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Conserved domains on  [gi|226718951|gb|ACO78122|]
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transcriptional regulator, LysR family [Azotobacter vinelandii DJ]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 3.16e-50

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.58  E-value: 3.16e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLED 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  81 LAHHMEQGWEAEVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSL 158
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 159 SEVEFVAVAHPDHPLhrpqrtltaadlesqmqvvirdtgrrqprdigwlgAEQRWTVGSLATAATFVGSGLGFAWLPCHL 238
Cdd:COG0583  161 GEERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 226718951 239 IRRELAEGLLKPLPLAEGATHRPrFQLYADKDKPLGPATRILVELIK 285
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 3.16e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.58  E-value: 3.16e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLED 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  81 LAHHMEQGWEAEVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSL 158
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 159 SEVEFVAVAHPDHPLhrpqrtltaadlesqmqvvirdtgrrqprdigwlgAEQRWTVGSLATAATFVGSGLGFAWLPCHL 238
Cdd:COG0583  161 GEERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 226718951 239 IRRELAEGLLKPLPLAEGATHRPrFQLYADKDKPLGPATRILVELIK 285
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 9-255 1.96e-27

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 108.11  E-value: 1.96e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   9 LQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKqagQLEDLAHHMEQ- 87
Cdd:PRK11074  10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK---KMQETRRQCQQv 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  88 --GWEAEVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAI---SSLSISG-YLGSSLSEV 161
Cdd:PRK11074  87 anGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIgatRAIPVGGrFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 162 EFVAVAHPDHPLHRPQRTLTAADLESQMQVVIRDTGRRQPRDIGWLGAEQ-RWTVGSLATAATFVGSGLGFAWLPCHLIR 240
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQrRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250
                 ....*....|....*
gi 226718951 241 RELAEGLLKPLPLAE 255
Cdd:PRK11074 247 PLINSGKLVELTLEN 261
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-285 2.82e-24

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: 97.36  E-value: 2.82e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   92 EVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSLSEVEFVAVAHP 169
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPddPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  170 DHPLHRpQRTLTAADLESQMQVVIRDTGRRQPRDIGWLGA-----EQRWTVGSLATAATFVGSGLGFAWLPCHLIRRELA 244
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 226718951  245 EGLLKPLPLAEGATHRPrFQLYADKDKPLGPATRILVELIK 285
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 92-255 4.17e-24

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: 96.57  E-value: 4.17e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  92 EVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISS---LSISGYLGSSLSEVEFVAVAH 168
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGAtgeLPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 169 PDHPLHRPQRTLTAADLESQMQVVIRDTGRRQP-RDIGWLGAEQRWTVGSLATAATFVGSGLGFAWLPCHLIRRELAEGL 247
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160


                 ....*...
gi 226718951 248 LKPLPLAE 255
Cdd:cd08431  161 LVEKALED 168
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 3.16e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.58  E-value: 3.16e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLED 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  81 LAHHMEQGWEAEVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSL 158
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 159 SEVEFVAVAHPDHPLhrpqrtltaadlesqmqvvirdtgrrqprdigwlgAEQRWTVGSLATAATFVGSGLGFAWLPCHL 238
Cdd:COG0583  161 GEERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 226718951 239 IRRELAEGLLKPLPLAEGATHRPrFQLYADKDKPLGPATRILVELIK 285
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 9-255 1.96e-27

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 108.11  E-value: 1.96e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   9 LQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKqagQLEDLAHHMEQ- 87
Cdd:PRK11074  10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK---KMQETRRQCQQv 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  88 --GWEAEVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAI---SSLSISG-YLGSSLSEV 161
Cdd:PRK11074  87 anGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIgatRAIPVGGrFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 162 EFVAVAHPDHPLHRPQRTLTAADLESQMQVVIRDTGRRQPRDIGWLGAEQ-RWTVGSLATAATFVGSGLGFAWLPCHLIR 240
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQrRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250
                 ....*....|....*
gi 226718951 241 RELAEGLLKPLPLAE 255
Cdd:PRK11074 247 PLINSGKLVELTLEN 261
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-285 2.82e-24

