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Conserved domains on  [gi|2084912661|ref|WP_221576036|]
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LysR family transcriptional regulator [Pseudomonas cichorii]

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];
7-289 4.78e-49

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 163.88  E-value: 4.78e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDL 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  87 AHHMEQGWEAEVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMS 164
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 165 TVEFIAVAHPEHPLhqakreltfqdlesqlqvvirdsgrqqprdigwlgAEQRWTVGSLGTATTFVSSGLGFAWLPRHMI 244
Cdd:COG0583   162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2084912661 245 ERELKEGVLKILPLDKGGSRNPsFYLYSSKDKPLGPATQILIDLI 289
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-289 4.78e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 163.88  E-value: 4.78e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDL 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  87 AHHMEQGWEAEVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMS 164
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 165 TVEFIAVAHPEHPLhqakreltfqdlesqlqvvirdsgrqqprdigwlgAEQRWTVGSLGTATTFVSSGLGFAWLPRHMI 244
Cdd:COG0583   162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2084912661 245 ERELKEGVLKILPLDKGGSRNPsFYLYSSKDKPLGPATQILIDLI 289
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFL 250
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-260 7.75e-30

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 114.65  E-value: 7.75e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  14 LQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHMEQG 93
Cdd:PRK11074   10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANG 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  94 WEAEVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFS-IP---GYLGTEMSTVEFI 169
Cdd:PRK11074   90 WRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRaIPvggRFAFRDMGMLSWA 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 170 AVAHPEHPLHQAKRELTFQDLESQLQVVIRDSGRQQPRDIGWLGAEQR------WTvgslgTATTFVSSGLGFAWLPRHM 243
Cdd:PRK11074  170 CVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRrlvvpdWE-----SAINCLSAGLCVGMVPTHF 244

                         250
                  ....*....|....*....
gi 2084912661 244 IERELKEGVL--KILPLDK 260
Cdd:PRK11074  245 AKPLINSGKLveLTLENPF 263
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-289 2.97e-25

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: 100.06  E-value: 2.97e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  97 EVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMSTVEFIAVAHP 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPddPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 175 EHPLHQaKRELTFQDLESQLQVVIRDSGRQQPRDIGWLGA-----EQRWTVGSLGTATTFVSSGLGFAWLPRHMIERELK 249
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084912661 250 EGVLKILPLDKGGSRNPsFYLYSSKDKPLGPATQILIDLI 289
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFL 200
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 97-260 4.82e-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: 93.87  E-value: 4.82e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  97 EVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAI--SGFSIPGYLGT-EMSTVEFIAVAH 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIgaTGELPPGGVKTrPLGEVEFVFAVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 174 PEHPLHQAKRELTFQDLESQLQVVIRDSGRQQP-RDIGWLGAEQRWTVGSLGTATTFVSSGLGFAWLPRHMIERELKEGV 252
Cdd:cd08431    81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160


                  ....*...
gi 2084912661 253 LKILPLDK 260
Cdd:cd08431   161 LVEKALED 168
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-289 4.78e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 163.88  E-value: 4.78e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDL 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  87 AHHMEQGWEAEVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMS 164
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPpdPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 165 TVEFIAVAHPEHPLhqakreltfqdlesqlqvvirdsgrqqprdigwlgAEQRWTVGSLGTATTFVSSGLGFAWLPRHMI 244
Cdd:COG0583   162 EERLVLVASPDHPL-----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2084912661 245 ERELKEGVLKILPLDKGGSRNPsFYLYSSKDKPLGPATQILIDLI 289
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFL 250
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-260 7.75e-30

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 114.65  E-value: 7.75e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  14 LQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHMEQG 93
Cdd:PRK11074   10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANG 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  94 WEAEVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFS-IP---GYLGTEMSTVEFI 169
Cdd:PRK11074   90 WRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRaIPvggRFAFRDMGMLSWA 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 170 AVAHPEHPLHQAKRELTFQDLESQLQVVIRDSGRQQPRDIGWLGAEQR------WTvgslgTATTFVSSGLGFAWLPRHM 243
Cdd:PRK11074  170 CVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRrlvvpdWE-----SAINCLSAGLCVGMVPTHF 244

