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Conserved domains on  [gi|489303259|ref|WP_003210710|]
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MULTISPECIES: LysR family transcriptional regulator [Pseudomonas]

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 1.70e-42

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 146.94  E-value: 1.70e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDL 86
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  87 AHHMEQGWEAEVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGFII--PGYLGTEMS 164
Cdd:COG0583   82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 165 DVEFVAVAHPEHPLhqlhrelsfqdleshmqvvirdsgrqqprdvgwlgAEQRWTVGSLPTAATFVSSGLGFAWLPRHLI 244
Cdd:COG0583  162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489303259 245 ERELKEGLLKLLPLERGGSRNPtFYLYSNKDKPLGPATQILVELLR 290
Cdd:COG0583  207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-290 1.70e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 146.94  E-value: 1.70e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDL 86
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  87 AHHMEQGWEAEVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGFII--PGYLGTEMS 164
Cdd:COG0583   82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 165 DVEFVAVAHPEHPLhqlhrelsfqdleshmqvvirdsgrqqprdvgwlgAEQRWTVGSLPTAATFVSSGLGFAWLPRHLI 244
Cdd:COG0583  162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489303259 245 ERELKEGLLKLLPLERGGSRNPtFYLYSNKDKPLGPATQILVELLR 290
Cdd:COG0583  207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-243 7.28e-30

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 114.65  E-value: 7.28e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  14 LQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKnasQLEDLAHHMEQ- 92
Cdd:PRK11074  10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK---KMQETRRQCQQv 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  93 --GWEAEVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGF-IIP---GYLGTEMSDV 166
Cdd:PRK11074  87 anGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATrAIPvggRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 167 EFVAVAHPEHPLHQLHRELSFQDLESHMQVVIRDSGRQQPRDVGWLGAEQRWTVgsLP---TAATFVSSGLGFAWLPRHL 243
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLV--VPdweSAINCLSAGLCVGMVPTHF 244
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 97-244 1.61e-23

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: 95.03  E-value: 1.61e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  97 EVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAI--SGFIIPGYLGT-EMSDVEFVAVAH 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIgaTGELPPGGVKTrPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489303259 174 PEHPLHQLHRELSFQDLESHMQVVIRDSGRQQP-RDVGWLGAEQRWTVGSLPTAATFVSSGLGFAWLPRHLI 244
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLA 152
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-290 8.33e-20

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: 85.42  E-value: 8.33e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   97 EVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGFII--PGYLGTEMSDVEFVAVAHP 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPddPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  175 EHPLHQlHRELSFQDLESHMQVVIRDSGRQQPRDVGWLGA-----EQRWTVGSLPTAATFVSSGLGFAWLPRHLIERELK 249
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 489303259  250 EGLLKLLPLERGGSRNPtFYLYSNKDKPLGPATQILVELLR 290
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-290 1.70e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 146.94  E-value: 1.70e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDL 86
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  87 AHHMEQGWEAEVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGFII--PGYLGTEMS 164
Cdd:COG0583   82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 165 DVEFVAVAHPEHPLhqlhrelsfqdleshmqvvirdsgrqqprdvgwlgAEQRWTVGSLPTAATFVSSGLGFAWLPRHLI 244
Cdd:COG0583  162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489303259 245 ERELKEGLLKLLPLERGGSRNPtFYLYSNKDKPLGPATQILVELLR 290
Cdd:COG0583  207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLR 251
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-243 7.28e-30

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 114.65  E-value: 7.28e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  14 LQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKnasQLEDLAHHMEQ- 92
Cdd:PRK11074  10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK---KMQETRRQCQQv 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  93 --GWEAEVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGF-IIP---GYLGTEMSDV 166
Cdd:PRK11074  87 anGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATrAIPvggRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 167 EFVAVAHPEHPLHQLHRELSFQDLESHMQVVIRDSGRQQPRDVGWLGAEQRWTVgsLP---TAATFVSSGLGFAWLPRHL 243
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLV--VPdweSAINCLSAGLCVGMVPTHF 244
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 97-244 1.61e-23