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: 97.36  E-value: 2.82e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   92 EVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSLSEVEFVAVAHP 169
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPddPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  170 DHPLHRpQRTLTAADLESQMQVVIRDTGRRQPRDIGWLGA-----EQRWTVGSLATAATFVGSGLGFAWLPCHLIRRELA 244
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 226718951  245 EGLLKPLPLAEGATHRPrFQLYADKDKPLGPATRILVELIK 285
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 92-255 4.17e-24

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: 96.57  E-value: 4.17e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  92 EVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISS---LSISGYLGSSLSEVEFVAVAH 168
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGAtgeLPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 169 PDHPLHRPQRTLTAADLESQMQVVIRDTGRRQP-RDIGWLGAEQRWTVGSLATAATFVGSGLGFAWLPCHLIRRELAEGL 247
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160


                 ....*...
gi 226718951 248 LKPLPLAE 255
Cdd:cd08431  161 LVEKALED 168
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
7-248 2.73e-23

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 97.18  E-value: 2.73e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   7 RTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLEDLAHHME 86
Cdd:PRK10094   8 RTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVN 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  87 QGWEAEVRLVVD----AAYPTLRLVRALSAFMPQSrgcRVRLREEVLSGVEEVLLEGGADLAI---SSLSISGYLGS-SL 158
Cdd:PRK10094  88 DGVERQVNIVINnllyNPQAVAQLLAWLNERYPFT---QFHISRQIYMGVWDSLLYEGFSLAIgvtGTEALANTFSLdPL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 159 SEVEFVAVAHPDHPLHRPQRTLTAADLESQMQVVIRDTGRRQPRDIGW-LGAEQRWTVGSLAT--AATFVGSGLGFawLP 235
Cdd:PRK10094 165 GSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWrLPGQKEIIVPDMETkiAAHLAGVGIGF--LP 242

                        250
                 ....*....|...
gi 226718951 236 CHLIRRELAEGLL 248
Cdd:PRK10094 243 KSLCQSMIDNQQL 255
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 2.64e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 2.64e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 226718951    3 LDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-284 1.77e-16

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: 76.10  E-value: 1.77e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  92 EVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSLSEVEFVAVAHP 169
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVddPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 170 DHPLHRpQRTLTAADLeSQMQVVIRDTGRRQPRDIGWLGAEQRWT------VGSLATAATFVGSGLGFAWLPcHLIRREL 243
Cdd:cd05466   81 DHPLAK-RKSVTLADL-ADEPLILFERGSGLRRLLDRAFAEAGFTpnialeVDSLEAIKALVAAGLGIALLP-ESAVEEL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 226718951 244 AEGLLKPLPLAEGATHRPrFQLYADKDKPLGPATRILVELI 284
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRT-IGLVWRKGRYLSPAARAFLELL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 2-248 1.80e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 75.06  E-value: 1.80e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   2 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLK------QA 75
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceetcRA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  76 gqLEDLaHHMEQGweaevRLVVDA-----AYPTLRLVRALSAFMPQSrgcRVRLREEVLSGVEEVLLEGGADLAISSLSI 150
Cdd:CHL00180  86 --LEDL-KNLQRG-----TLIIGAsqttgTYLMPRLIGLFRQRYPQI---NVQLQVHSTRRIAWNVANGQIDIAIVGGEV 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 151 SGYLGSSLS-----EVEFVAVAHPDHPLHRPQRTLT---------AADLESQMQVVIRDTGRRQPRDIGWLGAEQRwtVG 216
Cdd:CHL00180 155 PTELKKILEitpyvEDELALIIPKSHPFAKLKKIQKedlyrlnfiTLDSNSTIRKVIDNILIQNGIDSKRFKIEME--LN 232

                        250       260       270
                 ....*....|....*....|....*....|..
gi 226718951 217 SLATAATFVGSGLGFAWLPCHLIRRELAEGLL 248
Cdd:CHL00180 233 SIEAIKNAVQSGLGAAFVSVSAIEKELELGLL 264
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-188 1.25e-14

