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Conserved domains on  [gi|373916477|gb|EHQ48225|]
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hypothetical protein HMPREF0978_00931 [Coprobacillus sp. 8_2_54BFAA]

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
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];
2-257 2.47e-31

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 116.12  E-value: 2.47e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:COG0583   38 RLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARH 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMKKNASLAKKEYITskdlidlpliasar 161
Cdd:COG0583  118 PGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL-GEERLVLVASPDHPLARRAPLV-------------- 182
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 162 seaqtifsnwygtgyenlsfcatsDLTTTAAILVKNDVGYAVVVEGSI-CDAASDELCFRPL-YPSLNSHSLFVWKKYQS 239
Cdd:COG0583  183 ------------------------NSLEALLAAVAAGLGIALLPRFLAaDELAAGRLVALPLpDPPPPRPLYLVWRRRRH 238
                        250
                 ....*....|....*...
gi 373916477 240 FSLTVTKFIDFISKEIKK 257
Cdd:COG0583  239 LSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-257 2.47e-31

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 116.12  E-value: 2.47e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:COG0583   38 RLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARH 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMKKNASLAKKEYITskdlidlpliasar 161
Cdd:COG0583  118 PGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL-GEERLVLVASPDHPLARRAPLV-------------- 182
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 162 seaqtifsnwygtgyenlsfcatsDLTTTAAILVKNDVGYAVVVEGSI-CDAASDELCFRPL-YPSLNSHSLFVWKKYQS 239
Cdd:COG0583  183 ------------------------NSLEALLAAVAAGLGIALLPRFLAaDELAAGRLVALPLpDPPPPRPLYLVWRRRRH 238
                        250
                 ....*....|....*...
gi 373916477 240 FSLTVTKFIDFISKEIKK 257
Cdd:COG0583  239 LSPAVRAFLDFLREALAE 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
3-254 2.26e-24

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 98.84  E-value: 2.26e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   3 LEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIYP 82
Cdd:NF040786  39 LEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYP 118
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  83 HVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFNAEEKWgILMKKNASL--AKKEYITSKDLIDLPLI--- 157
Cdd:NF040786 119 NVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPFYKDRLV-LITPNGTEKyrMLKEEISISELQKEPFImre 197
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 158 -ASA-RSEAQTIFSNWyGTGYENLSFCATsdLTTTAAI--LVKNDVGYAVVVEgsicdAASDELCFRPLYPSLNSHSL-- 231
Cdd:NF040786 198 eGSGtRKEAEKALKSL-GISLEDLNVVAS--LGSTEAIkqSVEAGLGISVISE-----LAAEKEVERGRVLIFPIPGLpk 269
                        250       260
                 ....*....|....*....|....*...
gi 373916477 232 -----FVWKKYQSFSLTVTKFIDFISKE 254
Cdd:NF040786 270 nrdfyLVYNKNRQLSPTAEAFLQFVKER 297
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
56-251 1.17e-22

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 91.89  E-value: 1.17e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMK 135
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPL-FEEPLVLVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 136 KNASLAKKEYITSKDLIDLPLIA-----SARSEAQTIFSNwygTGYENLSFCATSDLTTTAAiLVKNDVGYAVVVEGSIC 210
Cdd:cd05466   80 PDHPLAKRKSVTLADLADEPLILfergsGLRRLLDRAFAE---AGFTPNIALEVDSLEAIKA-LVAAGLGIALLPESAVE 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 373916477 211 DAASDELCFRPL-YPSLNSHSLFVWKKYQSFSLTVTKFIDFI 251
Cdd:cd05466  156 ELADGGLVVLPLeDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
54-251 7.21e-19