                         250
                  ....*....|....*....
gi 2084912661 244 IERELKEGVL--KILPLDK 260
Cdd:PRK11074  245 AKPLINSGKLveLTLENPF 263
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-289 2.97e-25

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: 100.06  E-value: 2.97e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  97 EVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMSTVEFIAVAHP 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPddPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 175 EHPLHQaKRELTFQDLESQLQVVIRDSGRQQPRDIGWLGA-----EQRWTVGSLGTATTFVSSGLGFAWLPRHMIERELK 249
Cdd:pfam03466  83 DHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084912661 250 EGVLKILPLDKGGSRNPsFYLYSSKDKPLGPATQILIDLI 289
Cdd:pfam03466 162 DGRLVALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFL 200
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 97-260 4.82e-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: 93.87  E-value: 4.82e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  97 EVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAI--SGFSIPGYLGT-EMSTVEFIAVAH 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIgaTGELPPGGVKTrPLGEVEFVFAVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 174 PEHPLHQAKRELTFQDLESQLQVVIRDSGRQQP-RDIGWLGAEQRWTVGSLGTATTFVSSGLGFAWLPRHMIERELKEGV 252
Cdd:cd08431    81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPpRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160


                  ....*...
gi 2084912661 253 LKILPLDK 260
Cdd:cd08431   161 LVEKALED 168
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-301 3.47e-21

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 91.41  E-value: 3.47e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  12 RTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHME 91
Cdd:PRK10094    8 RTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  92 QGWEAEVRLVVD----AAYPTARLVRALTAFMPQSrgcRVRLREEVLSGVEEVLLEGTADLAIsgfsipGYLGTE----- 162
Cdd:PRK10094   88 DGVERQVNIVINnllyNPQAVAQLLAWLNERYPFT---QFHISRQIYMGVWDSLLYEGFSLAI------GVTGTEalant 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 163 -----MSTVEFIAVAHPEHPLHQAKRELTFQDLESQLQVVIRDSGRQQPRDIGW-LGAEQRWTVGSLGTATTFVSSGLGF 236
Cdd:PRK10094  159 fsldpLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWrLPGQKEIIVPDMETKIAAHLAGVGI 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2084912661 237 AWLPRHMIERELKEGVLKILPLDKGgsRNPSFYLYSSKDKPLGPATQILIDLISTfdTAPLTAAF 301
Cdd:PRK10094  239 GFLPKSLCQSMIDNQQLVSRVIPTM--RPPSPLSLAWRKFGSGKAVEDIVTLFTQ--RRPEISGF 299
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-259 2.27e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 80.83  E-value: 2.27e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   7 TLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQ---LVKQASQ- 82
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRilaLCEETCRa 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  83 LEDLaHHMEQGweaevRLVVDA-----AYPTARLVRALTAFMPQSrgcRVRLREEVLSGVEEVLLEGTADLAISGFSIPG 157
Cdd:CHL00180   86 LEDL-KNLQRG-----TLIIGAsqttgTYLMPRLIGLFRQRYPQI---NVQLQVHSTRRIAWNVANGQIDIAIVGGEVPT 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 158 YLGTEMSTVEF--------IAVAHPEHPLHQAKRE----LTFQDLESQLQV--VIRDSGRQQPRDIGWLGAEQRwtVGSL 223
Cdd:CHL00180  157 ELKKILEITPYvedelaliIPKSHPFAKLKKIQKEdlyrLNFITLDSNSTIrkVIDNILIQNGIDSKRFKIEME--LNSI 234

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 2084912661 224 GTATTFVSSGLGFAWLPRHMIERELKEGVLKILPLD 259
Cdd:CHL00180  235 EAIKNAVQSGLGAAFVSVSAIEKELELGLLHWIKIE 270
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-66 3.10e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 3.10e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2084912661   8 LDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAG 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 97-289 1.78e-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: 1.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  97 EVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMSTVEFIAVAHP 174
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVddPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 175 EHPLHQaKRELTFQDLESQlQVVIRDSGRQQPRDIGWLGAEQRWT------VGSLGTATTFVSSGLGFAWLPRHMIErEL 248
Cdd:cd05466    81 DHPLAK-RKSVTLADLADE-PLILFERGSGLRRLLDRAFAEAGFTpnialeVDSLEAIKALVAAGLGIALLPESAVE-EL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2084912661 249 KEGVLKILPLDKGGSRNPsFYLYSSKDKPLGPATQILIDLI 289
Cdd:cd05466   158 ADGGLVVLPLEDPPLSRT-IGLVWRKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-193 1.52e-14