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 72.68  E-value: 1.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLK--QAGQ- 77
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQdlEAGRr 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  78 -LEDlAHHMEQGweaEVRLVVD---AAYPTLRLVRALSAFMPqsrGCRVRLREEVLSGVEEVLLEGGADLAIsslsisGY 153
Cdd:PRK11242  81 aIHD-VADLSRG---SLRLAMTptfTAYLIGPLIDAFHARYP---GITLTIREMSQERIEALLADDELDVGI------AF 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 226718951 154 LGSSLSEVEFVA--------VAHPDHPLHRPQRTLTAADLESQ 188
Cdd:PRK11242 148 APVHSPEIEAQPlftetlalVVGRHHPLAARRKALTLDELADE 190
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-185 4.31e-13

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 68.46  E-value: 4.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAV-LTEAGTVLLRRSRQLLKQAGQL 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  79 ----EDLAHHmEQGweaevRLVVDAAYPTLR--LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSISG 152
Cdd:PRK12684  81 krvgKEFAAQ-DQG-----NLTIATTHTQARyaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIAD 154

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 226718951 153 YLG-SSLS--EVEFVAVAHPDHPLHRpQRTLTAADL 185
Cdd:PRK12684 155 YKElVSLPcyQWNHCVVVPPDHPLLE-RKPLTLEDL 189
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
4-95 1.55e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 63.64  E-value: 1.55e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   4 DQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLrIEGRKAVLTEAGTVLLRrsrqLLKQAGQLE-DLA 82
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQRLLR----HARQVRLLEaELL 79

                         90
                 ....*....|...
gi 226718951  83 HHMEQGWEAEVRL 95
Cdd:PRK03635  80 GELPALDGTPLTL 92
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 132-284 1.79e-11

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 62.12  E-value: 1.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 132 VEEVLLEGGADLAI-------SSLSISGYLgsslsEVEFVAVAHPDHPLHRPQRtLTAADLEsQMQVVIRDTG---RR-- 199
Cdd:cd08420   41 IAERVLDGEIDLGLvegpvdhPDLIVEPFA-----EDELVLVVPPDHPLAGRKE-VTAEELA-AEPWILREPGsgtREvf 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 200 ----QPRDIGWLGAEQRWTVGSLATAATFVGSGLGFAWLPCHLIRRELAEGLLKPLPLAEGATHRPrFQLYADKDKPLGP 275
Cdd:cd08420  114 eralAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVALPVEGLRLTRP-FSLIYHKDKYLSP 192


                 ....*....
gi 226718951 276 ATRILVELI 284
Cdd:cd08420  193 AAEAFLEFL 201
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-251 2.03e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.45  E-value: 2.03e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   2 TLD--QWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLrIEGRKAVLTEAGTVLLRrsrqLLKQAGQLE 79
Cdd:PRK13348   1 MLDykQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLR----HLRQVALLE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  80 -DLAHHMEQGWEAEVRLV--VDAAYPTLRLVRALSAFMPQSRgCRVRLREEVLSGVEEVLLEGGADLAISSLS--ISGYL 154
Cdd:PRK13348  76 aDLLSTLPAERGSPPTLAiaVNADSLATWFLPALAAVLAGER-ILLELIVDDQDHTFALLERGEVVGCVSTQPkpMRGCL 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 155 GSSLSEVEFVAVAHPD-HPLHRPQRTLTAADLESQMQVVIRDTGRRQprdiGWLGAEQRWTVGSLAT-----AATFVGS- 227
Cdd:PRK13348 155 AEPLGTMRYRCVASPAfAARYFAQGLTRHSALKAPAVAFNRKDTLQD----SFLEQLFGLPVGAYPRhyvpsTHAHLAAi 230