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: 81.95  E-value: 7.21e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   54 SGEIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGIL 133
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPL-GEEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  134 MKKNASLAKKEYITSKDLIDLPLIASARSEA-QTIFSNWYGTGYENLSFCATSDLTTTAAILVKNDVGYAVVVEGSICDA 212
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGlRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 373916477  213 -ASDELCFRPLY-PSLNSHSLFVWKKYQSFSLTVTKFIDFI 251
Cdd:pfam03466 160 lADGRLVALPLPePPLPRELYLVWRKGRPLSPAVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
2-158 3.38e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 73.52  E-value: 3.38e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:CHL00180  42 NLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRY 121
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLE--PVELEKLNFIHFNAEEKWGILMKKNASLAKKEYITSKDLIDLPLIA 158
Cdd:CHL00180 122 PQINVQLQVHSTRRIAWNVANGQIDIAIVGGevPTELKKILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFIT 200
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-257 2.47e-31

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 116.12  E-value: 2.47e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:COG0583   38 RLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARH 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMKKNASLAKKEYITskdlidlpliasar 161
Cdd:COG0583  118 PGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL-GEERLVLVASPDHPLARRAPLV-------------- 182
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 162 seaqtifsnwygtgyenlsfcatsDLTTTAAILVKNDVGYAVVVEGSI-CDAASDELCFRPL-YPSLNSHSLFVWKKYQS 239
Cdd:COG0583  183 ------------------------NSLEALLAAVAAGLGIALLPRFLAaDELAAGRLVALPLpDPPPPRPLYLVWRRRRH 238
                        250
                 ....*....|....*...
gi 373916477 240 FSLTVTKFIDFISKEIKK 257
Cdd:COG0583  239 LSPAVRAFLDFLREALAE 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
3-254 2.26e-24

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 98.84  E-value: 2.26e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   3 LEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIYP 82
Cdd:NF040786  39 LEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYP 118
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  83 HVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFNAEEKWgILMKKNASL--AKKEYITSKDLIDLPLI--- 157
Cdd:NF040786 119 NVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPFYKDRLV-LITPNGTEKyrMLKEEISISELQKEPFImre 197
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 158 -ASA-RSEAQTIFSNWyGTGYENLSFCATsdLTTTAAI--LVKNDVGYAVVVEgsicdAASDELCFRPLYPSLNSHSL-- 231
Cdd:NF040786 198 eGSGtRKEAEKALKSL-GISLEDLNVVAS--LGSTEAIkqSVEAGLGISVISE-----LAAEKEVERGRVLIFPIPGLpk 269
                        250       260
                 ....*....|....*....|....*...
gi 373916477 232 -----FVWKKYQSFSLTVTKFIDFISKE 254
Cdd:NF040786 270 nrdfyLVYNKNRQLSPTAEAFLQFVKER 297
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
56-251 1.17e-22

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 91.89  E-value: 1.17e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMK 135
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPL-FEEPLVLVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 136 KNASLAKKEYITSKDLIDLPLIA-----SARSEAQTIFSNwygTGYENLSFCATSDLTTTAAiLVKNDVGYAVVVEGSIC 210
Cdd:cd05466   80 PDHPLAKRKSVTLADLADEPLILfergsGLRRLLDRAFAE---AGFTPNIALEVDSLEAIKA-LVAAGLGIALLPESAVE 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 373916477 211 DAASDELCFRPL-YPSLNSHSLFVWKKYQSFSLTVTKFIDFI 251
Cdd:cd05466  156 ELADGGLVVLPLeDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
54-251 7.21e-19

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: 81.95  E-value: 7.21e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   54 SGEIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGIL 133
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPL-GEEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  134 MKKNASLAKKEYITSKDLIDLPLIASARSEA-QTIFSNWYGTGYENLSFCATSDLTTTAAILVKNDVGYAVVVEGSICDA 212
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGlRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 373916477  213 -ASDELCFRPLY-PSLNSHSLFVWKKYQSFSLTVTKFIDFI 251
Cdd:pfam03466 160 lADGRLVALPLPePPLPRELYLVWRKGRPLSPAVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
2-158 3.38e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 73.52  E-value: 3.38e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:CHL00180  42 NLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRY 121
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLE--PVELEKLNFIHFNAEEKWGILMKKNASLAKKEYITSKDLIDLPLIA 158
Cdd:CHL00180 122 PQINVQLQVHSTRRIAWNVANGQIDIAIVGGevPTELKKILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFIT 200
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
2-124 2.18e-13