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 72.68  E-value: 1.52e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  12 RTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHME 91
Cdd:PRK11242    7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  92 QGWEAEVRLVVD---AAYPTARLVRALTAFMPqsrGCRVRLREEVLSGVEEVLLEGTADLAIsGFSIPGYLGTEMST--V 166
Cdd:PRK11242   87 DLSRGSLRLAMTptfTAYLIGPLIDAFHARYP---GITLTIREMSQERIEALLADDELDVGI-AFAPVHSPEIEAQPlfT 162

                         170       180
                  ....*....|....*....|....*...
gi 2084912661 167 EFIA-VAHPEHPLHQAKRELTFQDLESQ 193
Cdd:PRK11242  163 ETLAlVVGRHHPLAARRKALTLDELADE 190
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 137-289 5.04e-14

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: 69.44  E-value: 5.04e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 137 VEEVLLEGTADLAISG--FSIPGYLGTEMSTVEFIAVAHPEHPLHQaKRELTFQDLEsQLQVVIRDSG---RQ------Q 205
Cdd:cd08420    41 IAERVLDGEIDLGLVEgpVDHPDLIVEPFAEDELVLVVPPDHPLAG-RKEVTAEELA-AEPWILREPGsgtREvferalA 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 206 PRDIGWLGAEQRWTVGSLGTATTFVSSGLGFAWLPRHMIERELKEGVLKILPLdKGGSRNPSFYLYSSKDKPLGPATQIL 285
Cdd:cd08420   119 EAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVALPV-EGLRLTRPFSLIYHKDKYLSPAAEAF 197


                  ....
gi 2084912661 286 IDLI 289
Cdd:cd08420   198 LEFL 201
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 111-289 1.42e-12

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: 65.37  E-value: 1.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 111 LVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAIS----GFSIPGYLGTEMSTVEFIAVAHPEHPLHQaKRELT 186
Cdd:cd08435    15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGrladDEQPPDLASEELADEPLVVVARPGHPLAR-RARLT 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 187 FQDLESQ--------------LQVVIRDSGRQQPRDIgwlgAEqrwtVGSLGTATTFVSSGLGFAWLPRHMIERELKEGV 252
Cdd:cd08435    94 LADLADYpwvlpppgtplrqrLEQLFAAAGLPLPRNV----VE----TASISALLALLARSDMLAVLPRSVAEDELRAGV 165

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2084912661 253 LKILPLDKGGSRNPsFYLYSSKDKPLGPATQILIDLI 289
Cdd:cd08435   166 LRELPLPLPTSRRP-IGITTRRGGPLSPAARALLDAL 201
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-190 8.45e-12

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 64.61  E-value: 8.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   8 LDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAV-LTEAGGVLLRRSRQLVKQASQL-- 83
Cdd:PRK12684    3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLkr 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  84 --EDLAHHmEQGweaevRLVVDAAYPTAR--LVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAI-----SGF- 153
Cdd:PRK12684   83 vgKEFAAQ-DQG-----NLTIATTHTQARyaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIateaiADYk 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084912661 154 ---SIPGYLGTEMstvefiAVAHPEHPLHQaKRELTFQDL 190
Cdd:PRK12684  157 elvSLPCYQWNHC------VVVPPDHPLLE-RKPLTLEDL 189
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-253 2.23e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.07  E-value: 2.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   7 TLD--QWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLrIDGRKAVLTEAGGVLLRrsrqLVKQASQLE 84
Cdd:PRK13348    1 MLDykQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLR----HLRQVALLE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  85 -DLAHHMEQGWEAEVRLV--VDAAYPTARLVRALTAFMPQSrgcrvRLREEVLsgVE------EVLLEGTADLAISGFS- 154
Cdd:PRK13348   76 aDLLSTLPAERGSPPTLAiaVNADSLATWFLPALAAVLAGE-----RILLELI--VDdqdhtfALLERGEVVGCVSTQPk 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 155 -IPGYLGTEMSTVEFIAVAHPE------------HPLHQA-----KRELTFQD--LESQLQVVIrdsgrqqprdigwlGA 214
Cdd:PRK13348  149 pMRGCLAEPLGTMRYRCVASPAfaaryfaqgltrHSALKApavafNRKDTLQDsfLEQLFGLPV--------------GA 214