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: 95.03  E-value: 1.61e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  97 EVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAI--SGFIIPGYLGT-EMSDVEFVAVAH 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIgaTGELPPGGVKTrPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489303259 174 PEHPLHQLHRELSFQDLESHMQVVIRDSGRQQP-RDVGWLGAEQRWTVGSLPTAATFVSSGLGFAWLPRHLI 244
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLA 152
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-245 2.77e-22

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 94.49  E-value: 2.77e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  12 RTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDLAHHME 91
Cdd:PRK10094   8 RTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVN 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  92 QGWEAEVRLVVDAAYPNARLVRALTAFMPQSRG-CRVRLREEVLSGVEELLMDGMADLAIsgfiipGYLGTE-------- 162
Cdd:PRK10094  88 DGVERQVNIVINNLLYNPQAVAQLLAWLNERYPfTQFHISRQIYMGVWDSLLYEGFSLAI------GVTGTEalantfsl 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 163 --MSDVEFVAVAHPEHPLHQLHRELSFQDLESHMQVVIRDSGRQQPRDVGW-LGAEQRWTVGSLPTAATFVSSGLGFAWL 239
Cdd:PRK10094 162 dpLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWrLPGQKEIIVPDMETKIAAHLAGVGIGFL 241


                 ....*.
gi 489303259 240 PRHLIE 245
Cdd:PRK10094 242 PKSLCQ 247
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-290 8.33e-20

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: 85.42  E-value: 8.33e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   97 EVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGFII--PGYLGTEMSDVEFVAVAHP 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPddPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  175 EHPLHQlHRELSFQDLESHMQVVIRDSGRQQPRDVGWLGA-----EQRWTVGSLPTAATFVSSGLGFAWLPRHLIERELK 249
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 489303259  250 EGLLKLLPLERGGSRNPtFYLYSNKDKPLGPATQILVELLR 290
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLR 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 6.64e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.88  E-value: 6.64e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259    8 LDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-239 1.22e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 72.75  E-value: 1.22e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQ---LVKNASQ- 82
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRilaLCEETCRa 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  83 LEDLaHHMEQGweaevRLVVDA-----AYPNARLVRALTAFMPQSrgcRVRLREEVLSGVEELLMDGMADLAISGFIIPG 157
Cdd:CHL00180  86 LEDL-KNLQRG-----TLIIGAsqttgTYLMPRLIGLFRQRYPQI---NVQLQVHSTRRIAWNVANGQIDIAIVGGEVPT 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 158 YLG-----TEMSDVEFVAVAHPEHPLHQLHR-------ELSFQDLESHMQV--VIRDSGRQQPRDVGWLGAEQRwtVGSL 223
Cdd:CHL00180 157 ELKkileiTPYVEDELALIIPKSHPFAKLKKiqkedlyRLNFITLDSNSTIrkVIDNILIQNGIDSKRFKIEME--LNSI 234

                        250
                 ....*....|....*.
gi 489303259 224 PTAATFVSSGLGFAWL 239
Cdd:CHL00180 235 EAIKNAVQSGLGAAFV 250
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-191 2.14e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 69.21  E-value: 2.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  12 RTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQlvknasQLEDLA---- 87
Cdd:PRK11242   7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARR------ALQDLEagrr 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  88 --HHMEQGWEAEVRLVVD---AAYPNARLVRALTAFMPqsrGCRVRLREEVLSGVEELLMDGMADLAIsGFIIPGYLGTE 162
Cdd:PRK11242  81 aiHDVADLSRGSLRLAMTptfTAYLIGPLIDAFHARYP---GITLTIREMSQERIEALLADDELDVGI-AFAPVHSPEIE 156

                        170       180       190
                 ....*....|....*....|....*....|..
gi 489303259 163 MSD--VEFVA-VAHPEHPLHQLHRELSFQDLE 191
Cdd:PRK11242 157 AQPlfTETLAlVVGRHHPLAARRKALTLDELA 188
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 97-289 2.92e-12

