IVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ 77
cbl PRK12679
HTH-type transcriptional regulator Cbl;
25-151 7.67e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.56  E-value: 7.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953  25 QAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAV-LTEAGEVLLRRSRQLVKQASQLEELAHHMEQgwEAEVRLVVD 103
Cdd:PRK12679   21 EVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTN--DTSGVLTIA 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1755689953 104 AAYPNAR--LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAIT 151
Cdd:PRK12679   99 TTHTQARysLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIA 148
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
1-92 1.30e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.41  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953   1 MKAPRVTLDQWRTLQAVVDHGG--FAQAAEATHRSQSSVSYTVARMqEQLGvpLLRIE-----GRK--AVLTEAGEVLLR 71
Cdd:COG1846    31 LAELGLTPAQFRVLAALAEAGGltQSELAERLGLTKSTVSRLLDRL-EEKG--LVEREpdpedRRAvlVRLTEKGRALLE 107

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1755689953  72 RSRQLVKQ----------ASQLEELAHHMEQ 92
Cdd:COG1846   108 EARPALEAllaellaglsEEELEALLRLLRR 138
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 141-289 1.37e-03

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 39.06  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 141 LLEGSADLAITGL--DIQGYLGAGLCSVEFVAVAHPDHPLHRlQRQINFQDLESQLQVVIRDT--GRT-----------Q 205
Cdd:cd08434    45 LKNGELDLALCSPvpDEPDIEWIPLFTEELVLVVPKDHPLAG-RDSVDLAELADEPFVLLSPGfgLRPivdelcaaagfT 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 206 PRnVGWLGAEqrwtvgsLSTAANFVSSGLGFAWLPRHLIERELKdgqLKPLPLEQGGSRHPsFYLYSNKDKALGPASQIL 285
Cdd:cd08434   124 PK-IAFEGEE-------DSTIAGLVAAGLGVAILPEMTLLNPPG---VKKIPIKDPDAERT-IGLAWLKDRYLSPAARRF 191


                  ....
gi 1755689953 286 VELI 289
Cdd:cd08434   192 KDFV 195
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 111-237 1.77e-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: 38.70  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755689953 111 LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGSADLAIT-------GLDIQgylgaGLCSVEFVAVAHPDHPLHRLqR 183
Cdd:cd08415    15 LPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLAslpldhpGLESE-----PLASGRAVCVLPPGHPLARK-D 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1755689953 184 QINFQDLESQLQVVIRDTGRTQPRNVGWLGAEQ-----RWTVGSLSTAANFVSSGLGFA 237
Cdd:cd08415    89 VVTPADLAGEPLISLGRGDPLRQRVDAAFERAGvepriVIETQLSHTACALVAAGLGVA 147
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 6-47 2.00e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 36.03  E-value: 2.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1755689953   6 VTLDQWRTLQAVVDHGG--FAQAAEATHRSQSSVSYTVARMQEQ 47
Cdd:pfam12802   3 LTPAQFRVLLALARNPGltVAELARRLGISKQTVSRLVKRLEAK 46
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 20-74 2.97e-03

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 38.67  E-value: 2.97e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1755689953  20 HGGFAQAAEATHRSQSSVSYTVARMQEQLGVPLLRIEGRKAVLTEAGEVLLRRSR 74
Cdd:PRK11139   20 HLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIR 74
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 217-271 3.73e-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 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 37.83  E-value: 3.73e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1755689953 217 RWTVGSLSTAANFVSSGLGFAWLPRHLIERELKDGQLKPLpLEQGGSRHPSFYLY 271
Cdd:cd08474   131 PLILNDSDLMLDAALDGLGIAYLFEDLVAEHLASGRLVRV-LEDWSPPFPGGYLY 184
 
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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