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 67.92  E-value: 2.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:PRK11716  14 RLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPPILDRFRAEH 93
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLEPvelEKL-NFIHF 124
Cdd:PRK11716  94 PLVEIKLTTGDAADAVEKVQSGEADLAIAAKP---ETLpASVAF 134
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
56-251 4.95e-13

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: 65.64  E-value: 4.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMK 135
Cdd:cd08434    1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPL-FTEELVLVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 136 KNASLAKKEYITSKDLIDLPLIAsarseaqtiFSNWYGTGYENLSFCATSDLT----------TTAAILVKNDVGYAVVV 205
Cdd:cd08434   80 KDHPLAGRDSVDLAELADEPFVL---------LSPGFGLRPIVDELCAAAGFTpkiafegeedSTIAGLVAAGLGVAILP 150
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 373916477 206 EGSICDAA-------SDELCFRPLYpslnshslFVWKKYQSFSLTVTKFIDFI 251
Cdd:cd08434  151 EMTLLNPPgvkkipiKDPDAERTIG--------LAWLKDRYLSPAARRFKDFV 195
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
3-157 5.10e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 67.32  E-value: 5.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   3 LEDELGAVLFIR-GKRKMVLTEEGMVLKRRAEeiIILSEKAELE-VGSQ-SHDISGEIAIGCGVTEATQTMGKLIKKFSE 79
Cdd:PRK12682  40 LEEELGIEIFIRhGKRLKGLTEPGKAVLDVIE--RILREVGNIKrIGDDfSNQDSGTLTIATTHTQARYVLPRVVAAFRK 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  80 IYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKlNFIHFNAEEkW--GILMKKNASLAKKEYITSKDLIDLPLI 157
Cdd:PRK12682 118 RYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDP-DLATLPCYD-WqhAVIVPPDHPLAQEERITLEDLAEYPLI 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
3-253 5.15e-13

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 67.10  E-value: 5.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   3 LEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELeVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIYP 82
Cdd:PRK09906  39 LENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL-RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHP 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  83 HVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFiHFNAEEKWGILMKKNASLAKKEYITSKDLIDLPLIASARS 162
Cdd:PRK09906 118 DTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDY-LELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPA 196
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 163 EAQT---IFSNWYGTGYENLSFCATSDLTTTAAILVKNDVGYAvVVEGSICDAASDELCFRPLYPSLNSHSLFV-WKKyQ 238
Cdd:PRK09906 197 YSGSlapIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT-IIPGYMNNFNTGQVVFRPLAGNVPSIALLMaWKK-G 274
                        250
                 ....*....|....*
gi 373916477 239 SFSLTVTKFIDFISK 253
Cdd:PRK09906 275 EMKPALRDFIAIVQE 289
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
3-157 6.95e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 66.99  E-value: 6.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   3 LEDELGAVLFIR-GKRKMVLTEEGMVLKRRAEEIIILSEKAElEVGSQ--SHDiSGEIAIGCGVTEATQTMGKLIKKFSE 79
Cdd:PRK12683  40 LEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAENLR-RLAEQfaDRD-SGHLTVATTHTQARYALPKVVRQFKE 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  80 IYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKlNFIHFNAEEkW--GILMKKNASLAKKEYITSKDLIDLPLI 157
Cdd:PRK12683 118 VFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREP-DLVSFPYYS-WhhVVVVPKGHPLTGRENLTLEAIAEYPII 195
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
56-222 8.88e-12

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


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 62.52  E-value: 8.88e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMK 135
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPL-LREPLVVALP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 136 KNASLAKKEYITSKDLIDLPLIASARSEAQTIFSNWygtgyenLSFCA-----------TSDLTTTAAiLVKNDVGYAVV 204
Cdd:cd08414   80 ADHPLAARESVSLADLADEPFVLFPREPGPGLYDQI-------LALCRragftprivqeASDLQTLLA-LVAAGLGVALV 151
                        170
                 ....*....|....*...
gi 373916477 205 VEgSICDAASDELCFRPL 222
Cdd:cd08414  152 PA-SVARLQRPGVVYRPL 168
cbl PRK12679
HTH-type transcriptional regulator Cbl;
2-157 9.52e-12