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 64.54  E-value: 2.92e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  97 EVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGFII--PGYLGTEMSDVEFVAVAHP 174
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVddPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 175 EHPLHQlHRELSFQDLeSHMQVVIRDSGRQQPRDVGWLGAEQRWT------VGSLPTAATFVSSGLGFAWLPRHLIEREL 248
Cdd:cd05466   81 DHPLAK-RKSVTLADL-ADEPLILFERGSGLRRLLDRAFAEAGFTpnialeVDSLEAIKALVAAGLGIALLPESAVEELA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 489303259 249 KEGLLKLLPLERGGSRnpTFYLYSNKDKPLGPATQILVELL 289
Cdd:cd05466  159 DGGLVVLPLEDPPLSR--TIGLVWRKGRYLSPAARAFLELL 197
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-100 6.90e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.79  E-value: 6.90e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   9 DQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLrIDGRKAVLTEAGEVLLRRSRQLvknaSQLE-DLA 87
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQRLLRHARQV----RLLEaELL 79

                         90
                 ....*....|...
gi 489303259  88 HHMEQGWEAEVRL 100
Cdd:PRK03635  80 GELPALDGTPLTL 92
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-190 2.00e-11

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 63.46  E-value: 2.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   8 LDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAV-LTEAGEVLLR---RSRQLVKNASQ 82
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILAsveRILQEVENLKR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  83 LEDLAHHMEQGweaevRLVVDAAYPNAR--LVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAI-----SGF-- 153
Cdd:PRK12684  83 VGKEFAAQDQG-----NLTIATTHTQARyaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIateaiADYke 157

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489303259 154 --IIPGYlgtemsDVEFVAVAHPEHPLHQLhRELSFQDL 190
Cdd:PRK12684 158 lvSLPCY------QWNHCVVVPPDHPLLER-KPLTLEDL 189
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-76 8.29e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 61.53  E-value: 8.29e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489303259   7 TLD--QWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLrIDGRKAVLTEAGEVLLRRSRQL 76
Cdd:PRK13348   1 MLDykQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLRHLRQV 71
PRK09986 PRK09986
LysR family transcriptional regulator;
2-82 1.33e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 60.89  E-value: 1.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   2 KAPRVTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNAS 81
Cdd:PRK09986   3 RLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAE 82


                 .
gi 489303259  82 Q 82
Cdd:PRK09986  83 Q 83
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-178 7.96e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 58.88  E-value: 7.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   6 VTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLED 85
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  86 LAHHMEQgweAEVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGFIIP--GYLGTEM 163
Cdd:PRK15421  82 ACNEPQQ---TRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPrsGLHYSPM 158

                        170
                 ....*....|....*
gi 489303259 164 SDVEFVAVAHPEHPL 178
Cdd:PRK15421 159 FDYEVRLVLAPDHPL 173
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 126-289 1.13e-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: 1.13e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 126 RVRLREEVLSGVEELLMDGMADLAIsgfiipGYLGTEMSDVE--------FVAVAHPEHPLHQlHRELSFQDLESHMQVV 197
Cdd:cd08440   30 RVRLRDVSAEQVIEAVRSGEVDFGI------GSEPEADPDLEfepllrdpFVLVCPKDHPLAR-RRSVTWAELAGYPLIA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 198 ------IRDSGRQQPRDVGWLgAEQRWTVGSLPTAATFVSSGLGFAWLPRHLIERELKEGLLKLLPLERGGSRnpTFYLY 271
Cdd:cd08440  103 lgrgsgVRALIDRALAAAGLT-LRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPGLVARPLTEPVVTR--TVGLI 179

                        170
                 ....*....|....*...
gi 489303259 272 SNKDKPLGPATQILVELL 289
Cdd:cd08440  180 RRRGRSLSPAAQAFLDLL 197
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 25-193 2.34e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 57.36  E-value: 2.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  25 QAAEALHRSQSSVSYTVARMQDQLGVPLL-RIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDLAHHMEQGWEAevRLVVD 103
Cdd:PRK12683  21 EVANALYTSQSGVSKQIKDLEDELGVEIFiRRGKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSG--HLTVA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 104 AAYPNAR--LVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISgfiiPGYLGTEMSDVEF-------VAVAHP 174
Cdd:PRK12683  99 TTHTQARyaLPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIA----TEALDREPDLVSFpyyswhhVVVVPK 174