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 2084912661 215 EQRWTVGSLGTATTFVSSGLGFAWLPRHMIERELKEGVL 253
Cdd:PRK13348  215 YPRHYVPSTHAHLAAIRHGLGYGMVPELLIGPLLAAGRL 253
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-100 2.86e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 62.87  E-value: 2.86e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   9 DQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLrIDGRKAVLTEAGGVLLRrsrqLVKQASQLE-DLA 87
Cdd:PRK03635    5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQRLLR----HARQVRLLEaELL 79

                          90
                  ....*....|...
gi 2084912661  88 HHMEQGWEAEVRL 100
Cdd:PRK03635   80 GELPALDGTPLTL 92
PRK09986 PRK09986
LysR family transcriptional regulator;
2-193 3.84e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 62.43  E-value: 3.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   2 KAPRVTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQAS 81
Cdd:PRK09986    3 RLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  82 Q----LEDLAHHmEQGwEAEVRLVVDAAYptARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI-- 155
Cdd:PRK09986   83 QslarVEQIGRG-EAG-RIEIGIVGTALW--GRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADle 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084912661 156 --PGYLGTEMSTVEFIAVAHPEHPLHQAKReLTFQDLESQ 193
Cdd:PRK09986  159 pnPGFTSRRLHESAFAVAVPEEHPLASRSS-VPLKALRNE 197
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 126-289 1.92e-10

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 59.08  E-value: 1.92e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 126 RVRLREEVLSGVEEVLLEGTADLAIsgfsipGYLGTEMSTVE--------FIAVAHPEHPLHQaKRELTFQDL------- 190
Cdd:cd08440    30 RVRLRDVSAEQVIEAVRSGEVDFGI------GSEPEADPDLEfepllrdpFVLVCPKDHPLAR-RRSVTWAELagyplia 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 191 ---ESQLQVVIRDSGRQQPRDIGWlgaeqRWTVGSLGTATTFVSSGLGFAWLPRHMIERELKEGvLKILPLDK-GGSRNp 266
Cdd:cd08440   103 lgrGSGVRALIDRALAAAGLTLRP-----AYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG-LVARPLTEpVVTRT- 175

                         170       180
                  ....*....|....*....|...
gi 2084912661 267 sFYLYSSKDKPLGPATQILIDLI 289
Cdd:cd08440   176 -VGLIRRRGRSLSPAAQAFLDLL 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-261 3.60e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.03  E-value: 3.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   6 VTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLED 85
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  86 LAHHMEQgweAEVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSIP--GYLGTEM 163
Cdd:PRK15421   82 ACNEPQQ---TRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPrsGLHYSPM 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 164 STVEFIAVAHPEHPLhQAKRELTFQDLESQ------LQVVIRDSGRQ--QPRDIgwlgAEQRWTVGSLGTATTFVSSGLG 235
Cdd:PRK15421  159 FDYEVRLVLAPDHPL-AAKTRITPEDLASEtlliypVQRSRLDVWRHflQPAGV----SPSLKSVDNTLLLIQMVAARMG 233

                         250       260
                  ....*....|....*....|....*.
gi 2084912661 236 FAWLPRHMIERELKEGVLKILPLDKG 261
Cdd:PRK15421  234 IAALPHWVVESFERQGLVVTKTLGEG 259
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-78 1.90e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 57.73  E-value: 1.90e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2084912661   8 LDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVK 78
Cdd:PRK15092   13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR 83
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-243 7.09e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 55.93  E-value: 7.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  12 RTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHME 91
Cdd:PRK09906    7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  92 QgweAEVRLVVdAAYPTARlVRALTAFMPQSR----GCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMST 165
Cdd:PRK09906   87 Q---EDRQLTI-GFVPSAE-VNLLPKVLPMFRlrhpDTLIELVSLITTQQEEKLRRGELDVGFMRHPVysDEIDYLELLD 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 166 VEFIAVAHPEHPLHQAKReLTFQDLESqLQVVIRD---SGRQQPRDIGWLGAEQR-----WTVGSLGTATTFVSSGLGFA 237
Cdd:PRK09906  162 EPLVVVLPVDHPLAHEKE-ITAAQLDG-VNFISTDpaySGSLAPIIKAWFAQHNSqpnivQVATNILVTMNLVGMGLGCT 239