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 63.68  E-value: 9.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIR-GKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEI 80
Cdd:PRK12679  39 ELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFREL 118
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  81 YPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKL--NFIHFNaeekW--GILMKKNASLAKKEYITSKDLIDLPL 156
Cdd:PRK12679 119 FPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQlvAFPWFR----WhhSLLVPHDHPLTQITPLTLESIAKWPL 194

                 .
gi 373916477 157 I 157
Cdd:PRK12679 195 I 195
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
57-222 1.99e-10

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 58.69  E-value: 1.99e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  57 IAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMKK 136
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPL-LRDPFVLVCPK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 137 NASLAKKEYITSKDLIDLPLIASAR--SEAQTIFSNWYGTGYENLSFCATSdLTTTAAILVKNDVGYAVVVEGSICDAAS 214
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRgsGVRALIDRALAAAGLTLRPAYEVS-HMSTALGMVAAGLGVAVLPALALPLADH 159

                 ....*...
gi 373916477 215 DELCFRPL 222
Cdd:cd08440  160 PGLVARPL 167
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
66-157 4.42e-10

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: 57.50  E-value: 4.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  66 ATQTMG-----KLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMKKNASL 140
Cdd:cd08420    6 ASTTIGeyllpRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPF-AEDELVLVVPPDHPL 84
                         90
                 ....*....|....*..
gi 373916477 141 AKKEYITSKDLIDLPLI 157
Cdd:cd08420   85 AGRKEVTAEELAAEPWI 101
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
2-118 4.49e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 58.83  E-value: 4.49e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIR-GKRKMVLTEEGMVLKRRAEEIiiLSEKAELE-VGSQ-SHDISGEIAIGCGVTEATQTMGKLIKKFS 78
Cdd:PRK12684  39 ELEDELGVEIFTRhGKRLRGLTEPGRIILASVERI--LQEVENLKrVGKEfAAQDQGNLTIATTHTQARYALPAAIKEFK 116
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 373916477  79 EIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEK 118
Cdd:PRK12684 117 KRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYK 156
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
72-251 6.59e-10

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


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 57.18  E-value: 6.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  72 KLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFNAEEKWGILMKKNAsLAKKEYITSKDL 151
Cdd:cd08438   17 PLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHP-LAGRKTVSLADL 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 152 IDLPLI--ASARSEAQTIFSNWYGTGYENLSFCATSDLTTTAAiLVKNDVGYAVVVEgSICDAASDE-LCFRPL-YPSLN 227
Cdd:cd08438   96 ADEPFIlfNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAE-LVAAGLGVALLPR-SIAQRLDNAgVKVIPLtDPDLR 173
                        170       180
                 ....*....|....*....|....
gi 373916477 228 SHSLFVWKKYQSFSLTVTKFIDFI 251
Cdd:cd08438  174 WQLALIWRKGRYLSHAARAWLALL 197
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
70-249 4.39e-09