                        250       260
                 ....*....|....*....|....*.
gi 226718951 228 --GLGFAWLPCHLIRRELAEGLLKPL 251
Cdd:PRK13348 231 rhGLGYGMVPELLIGPLLAAGRLVDL 256
PRK09986 PRK09986
LysR family transcriptional regulator;
7-182 3.59e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 62.43  E-value: 3.59e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   7 RTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQ----LEDLA 82
Cdd:PRK09986  13 RYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQslarVEQIG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  83 HHmEQGwEAEVRLVVDAAYPTLRLvrALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAI---SSLSISGYLGSSLS 159
Cdd:PRK09986  93 RG-EAG-RIEIGIVGTALWGRLRP--AMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrmADLEPNPGFTSRRL 168

                        170       180
                 ....*....|....*....|....*
gi 226718951 160 EVEFVAVAHP-DHPL-HRPQRTLTA 182
Cdd:PRK09986 169 HESAFAVAVPeEHPLaSRSSVPLKA 193
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-186 6.49e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 61.71  E-value: 6.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLED 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  81 LAHHMEQGWE---------AEVRlVVDAAYPTLRLvralsafmpQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI- 150
Cdd:PRK09906  81 RARKIVQEDRqltigfvpsAEVN-LLPKVLPMFRL---------RHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVy 150

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 226718951 151 SGYLGSSLSEVEFVAVAHP-DHPLHRPQRtLTAADLE 186
Cdd:PRK09906 151 SDEIDYLELLDEPLVVVLPvDHPLAHEKE-ITAAQLD 186
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-188 9.72e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 61.57  E-value: 9.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   7 RTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLEDLAHHME 86
Cdd:PRK15421   8 KTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQ 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  87 QgweAEVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISS--LSISGYLGSSLSEVEFV 164
Cdd:PRK15421  88 Q---TRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSdiLPRSGLHYSPMFDYEVR 164

                        170       180
                 ....*....|....*....|....
gi 226718951 165 AVAHPDHPLHRPQRtLTAADLESQ 188
Cdd:PRK15421 165 LVLAPDHPLAAKTR-ITPEDLASE 187
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 3-73 1.83e-10

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 60.81  E-value: 1.83e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 226718951   3 LDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLK 73
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR 83
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 121-284 1.06e-09

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: 57.15  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 121 RVRLREEVLSGVEEVLLEGGADLAIsslsisGYLGSSLSEVE--------FVAVAHPDHPLHRpQRTLTAADLESQMQVV 192
Cdd:cd08440   30 RVRLRDVSAEQVIEAVRSGEVDFGI------GSEPEADPDLEfepllrdpFVLVCPKDHPLAR-RRSVTWAELAGYPLIA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 193 I-RDTGRRQPRDIGWLGAEQR----WTVGSLATAATFVGSGLGFAWLPcHLIRRELAEGLLKPLPLAEGATHRpRFQLYA 267
Cdd:cd08440  103 LgRGSGVRALIDRALAAAGLTlrpaYEVSHMSTALGMVAAGLGVAVLP-ALALPLADHPGLVARPLTEPVVTR-TVGLIR 180

                        170
                 ....*....|....*..
gi 226718951 268 DKDKPLGPATRILVELI 284
Cdd:cd08440  181 RRGRSLSPAAQAFLDLL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-81 1.19e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 58.16  E-value: 1.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLED 80
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQ 82


                 .
gi 226718951  81 L 81
Cdd:PRK10837  83 L 83
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 106-284 2.90e-09

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: 55.74  E-value: 2.90e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 106 LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLS----ISGYLGSSLSEVEFVAVAHPDHPLHRPQRtLT 181
Cdd:cd08435   15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLAddeqPPDLASEELADEPLVVVARPGHPLARRAR-LT 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 182 AADLESQ--------------MQVVIRDTGRRQPRDIgwlgAEqrwtVGSLATAATFVGSGLGFAWLPCHLIRRELAEGL 247
Cdd:cd08435   94 LADLADYpwvlpppgtplrqrLEQLFAAAGLPLPRNV----VE----TASISALLALLARSDMLAVLPRSVAEDELRAGV 165