                  ....*.
gi 2084912661 238 WLPRHM 243
Cdd:PRK09906  240 IIPGYM 245
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 25-190 7.74e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 55.82  E-value: 7.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  25 QAAEALHRSQSSVSYTVARMQDQLGVPLL-RIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHMEQGWEAevRLVVD 103
Cdd:PRK12683   21 EVANALYTSQSGVSKQIKDLEDELGVEIFiRRGKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSG--HLTVA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 104 AAYPTAR--LVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSipgyLGTEMSTVEF-------IAVAHP 174
Cdd:PRK12683   99 TTHTQARyaLPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEA----LDREPDLVSFpyyswhhVVVVPK 174

                         170
                  ....*....|....*.
gi 2084912661 175 EHPLHQAkRELTFQDL 190
Cdd:PRK12683  175 GHPLTGR-ENLTLEAI 189
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-86 1.35e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.08  E-value: 1.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   5 RVTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLE 84
Cdd:PRK10837    2 HITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE 81


                  ..
gi 2084912661  85 DL 86
Cdd:PRK10837   82 QL 83
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-287 7.40e-08

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: 51.75  E-value: 7.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  98 VRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSIPGYlGTEM---STVEFIAVAHP 174
Cdd:cd08421     2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAA-GLETrpyRTDRLVVVVPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 175 EHPLhQAKRELTFQDL----------ESQLQVVIRDSGRQQPRDIgwlgaEQRWTVGSLGTATTFVSSGLGFAWLPRHMI 244
Cdd:cd08421    81 DHPL-AGRASVAFADTldhdfvglpaGSALHTFLREAAARLGRRL-----RLRVQVSSFDAVCRMVAAGLGIGIVPESAA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2084912661 245 ERELKEGVLKILPLDKGGSRNPsFYLYSSKDKPLGPATQILID 287
Cdd:cd08421   155 RRYARALGLRVVPLDDAWARRR-LLLCVRSFDALPPAARALVD 196
PRK12680 PRK12680
LysR family transcriptional regulator;
6-239 1.41e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.93  E-value: 1.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   6 VTLDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRK-AVLTEAGGVLLRRSRQLVKQASQL 83
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSlESVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  84 EDLAHHmeQGWEAEVRLVVDAAYPTARLV--RALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAI---------SG 152
Cdd:PRK12680   81 RTYAAN--QRRESQGQLTLTTTHTQARFVlpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvstaggepsAG 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 153 FSIPGYLGTEMSTVefiavahPE-HPLHQAKRELTFQDLESQLQVVIRDSGRQQP---RDIGWLGAEQRWTVGSLGT--A 226
Cdd:PRK12680  159 IAVPLYRWRRLVVV-------PRgHALDTPRRAPDMAALAEHPLISYESSTRPGSslqRAFAQLGLEPSIALTALDAdlI 231

                         250
                  ....*....|...
gi 2084912661 227 TTFVSSGLGFAWL 239
Cdd:PRK12680  232 KTYVRAGLGVGLL 244
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 113-289 1.65e-07

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


Pssm-ID: 176111  Cd Length: 197  Bit Score: 50.58  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 113 RALTAFMPQSRGCRVRL----REEVLsgveEVLLEGTADLAISGfSIPGYLGTEmsTVEF-----IAVAHPEHPLHQAKR 183
Cdd:cd08419    16 RLLGAFCRRHPGVEVSLrvgnREQVL----ERLADNEDDLAIMG-RPPEDLDLV--AEPFldnplVVIAPPDHPLAGQKR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 184 eLTFQDLESQlQVVIRDSGRQQPRDIGWLGAEQRWT------VGSLGTATTFVSSGLGFAWLPRHMIERELKEGVLKILP 257
Cdd:cd08419    89 -IPLERLARE-PFLLREPGSGTRLAMERFFAEHGVTlrvrmeLGSNEAIKQAVMAGLGLSVLSLHTLALELATGRLAVLD 166