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: 54.88  E-value: 4.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  70 MGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMKKNASLAKKEYITSK 149
Cdd:cd08415   15 LPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPL-ASGRAVCVLPPGHPLARKDVVTPA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 150 DLIDLPLIASARSeaqtifsnwYGTGYE----------NLSFCATSDLTTTAAILVKNDVGYAVVVEGSICDAASDELCF 219
Cdd:cd08415   94 DLAGEPLISLGRG---------DPLRQRvdaaferagvEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAGAGLVV 164
                        170       180       190
                 ....*....|....*....|....*....|
gi 373916477 220 RPLYPSLNSHSLFVWKKYQSFSLTVTKFID 249
Cdd:cd08415  165 RPFRPAIPFEFALVRPAGRPLSRLAQAFID 194
PRK09791 PRK09791
LysR family transcriptional regulator;
2-109 7.83e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.15  E-value: 7.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEeiIILSE--KAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSE 79
Cdd:PRK09791  42 ELEEGLAAQLFFRRSKGVTLTDAGESFYQHAS--LILEElrAAQEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQ 119
                         90       100       110
                 ....*....|....*....|....*....|
gi 373916477  80 IYPHVSFRIRNGNSDFILENIDNGLLDIGV 109
Cdd:PRK09791 120 QHPQVKVRIMEGQLVSMINELRQGELDFTI 149
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-101 1.40e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 51.54  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEG----MVLKRRAEEIiilsEKAELEVGSQshDISGEIAIGCGVTEATQTMGKLIKKF 77
Cdd:PRK10086  51 QLEEELGIKLFVRSHRKVELTEEGkrvfWALKSSLDTL----NQEILDIKNQ--ELSGTLTVYSRPSIAQCWLVPRLADF 124
                         90       100
                 ....*....|....*....|....
gi 373916477  78 SEIYPHVSFRIRNGNsdfilENID 101
Cdd:PRK10086 125 TRRYPSISLTILTGN-----ENVN 143
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
2-157 2.82e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 50.34  E-value: 2.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEG---MVLKRRAEEiiilsekaELEVGSQS-HDIS----GEIAIGCGVTEATQTMGKL 73
Cdd:PRK11242  38 QLEESLGVQLFDRSGRTVRLTDAGevyLRYARRALQ--------DLEAGRRAiHDVAdlsrGSLRLAMTPTFTAYLIGPL 109
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  74 IKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPV---ELEKLNFIhfnaEEKWGILMKKNASLAKKE-YITSK 149
Cdd:PRK11242 110 IDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVhspEIEAQPLF----TETLALVVGRHHPLAARRkALTLD 185

                 ....*...
gi 373916477 150 DLIDLPLI 157
Cdd:PRK11242 186 ELADEPLV 193
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
56-251 5.76e-07

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 48.84  E-value: 5.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNfIHFNAEEKWGILMK 135
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIR-VHSRQPAPIGAVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 136 KNASLAKKEYITSKDLIDLPLIASARS-EAQTIFSNWYGTGYENLSFCATSDLTTTAAILVKNDVGYAVVVEGSICDA-A 213
Cdd:cd08426   80 PGHPLARQPSVTLAQLAGYPLALPPPSfSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREiR 159
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 373916477 214 SDELCFRPL-YPSLNSHSL-FVWKKYQSFSLTVTKFIDFI 251
Cdd:cd08426  160 RGQLVAVPLaDPHMNHRQLeLQTRAGRQLPAAASAFLQLL 199
cysB PRK12681
HTH-type transcriptional regulator CysB;
3-170 1.50e-06

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 48.36  E-value: 1.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   3 LEDELGAVLFIR-GKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:PRK12681  40 LEDELGIQIFARsGKHLTQVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERY 119
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVEL-EKLNFI---HFNAeekwGILMKKNASLAKKEYITSKDLIDLPLI 157
Cdd:PRK12681 120 PRVSLHMHQGSPTQIAEAAAKGNADFAIATEALHLyDDLIMLpcyHWNR----SVVVPPDHPLAKKKKLTIEELAQYPLV 195
                        170
                 ....*....|....*...
gi 373916477 158 A-----SARSEAQTIFSN 170
Cdd:PRK12681 196 TyvfgfTGRSELDTAFNR 213
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
57-204 2.05e-06