                        170
                 ....*....|....*....
gi 489303259 175 EHPLHQLHrELSFQDLESH 193
Cdd:PRK12683 175 GHPLTGRE-NLTLEAIAEY 192
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-92 7.49e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 55.93  E-value: 7.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  12 RTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDLAHHME 91
Cdd:PRK09906   7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIV 86


                 .
gi 489303259  92 Q 92
Cdd:PRK09906  87 Q 87
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-78 8.69e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.80  E-value: 8.69e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489303259   8 LDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVK 78
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR 83
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-86 7.74e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 52.77  E-value: 7.74e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   5 RVTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLE 84
Cdd:PRK10837   2 HITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE 81


                 ..
gi 489303259  85 DL 86
Cdd:PRK10837  82 QL 83
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
17-83 1.93e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 51.68  E-value: 1.93e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489303259  17 VVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQL 83
Cdd:PRK10632  13 VVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDV 79
PRK12680 PRK12680
LysR family transcriptional regulator;
6-239 3.07e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.16  E-value: 3.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   6 VTLDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRK-AVLTEAGEVLLRRSRQLVKNASQL 83
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSlESVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  84 EDLAHHmeQGWEAEVRLVVDAAYPNARLV--RALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAI---------SG 152
Cdd:PRK12680  81 RTYAAN--QRRESQGQLTLTTTHTQARFVlpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvstaggepsAG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 153 FIIPGYLGTEMsdvefvAVAHPEHPLHQLHRELSFQDLESHMQVVIRDSGRQQP---RDVGWLGAEQRWTVGSLPT--AA 227
Cdd:PRK12680 159 IAVPLYRWRRL------VVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSslqRAFAQLGLEPSIALTALDAdlIK 232

                        250
                 ....*....|..
gi 489303259 228 TFVSSGLGFAWL 239
Cdd:PRK12680 233 TYVRAGLGVGLL 244
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 111-289 8.14e-07

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 48.81  E-value: 8.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 111 LVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAIS----GFIIPGYLGTEMSDVEFVAVAHPEHPLHQLHReLS 186
Cdd:cd08435   15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGrladDEQPPDLASEELADEPLVVVARPGHPLARRAR-LT 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 187 FQDLE--------------SHMQVVIRDSGRQQPRDVgwlgAEqrwtVGSLPTAATFVSSGLGFAWLPRHLIERELKEGL 252
Cdd:cd08435   94 LADLAdypwvlpppgtplrQRLEQLFAAAGLPLPRNV----VE----TASISALLALLARSDMLAVLPRSVAEDELRAGV 165

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489303259 253 LKLLPLERGGSRNPtFYLYSNKDKPLGPATQILVELL 289
Cdd:cd08435  166 LRELPLPLPTSRRP-IGITTRRGGPLSPAARALLDAL 201
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 14-87 1.04e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 49.26  E-value: 1.04e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489303259  14 LQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDLA 87
Cdd:PRK11151   9 LVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 17-129 1.28e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 49.22  E-value: 1.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  17 VVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDLAHHMEQGWEA 96
Cdd:PRK14997  13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489303259  97 EVRLVVDAAYPNARLVRALTAFMPQSRGCRVRL 129
Cdd:PRK14997  93 IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PRK10341 PRK10341
transcriptional regulator TdcA;
15-172 6.87e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 46.78  E-value: 6.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  15 QAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRS----RQLVKNASQLEDLAHhm 90
Cdd:PRK10341  16 QEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSesitREMKNMVNEINGMSS-- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  91 eqgweaevRLVVDAAYPNARLVrALTaFMPQ--------SRGCRVRLREEVLSGVEELLMDGMADLAIsgfiipGYLGTE 162
Cdd:PRK10341  94 --------EAVVDVSFGFPSLI-GFT-FMSDminkfkevFPKAQVSMYEAQLSSFLPAIRDGRLDFAI------GTLSNE 157