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 226718951 248 LKPLPLAEGATHRPrFQLYADKDKPLGPATRILVELI 284
Cdd:cd08435  166 LRELPLPLPTSRRP-IGITTRRGGPLSPAARALLDAL 201
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-182 3.21e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 56.98  E-value: 3.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAV-LTEAGTVLLRRSRQLLKQAGQL 78
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  79 EDLAHHMEQGWEAevRLVV-----DAAYPTLRLVRALSAFMPQsrgCRVRLREEVLSGVEEVLLEGGADLAISSLSISGY 153
Cdd:PRK12683  81 RRLAEQFADRDSG--HLTVatthtQARYALPKVVRQFKEVFPK---VHLALRQGSPQEIAEMLLNGEADIGIATEALDRE 155

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 226718951 154 lgSSLSEVEF-----VAVAHPDHPL-HRPQRTLTA 182
Cdd:PRK12683 156 --PDLVSFPYyswhhVVVVPKGHPLtGRENLTLEA 188
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-185 6.34e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 56.15  E-value: 6.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAV-LTEAGTVLLRRSRQLLKQAGQL 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  79 EDLAhhmEQGWEAEV-RLVV-----DAAYPTLRLVRALSAFMPQsrgCRVRLREEVLSGVEEVLLEGGADLAISSLSISG 152
Cdd:PRK12682  81 KRIG---DDFSNQDSgTLTIatthtQARYVLPRVVAAFRKRYPK---VNLSLHQGSPDEIARMVISGEADIGIATESLAD 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 226718951 153 YlgSSLS-----EVEFVAVAHPDHPLHRPQRtLTAADL 185
Cdd:PRK12682 155 D--PDLAtlpcyDWQHAVIVPPDHPLAQEER-ITLEDL 189
PRK12680 PRK12680
LysR family transcriptional regulator;
1-234 1.00e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 55.40  E-value: 1.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   1 MTLDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRK-AVLTEAGTVLLRRSRQLLKQAGQL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSlESVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  79 EDLAHHMEQGWEAEVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLS---ISGYLG 155
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAggePSAGIA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 156 SSLSEVEFVAVAHPDHPLHRPQRTLTAADLESQMQVVIRDTGRRQP---RDIGWLGAEQRWTVGSLAT--AATFVGSGLG 230
Cdd:PRK12680 161 VPLYRWRRLVVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSslqRAFAQLGLEPSIALTALDAdlIKTYVRAGLG 240


                 ....
gi 226718951 231 FAWL 234
Cdd:PRK12680 241 VGLL 244
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 9-82 1.26e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 51.95  E-value: 1.26e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 226718951   9 LQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLEDLA 82
Cdd:PRK11151   9 LVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 12-145 1.82e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 51.53  E-value: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  12 VVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLEDLAHHMEQGWEA 91
Cdd:PRK14997  13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226718951  92 EVRLVVDAAYPTLRLVRALSAFMPQSRGcrVRLREEVLSGVEEVLLEgGADLAI 145
Cdd:PRK14997  93 IVKLTCPVTLLHVHIGPMLAKFMARYPD--VSLQLEATNRRVDVVGE-GVDVAI 143
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-284 5.94e-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: 49.23  E-value: 5.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  92 EVRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAI--SSLSISGYLGSSLSEVEFVAVAHP 169
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLafSPPPEPGIRVHSRQPAPIGAVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 170 DHPLHRpQRTLTAADLeSQMQVVI--RDTGRRQPRDIgwLGAEQRWTVG------SLATAATFVGSGLGFAWLPCHLIRR 241
Cdd:cd08426   81 GHPLAR-QPSVTLAQL-AGYPLALppPSFSLRQILDA--AFARAGVQLEpvlisnSIETLKQLVAAGGGISLLTELAVRR 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 226718951 242 ELAEGLLKPLPLAE-GATHRPrFQLYADKDKPLGPATRILVELI 284
Cdd:cd08426  157 EIRRGQLVAVPLADpHMNHRQ-LELQTRAGRQLPAAASAFLQLL 199
PRK10341 PRK10341
transcriptional regulator TdcA;
10-182 1.73e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 48.71  E-value: 1.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  10 QAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKqagQLEDLAHHMEQGW 89
Cdd:PRK10341  16 QEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITR---EMKNMVNEINGMS 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  90 EAEVrLVVDAAYPTL----RLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLS----ISGYLGSSLSEV 161
Cdd:PRK10341  93 SEAV-VDVSFGFPSLigftFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSnemkLQDLHVEPLFES 171

                        170       180
                 ....*....|....*....|.
gi 226718951 162 EFVAVAHPDHPLHRPqRTLTA 182
Cdd:PRK10341 172 EFVLVASKSRTCTGT-TTLES 191
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-282 1.82e-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: 176113  Cd Length: 198  Bit Score: 47.52  E-value: 1.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  93 VRLVVDAAYPTLRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSISGylgSSL-----SEVEFVAVA 167
Cdd:cd08421    2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDA---AGLetrpyRTDRLVVVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 168 HPDHPLHRpQRTLTAADL----------ESQMQVVIRDTGRRQPRDIgwlgaEQRWTVGSLATAATFVGSGLGFAWLPCH 237
Cdd:cd08421   79 PRDHPLAG-RASVAFADTldhdfvglpaGSALHTFLREAAARLGRRL-----RLRVQVSSFDAVCRMVAAGLGIGIVPES 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 226718951 238 LIRRELAEGLLKPLPLAEGATHRpRFQLYADKDKPLGPATRILVE 282
Cdd:cd08421  153 AARRYARALGLRVVPLDDAWARR-RLLLCVRSFDALPPAARALVD 196
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
12-78 3.60e-06

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 47.83  E-value: 3.60e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 226718951  12 VVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQL 78
Cdd:PRK10632  13 VVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDV 79
cbl PRK12679
HTH-type transcriptional regulator Cbl;
20-153 1.73e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 45.57  E-value: 1.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  20 QAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAV-LTEAGTVLLRRSRQLLKQAGQLEDLAHHMEQgwEAEVRLVVD 98
Cdd:PRK12679  21 EVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTN--DTSGVLTIA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 226718951  99 AAYPTLR--LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSISGY 153
Cdd:PRK12679  99 TTHTQARysLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSND 155
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-145 2.06e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 45.38  E-value: 2.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951   8 TLQAVVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVL---LRRSRQLLKQAgqLEDLAHH 84
Cdd:PRK10086  21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwaLKSSLDTLNQE--ILDIKNQ 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 226718951  85 MEQGweaevRLVVdAAYPTLR---LVRALSAFM---PQsrgcrvrLREEVLSGVEEVLLEG-GADLAI 145
Cdd:PRK10086  99 ELSG-----TLTV-YSRPSIAqcwLVPRLADFTrryPS-------ISLTILTGNENVNFQRaGIDLAI 153
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 12-145 2.65e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 45.06  E-value: 2.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  12 VVDHGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLEDLAHHMEQGWEA 91
Cdd:PRK11233  12 IVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSG 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 226718951  92 EVRLVVD----AAYPTLRLVRALSAFMPqsrGCRVRLREEVLSGVEEVLLEGGADLAI 145
Cdd:PRK11233  92 QVSIGLApgtaASSLTMPLLQAVRAEFP---GIVLYLHENSGATLNEKLMNGQLDMAV 146
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 99-232 4.09e-05

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: 43.70  E-value: 4.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  99 AAYPTLR---LVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSLSEVEFVAVAHPDHPL 173
Cdd:cd08415    5 AALPALAlslLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLdhPGLESEPLASGRAVCVLPPGHPL 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 226718951 174 HRpQRTLTAADLESQMQVVI---RDTGRRQPRDIGWLGAEQRWT--VGSLATAATFVGSGLGFA 232
Cdd:cd08415   85 AR-KDVVTPADLAGEPLISLgrgDPLRQRVDAAFERAGVEPRIVieTQLSHTACALVAAGLGVA 147
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 105-254 4.99e-05