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2084912661 258 LdKGGSRNPSFYLYSSKDKPLGPATQILIDLI 289
Cdd:cd08419   167 V-EGFPIRRQWYVVHRKGKRLSPAAQAFLDFL 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
17-83 1.98e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 51.68  E-value: 1.98e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2084912661  17 VVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQL 83
Cdd:PRK10632   13 VVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDV 79
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 14-87 6.43e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 50.03  E-value: 6.43e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2084912661  14 LQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLA 87
Cdd:PRK11151    9 LVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-289 8.87e-07

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 48.46  E-value: 8.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  97 EVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAIsGFSIPGYLGTEM---STVEFIAVAH 173
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGL-AFSPPPEPGIRVhsrQPAPIGAVVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 174 PEHPLhQAKRELTFQDL-ESQLQVVIRDSGRQQPRDIgwLGAEQRWTVG------SLGTATTFVSSGLGFAWLPRHMIER 246
Cdd:cd08426    80 PGHPL-ARQPSVTLAQLaGYPLALPPPSFSLRQILDA--AFARAGVQLEpvlisnSIETLKQLVAAGGGISLLTELAVRR 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2084912661 247 ELKEGVLKILPLDKGGSRNPSFYLYSSKDKPLGPATQILIDLI 289
Cdd:cd08426   157 EIRRGQLVAVPLADPHMNHRQLELQTRAGRQLPAAASAFLQLL 199
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 17-150 1.86e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 48.45  E-value: 1.86e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  17 VVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHMEQGWEA 96
Cdd:PRK14997   13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2084912661  97 EVRLVVDAAYPTARLVRALTAFMPQSRGcrVRLREEVLSGVEEVLLEGTaDLAI 150
Cdd:PRK14997   93 IVKLTCPVTLLHVHIGPMLAKFMARYPD--VSLQLEATNRRVDVVGEGV-DVAI 143
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 110-258 3.64e-06

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: 46.82  E-value: 3.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 110 RLVRALTAFMPqsrGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMSTVEFIAVAHPEHPLhqAKRELTF 187
Cdd:cd08417    17 PLLARLRQEAP---GVRLRFVPLDRDDLEEALESGEIDLAIGVFPElpPGLRSQPLFEDRFVCVARKDHPL--AGGPLTL 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2084912661 188 QDLESQLQVVIRDSGRQQPRDIGWLGAEQ-----RWTVGSLGTATTFVSSGLGFAWLPRHMIERELKEGVLKILPL 258
Cdd:cd08417    92 EDYLAAPHVLVSPRGRGHGLVDDALAELGlsrrvALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLPL 167
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 141-289 4.17e-05

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 43.68  E-value: 4.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 141 LLEGTADLAISgfSIP----GYLGTEMSTVEFIAVAHPEHPLHQaKRELTFQDLESQLQVVIRD-SG-RQ---------- 204
Cdd:cd08434    45 LKNGELDLALC--SPVpdepDIEWIPLFTEELVLVVPKDHPLAG-RDSVDLAELADEPFVLLSPgFGlRPivdelcaaag 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 205 -QPRdIGWLGAEqrwtvgsLGTATTFVSSGLGFAWLPRHMIERELKegvLKILPL-DKGGSRnpSFYLYSSKDKPLGPAT 282
Cdd:cd08434   122 fTPK-IAFEGEE-------DSTIAGLVAAGLGVAILPEMTLLNPPG---VKKIPIkDPDAER--TIGLAWLKDRYLSPAA 188


                  ....*..
gi 2084912661 283 QILIDLI 289
Cdd:cd08434   189 RRFKDFV 195
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-289 5.28e-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: 43.36  E-value: 5.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 110 RLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFS---IPGYLGTEMSTVEFIAVAHPEHPLHQAkRELT 186
Cdd:cd08436    14 DLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPerrPPGLASRELAREPLVAVVAPDHPLAGR-RRVA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 187 FQDLESQLQV------VIRDSGRQQPRDIGwLGAEQRWTVGSLGTATTFVSSGLGFAWLPRHMIERelkEGVLKILPLDK 260
Cdd:cd08436    93 LADLADEPFVdfppgtGARRQVDRAFAAAG-VRRRVAFEVSDVDLLLDLVARGLGVALLPASVAAR---LPGLAALPLEP 168