                        170       180
                 ....*....|....*....|
gi 489303259 163 MS----------DVEFVAVA 172
Cdd:PRK10341 158 MKlqdlhveplfESEFVLVA 177
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 137-289 1.60e-05

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: 44.79  E-value: 1.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 137 VEELLMDGMADLA-ISGFII-PGYLGTEMSDVEFVAVAHPEHPLHQLhRELSFQDLEsHMQVVIRDSG---RQ------Q 205
Cdd:cd08420   41 IAERVLDGEIDLGlVEGPVDhPDLIVEPFAEDELVLVVPPDHPLAGR-KEVTAEELA-AEPWILREPGsgtREvferalA 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 206 PRDVGWLGAEQRWTVGSlpTAA--TFVSSGLGFAWLPRHLIEReLKEGLLKLLPLERGGSRNPTFYLYSNKDKPLGPATQ 283
Cdd:cd08420  119 EAGLDGLDLNIVMELGS--TEAikEAVEAGLGISILSRLAVRK-ELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAE 195


                 ....*.
gi 489303259 284 ILVELL 289
Cdd:cd08420  196 AFLEFL 201
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 110-246 1.82e-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: 44.90  E-value: 1.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 110 RLVRALTAFMPqsrGCRVRLREEVLSGVEELLMDGMADLAISGFII--PGYLGTEMSDVEFVAVAHPEHPLhqLHRELSF 187
Cdd:cd08417   17 PLLARLRQEAP---GVRLRFVPLDRDDLEEALESGEIDLAIGVFPElpPGLRSQPLFEDRFVCVARKDHPL--AGGPLTL 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489303259 188 QDLESHMQVVIRDSGRQQPRDVGWLGAEQ-----RWTVGSLPTAATFVSSGLGFAWLPRHLIER 246
Cdd:cd08417   92 EDYLAAPHVLVSPRGRGHGLVDDALAELGlsrrvALTVPHFLAAPALVAGTDLIATVPRRLAEA 155
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-106 2.17e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 45.19  E-value: 2.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  31 HRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVknaSQLEDLAHHMEQGWEA---EVRLV--VDAA 105
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTL---LQWQQLRHTLDQQGPSlsgELSLFcsVTAA 78


                 .
gi 489303259 106 Y 106
Cdd:PRK11716  79 Y 79
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
13-67 4.64e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 44.22  E-value: 4.64e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489303259  13 TLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGE 67
Cdd:PRK10086  21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK 75
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-70 5.77e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 43.83  E-value: 5.77e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489303259   8 LDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAV-LTEAGEVLL 70
Cdd:PRK12682   3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVL 67
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 17-150 5.81e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.90  E-value: 5.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  17 VVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDLAHHMEQGWEA 96
Cdd:PRK11233  12 IVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSG 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489303259  97 EVRL-------VVDAAYPNARLVRAltafmpQSRGCRVRLREEVLSGVEELLMDGMADLAI 150
Cdd:PRK11233  92 QVSIglapgtaASSLTMPLLQAVRA------EFPGIVLYLHENSGATLNEKLMNGQLDMAV 146
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 20-74 7.38e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 43.68  E-value: 7.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489303259  20 HGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSR 74
Cdd:PRK11139  20 HLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIR 74
cbl PRK12679
HTH-type transcriptional regulator Cbl;
25-151 1.59e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 42.87  E-value: 1.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  25 QAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAV-LTEAGEVLLRRSRQLVKNASQLEDLAHHMEQgwEAEVRLVVD 103
Cdd:PRK12679  21 EVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTN--DTSGVLTIA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 489303259 104 AAYPNAR--LVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAIS 151
Cdd:PRK12679  99 TTHTQARysLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIA 148
PRK09801 PRK09801
LysR family transcriptional regulator;
12-200 4.03e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 41.56  E-value: 4.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  12 RTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLLRRSRQLVKNASQLEDLAHHME 91
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  92 QGWEAEVRLVVDAAYPNARLVRALTAFMPQSRGCRVRLreEVLSGVEELLMDGM-ADLAISGFIIPGYLGTEMSDVEFVA 170
Cdd:PRK09801  92 TRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF--ELFDRQIDLVQDNIdLDIRINDEIPDYYIAHLLTKNKRIL 169