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: 43.36  E-value: 4.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 105 RLVRALSAFMPqsrGCRVRLREEVLSGVEEVLLEGGADLAISSLSI--SGYLGSSLSEVEFVAVAHPDHPlhRPQRTLTA 182
Cdd:cd08417   17 PLLARLRQEAP---GVRLRFVPLDRDDLEEALESGEIDLAIGVFPElpPGLRSQPLFEDRFVCVARKDHP--LAGGPLTL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 183 ADLESQMQVVIRDTGRRQPRDIGWLGAEQ-----RWTVGSLATAATFVGSGLGFAWLPCHLIRReLAEGL---LKPLPLA 254
Cdd:cd08417   92 EDYLAAPHVLVSPRGRGHGLVDDALAELGlsrrvALTVPHFLAAPALVAGTDLIATVPRRLAEA-LAERLglrVLPLPFE 170
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 102-260 5.45e-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: 5.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 102 PTL------RLVRALSAFMPQSRgcrVRLREEVLSGVEEVLLEGGADLAISSLSISGylgSSLSEV-----EFVAVAHPD 170
Cdd:cd08411    9 PTIapyllpRLLPALRQAYPKLR---LYLREDQTERLLEKLRSGELDAALLALPVDE---PGLEEEplfdePFLLAVPKD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 171 HPLhRPQRTLTAADLESQmQVVIRDTG---RRQPRDI-GWLGAEQRWTV--GSLATAATFVGSGLGFAWLPCHLIR-REL 243
Cdd:cd08411   83 HPL-AKRKSVTPEDLAGE-RLLLLEEGhclRDQALELcRLAGAREQTDFeaTSLETLRQMVAAGLGITLLPELAVPsEEL 160

                        170
                 ....*....|....*..
gi 226718951 244 AEGLLKPLPLAEGATHR 260
Cdd:cd08411  161 RGDRLVVRPFAEPAPSR 177
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-284 5.79e-05

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 42.97  E-value: 5.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 104 LRLVRALSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLS---ISGYLGSSLSEVEFVAVAHPDHPLHRPqRTL 180
Cdd:cd08436   13 VDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPerrPPGLASRELAREPLVAVVAPDHPLAGR-RRV 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 181 TAADLESQMQV------VIRDTGRRQPRDIGwLGAEQRWTVGSLATAATFVGSGLGFAWLPCHLIRRelAEGLLKpLPLA 254
Cdd:cd08436   92 ALADLADEPFVdfppgtGARRQVDRAFAAAG-VRRRVAFEVSDVDLLLDLVARGLGVALLPASVAAR--LPGLAA-LPLE 167

                        170       180       190
                 ....*....|....*....|....*....|.
gi 226718951 255 EGathrPRFQLY-ADKDKPLGPATRILVELI 284
Cdd:cd08436  168 PA----PRRRLYlAWSAPPPSPAARAFLELL 194
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 15-74 7.20e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 43.68  E-value: 7.20e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951  15 HGGFAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQ 74
Cdd:PRK11139  20 HLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQ 79
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 110-285 2.03e-04

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 41.57  E-value: 2.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 110 LSAFMPQSRGCRVRLREEVLSGVEEVLLEGGADLAISSLSISGYLGSSLSEV----EFVAVAHPDHPLHRPQR------- 178
Cdd:cd08418   19 INRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPlfesDFVVVARKDHPLQGARSleellda 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 179 --TLTAADLESQMQvvIRDTGRRQ---PRDIgwLGAEQRWTVGSLATAATFVgsglgfAWLPCHLIRRELAEGLLKPLPL 253
Cdd:cd08418   99 swVLPGTRMGYYNN--LLEALRRLgynPRVA--VRTDSIVSIINLVEKADFL------TILSRDMGRGPLDSFRLITIPV 168