                         170       180
                  ....*....|....*....|....*....
gi 2084912661 261 GGSRnpSFYLYSSKDKPlGPATQILIDLI 289
Cdd:cd08436   169 APRR--RLYLAWSAPPP-SPAARAFLELL 194
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 20-66 6.10e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 43.68  E-value: 6.10e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2084912661  20 HGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAG 66
Cdd:PRK11139   20 HLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG 66
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 17-82 8.80e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.52  E-value: 8.80e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2084912661  17 VVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQ 82
Cdd:PRK11233   12 IVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ 77
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
13-66 1.26e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 43.07  E-value: 1.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2084912661  13 TLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAG 66
Cdd:PRK10086   21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG 74
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-190 1.26e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 43.06  E-value: 1.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   8 LDQWRTLQAVVDHG-GFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAV-LTEAGGVLLRRSRQLVKQASQLED 85
Cdd:PRK12682    3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  86 LAhhmEQGWEAEV-RLVVDAAYPTARLV--RALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSIPGYlgTE 162
Cdd:PRK12682   83 IG---DDFSNQDSgTLTIATTHTQARYVlpRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADD--PD 157

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2084912661 163 MSTV-----EFIAVAHPEHPLHQAKReLTFQDL 190
Cdd:PRK12682  158 LATLpcydwQHAVIVPPDHPLAQEER-ITLEDL 189
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 111-237 1.29e-04

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: 42.16  E-value: 1.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 111 LVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSI--PGYLGTEMSTVEFIAVAHPEHPLhQAKRELTFQ 188
Cdd:cd08415    15 LPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLdhPGLESEPLASGRAVCVLPPGHPL-ARKDVVTPA 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2084912661 189 DLESQLQVVI--RDSGRQQPRDI-GWLGAEQRWT--VGSLGTATTFVSSGLGFA 237
Cdd:cd08415    94 DLAGEPLISLgrGDPLRQRVDAAfERAGVEPRIVieTQLSHTACALVAAGLGVA 147
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-152 1.37e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 42.50  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  31 HRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQASQLEDLAHHMEQGWEAEVRLV--VDAAYpt 108
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFcsVTAAY-- 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2084912661 109 ARLVRALTAFMPQSRGCRVRLR--------EEVLSgveevlleGTADLAISG 152
Cdd:PRK11716   80 SHLPPILDRFRAEHPLVEIKLTtgdaadavEKVQS--------GEADLAIAA 123
cbl PRK12679
HTH-type transcriptional regulator Cbl;
25-151 2.92e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 41.72  E-value: 2.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  25 QAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAV-LTEAGGVLLRRSRQLVKQASQLEDLAHHMEQgwEAEVRLVVD 103
Cdd:PRK12679   21 EVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTN--DTSGVLTIA 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2084912661 104 AAYPTAR--LVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAIS 151
Cdd:PRK12679   99 TTHTQARysLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIA 148
PRK10341 PRK10341
transcriptional regulator TdcA;
15-163 3.37e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.77  E-value: 3.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  15 QAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRS----RQLVKQASQLEDLAHhm 90
Cdd:PRK10341   16 QEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSesitREMKNMVNEINGMSS-- 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  91 eqgweaevRLVVDAAYPTARLVrALTaFMPQ--------SRGCRVRLREEVLSGVEEVLLEGTADLAIsgfsipGYLGTE 162
Cdd:PRK10341   94 --------EAVVDVSFGFPSLI-GFT-FMSDminkfkevFPKAQVSMYEAQLSSFLPAIRDGRLDFAI------GTLSNE 157


                  .
gi 2084912661 163 M 163
Cdd:PRK10341  158 M 158
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 108-289 4.27e-04