                        170       180       190
                 ....*....|....*....|....*....|
gi 489303259 171 VAHPEHpLHQLHRELSFQDLESHMQVVIRD 200
Cdd:PRK09801 170 CAAPEY-LQKYPQPQSLQELSRHDCLVTKE 198
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
23-70 9.22e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 40.00  E-value: 9.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 489303259  23 FAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGEVLL 70
Cdd:PRK03601  18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL 65
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 6-47 1.56e-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: 1.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 489303259    6 VTLDQWRTLQAVVDHGG--FAQAAEALHRSQSSVSYTVARMQDQ 47
Cdd:pfam12802   3 LTPAQFRVLLALARNPGltVAELARRLGISKQTVSRLVKRLEAK 46
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
1-77 1.95e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.03  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259   1 MKAPRVTLDQWRTLQAVVDHGG--FAQAAEALHRSQSSVSYTVARMQDQlGvpLLRI-----DGRK--AVLTEAGEVLLR 71
Cdd:COG1846   31 LAELGLTPAQFRVLAALAEAGGltQSELAERLGLTKSTVSRLLDRLEEK-G--LVERepdpeDRRAvlVRLTEKGRALLE 107


                 ....*.
gi 489303259  72 RSRQLV 77
Cdd:COG1846  108 EARPAL 113
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-246 3.09e-03

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 37.97  E-value: 3.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 110 RLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAISGF---IIPGYLGTEMSDVEFVAVAHPEHPLHQLhRELS 186
Cdd:cd08436   14 DLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLperRPPGLASRELAREPLVAVVAPDHPLAGR-RRVA 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489303259 187 FQDLESHMQV------VIRDSGRQQPRDVGwLGAEQRWTVGSLPTAATFVSSGLGFAWLPRHLIER 246
Cdd:cd08436   93 LADLADEPFVdfppgtGARRQVDRAFAAAG-VRRRVAFEVSDVDLLLDLVARGLGVALLPASVAAR 157
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 113-245 4.66e-03

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: 37.49  E-value: 4.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 113 RALTAFMPQSRGCRVRL----REEVLsgveELLMDGMADLAISGFIiPGYLGTE---MSDVEFVAVAHPEHPLHQLHReL 185
Cdd:cd08419   16 RLLGAFCRRHPGVEVSLrvgnREQVL----ERLADNEDDLAIMGRP-PEDLDLVaepFLDNPLVVIAPPDHPLAGQKR-I 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489303259 186 SFQDLESHmQVVIRDSGRQQPRDVGWLGAEQRWT------VGSLPTAATFVSSGLGFAWLPRHLIE 245
Cdd:cd08419   90 PLERLARE-PFLLREPGSGTRLAMERFFAEHGVTlrvrmeLGSNEAIKQAVMAGLGLSVLSLHTLA 154
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-246 6.72e-03

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 37.12  E-value: 6.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259  98 VRLVVDAAYPNARLVRALTAFMPQSRGCRVRLREEVLSGVEELLMDGMADLAI-SGFIIPGYLGTEM-SDVEFVAVAHPE 175
Cdd:cd08421    2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIvAGNVDAAGLETRPyRTDRLVVVVPRD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489303259 176 HPLHQLhRELSFQDL----------ESHMQVVIRDSGRQQPRDVgwlgaEQRWTVGSLPTAATFVSSGLGFAWLPRHLIE 245
Cdd:cd08421   82 HPLAGR-ASVAFADTldhdfvglpaGSALHTFLREAAARLGRRL-----RLRVQVSSFDAVCRMVAAGLGIGIVPESAAR 155


                 .
gi 489303259 246 R 246
Cdd:cd08421  156 R 156
 
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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