                        170       180       190
                 ....*....|....*....|....*....|....
gi 226718951 254 AEgatHRPRFQLYA--DKDKPLGPATRILVELIK 285
Cdd:cd08418  169 EE---PLPSADYYLiyRKKSRLTPLAEQLVELFR 199
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-101 4.53e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.96  E-value: 4.53e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 226718951  26 HRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLLRRSRQLLKQAGQLEDLAHHMEQGWEAEVRLV--VDAAY 101
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFcsVTAAY 79
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 136-284 9.81e-04

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 39.35  E-value: 9.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 136 LLEGGADLAI--SSLSISGYLGSSLSEVEFVAVAHPD----HPL-HRPQ-----RTLTAADLESQMQVVIRDTGRRQPRD 203
Cdd:cd08422   43 LVEEGFDLAIriGELPDSSLVARRLGPVRRVLVASPAylarHGTpQTPEdlarhRCLGYRLPGRPLRWRFRRGGGEVEVR 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 204 IgwlgaEQRWTVGSLATAATFVGSGLGFAWLPCHLIRRELAEGLLKPLpLAEGATHRPRFQLYADKDKPLGPATRILVEL 283
Cdd:cd08422  123 V-----RGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRV-LPDWRPPPLPIYAVYPSRRHLPAKVRAFIDF 196


                 .
gi 226718951 284 I 284
Cdd:cd08422  197 L 197
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 1-42 1.48e-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: 36.41  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 226718951    1 MTLDQWRTLQAVVDHGG--FAQAAEALHRSQSSVSYAIARMQEQ 42
Cdd:pfam12802   3 LTPAQFRVLLALARNPGltVAELARRLGISKQTVSRLVKRLEAK 46
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 103-284 2.37e-03

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. 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: 176124  Cd Length: 198  Bit Score: 38.35  E-value: 2.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 103 TLRLVRALSAFMPqsrGCRVRLREEVLSGVEEVLLEGGADLAI--SSLSISGYLGSSLSEVEFVAVAHPDHPLhRPQRTL 180
Cdd:cd08433   15 AVPLLRAVRRRYP---GIRLRIVEGLSGHLLEWLLNGRLDLALlyGPPPIPGLSTEPLLEEDLFLVGPADAPL-PRGAPV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 181 TAADLESQMQVV------IRDTGRRQPRDIGwLGAEQRWTVGSLATAATFVGSGLGFAWLPCHLIRRELAEGLLKPLPLA 254
Cdd:cd08433   91 PLAELARLPLILpsrghgLRRLVDEAAARAG-LTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGRLVAAPIV 169

                        170       180       190
                 ....*....|....*....|....*....|
gi 226718951 255 EGATHRpRFQLYADKDKPLGPATRILVELI 284
Cdd:cd08433  170 DPALTR-TLSLATPRDRPLSPAALAVRDLL 198
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
18-65 3.55e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.46  E-value: 3.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 226718951  18 FAQAAEALHRSQSSVSYAIARMQEQLGVPLLRIEGRKAVLTEAGTVLL 65
Cdd:PRK03601  18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL 65
PBP2_DntR_like_1 cd08460
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-253 6.99e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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. 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: 176149 [Multi-domain]  Cd Length: 200  Bit Score: 36.80  E-value: 6.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226718951 105 RLVRALSAFMPqsrGCRVRLREEVLSGVEEvLLEGGADLAISSLSISG--YLGSSLSEVEFVAVAHPDHPLHRpqRTLTA 182
Cdd:cd08460   17 ALLAAVAAEAP---GVRLRFVPESDKDVDA-LREGRIDLEIGVLGPTGpeIRVQTLFRDRFVGVVRAGHPLAR--GPITP 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 226718951 183 ADLESQMQVVIRDTGR-RQPRD--IGWLGAEQR--WTVGSLATAATFV-GSGLgFAWLPCHLIRRELAEGLLKPLPL 253
Cdd:cd08460   91 ERYAAAPHVSVSRRGRlHGPIDdaLAALGLTRRvvAVVPTFAAALFLArGSDL-IALVPERVTAAARAGLGLRTFPL 166
 
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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