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: 40.66  E-value: 4.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 108 TARLVRALTAFMPqsrGCRVRLREEVLSGVEEVLLEGTADLAISgfsipgYLGTEMSTVEFIAVAH-------PEHPLHQ 180
Cdd:cd08433    15 AVPLLRAVRRRYP---GIRLRIVEGLSGHLLEWLLNGRLDLALL------YGPPPIPGLSTEPLLEedlflvgPADAPLP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 181 AKRELTFQDLESQ----------LQVVIRDSGRQqprdIGwLGAEQRWTVGSLGTATTFVSSGLGFAWLPRHMIERELKE 250
Cdd:cd08433    86 RGAPVPLAELARLplilpsrghgLRRLVDEAAAR----AG-LTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAA 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084912661 251 GVLKILPL-DKGGSRnpSFYLYSSKDKPLGPATQILIDLI 289
Cdd:cd08433   161 GRLVAAPIvDPALTR--TLSLATPRDRPLSPAALAVRDLL 198
PRK09791 PRK09791
LysR family transcriptional regulator;
6-288 6.84e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 40.52  E-value: 6.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   6 VTLDQWRTLQAVVDHGGFAQAAEALHRSQSSVSYTVARMQDQLGVPLLRIDGRKAVLTEAGGVLLRRSRQLVKQ--ASQl 83
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEElrAAQ- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661  84 EDLAHHMEQGwEAEVRLVVDAAYPTARLVRALTAFMPQSRGCRVRLREEVLSGVEEVLLEGTADLAISGFSiPGYLGTEM 163
Cdd:PRK09791   84 EDIRQRQGQL-AGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYY-QGPYDHEF 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 164 S-----TVEFIAVAHPEHPLHQAKRELTFQDLE-----------SQLQVVIRDSGrQQPRdIGwLGAEQRWTVGSLGTAT 227
Cdd:PRK09791  162 TfekllEKQFAVFCRPGHPAIGARSLKQLLDYSwtmptphgsyyKQLSELLDDQA-QTPQ-VG-VVCETFSACISLVAKS 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2084912661 228 TFVSSglgfawLPRHMIERELKEGVLKILPLDKGGSRnPSFYLYSSKDKPLGPATQILIDL 288
Cdd:PRK09791  239 DFLSI------LPEEMGCDPLHGQGLVMLPVSEILPK-ATYYLIQRRDTRQTPLTASLITL 292
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 6-47 1.64e-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: 1.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2084912661   6 VTLDQWRTLQAVVDHGG--FAQAAEALHRSQSSVSYTVARMQDQ 47
Cdd:pfam12802   3 LTPAQFRVLLALARNPGltVAELARRLGISKQTVSRLVKRLEAK 46
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 110-259 3.80e-03

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 37.89  E-value: 3.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 110 RLVRALTAFMPQSRgcrVRLREEVLSGVEEVLLEGTADLAISG--FSIPGYLGTEMSTVEFIAVAHPEHPLhqAKRE-LT 186
Cdd:cd08411    18 RLLPALRQAYPKLR---LYLREDQTERLLEKLRSGELDAALLAlpVDEPGLEEEPLFDEPFLLAVPKDHPL--AKRKsVT 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 187 FQDLESQlQVVIRDSG---RQQPRDI-GWLGAEQRWTV--GSLGTATTFVSSGLGFAWLPRHMIE-RELKEGVLKILPLD 259
Cdd:cd08411    93 PEDLAGE-RLLLLEEGhclRDQALELcRLAGAREQTDFeaTSLETLRQMVAAGLGITLLPELAVPsEELRGDRLVVRPFA 171
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
1-80 3.91e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.87  E-value: 3.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661   1 MKAPRVTLDQWRTLQAVVDHGG--FAQAAEALHRSQSSVSYTVARMQDQlGvpLLRI-----DGRK--AVLTEAGGVLLR 71
Cdd:COG1846    31 LAELGLTPAQFRVLAALAEAGGltQSELAERLGLTKSTVSRLLDRLEEK-G--LVERepdpeDRRAvlVRLTEKGRALLE 107


                  ....*....
gi 2084912661  72 RSRQLVKQA 80
Cdd:COG1846   108 EARPALEAL 116
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 167-287 7.62e-03

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 36.79  E-value: 7.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084912661 167 EFIAVAHPEhpLHQAKRELTFQDLesqLQVV-IRDSGRqqPRDIGWLGAEQRWTVGSLGTATTFVSS---------GLGF 236
Cdd:cd08432    70 ELVPVCSPA--LLAGLPLLSPADL---ARHTlLHDATR--PEAWQWWLWAAGVADVDARRGPRFDDSslalqaavaGLGV 142

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2084912661 237 AWLPRHMIERELKEGVLkILPLDKGGSRNPSFYLYSSKDKPLGPATQILID 287
Cdd:cd08432   143 ALAPRALVADDLAAGRL-VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRD 192
 
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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