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 47.17  E-value: 2.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  57 IAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEkLNFIHFNAeEKWG--ILM 134
Cdd:cd08443    2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDY-DDLITLPC-YHWNrcVVV 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 373916477 135 KKNASLAKKEYITSKDLIDLPLIA-----SARSEAQTIFSNwygTGYE-NLSFCAT-SDLTTTaaiLVKNDVGYAVV 204
Cdd:cd08443   80 KRDHPLADKQSISIEELATYPIVTytfgfTGRSELDTAFNR---AGLTpNIVLTATdADVIKT---YVRLGLGVGVI 150
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
2-110 3.39e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 47.33  E-value: 3.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVL----KRRAEEIIILSEKAELevgsQSHDISGEIAIGCGVTEATQTMGKLIKKF 77
Cdd:PRK11151  38 KLEDELGVMLLERTSRKVLFTQAGLLLvdqaRTVLREVKVLKEMASQ----QGETMSGPLHIGLIPTVGPYLLPHIIPML 113
                         90       100       110
                 ....*....|....*....|....*....|...
gi 373916477  78 SEIYPHVSFRIRNGNSDFILENIDNGLLDIGVV 110
Cdd:PRK11151 114 HQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIL 146
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
2-101 3.95e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 46.91  E-value: 3.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:PRK14997  39 QLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARY 118
                         90       100
                 ....*....|....*....|..
gi 373916477  82 PHVSFRIRNGNS--DFILENID 101
Cdd:PRK14997 119 PDVSLQLEATNRrvDVVGEGVD 140
PRK12680 PRK12680
LysR family transcriptional regulator;
2-110 4.18e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 46.92  E-value: 4.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKM-VLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEI 80
Cdd:PRK12680  39 QLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQA 118
                         90       100       110
                 ....*....|....*....|....*....|
gi 373916477  81 YPHVSFRIRNGNSDFILENIDNGLLDIGVV 110
Cdd:PRK12680 119 YPQVSVHLQQAAESAALDLLGQGDADIAIV 148
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
56-249 4.88e-06

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 45.87  E-value: 4.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVV---LEPVELEKLNFIhfnaEEKWGI 132
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVstlHEPPGIERERLL----RIDGVC 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 133 LMKKNASLAKKEYITSKDLIDLPLIASARSEA--QTIFSNWYGTGYENLSFCATSDLTTTAAiLVKNDVGYAVVVEGSIC 210
Cdd:cd08456   77 VLPPGHRLAVKKVLTPSDLEGEPFISLARTDGtrQRVDALFEQAGVKRRIVVETSYAATICA-LVAAGVGVSVVNPLTAL 155
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 373916477 211 DAASDELCFRPLYPSLNSHSLFVWKKYQSFSLTVTKFID 249
Cdd:cd08456  156 DYAAAGLVVRRFSPAVPFEVSLIRPKHRPSSALVAAFSA 194
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
56-170 6.38e-06

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 45.69  E-value: 6.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKlNFIHFNAEEkW--GIL 133
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHP-DLVTLPCYR-WnhCVI 78
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 373916477 134 MKKNASLAKKEYITSKDLIDLPLI-----ASARSEAQTIFSN 170
Cdd:cd08413   79 VPPGHPLADLGPLTLEDLAQYPLItydfgFTGRSSIDRAFAR 120
PRK09986 PRK09986
LysR family transcriptional regulator;
2-157 7.23e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 46.25  E-value: 7.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:PRK09986  44 ELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKEN 123
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFN-AEEKWGILMKKNASLAKKEYITSKDLIDLPLI 157
Cdd:PRK09986 124 PNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRRlHESAFAVAVPEEHPLASRSSVPLKALRNEYFI 200
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
2-25 1.00e-05

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 41.99  E-value: 1.00e-05
                          10        20
                  ....*....|....*....|....
gi 373916477    2 QLEDELGAVLFIRGKRKMVLTEEG 25
Cdd:pfam00126  36 RLEEELGVPLFERTTRGVRLTEAG 59
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
1-109 1.29e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 45.40  E-value: 1.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   1 MQ-LEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVgsQSHDISGEIAIGCGVTEATQTMGKLIKKFSE 79
Cdd:PRK15092  46 MQrLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSL--MYSNLQGVLTIGASDDTADTILPFLLNRVSS 123
                         90       100       110
                 ....*....|....*....|....*....|
gi 373916477  80 IYPHVSFRIRNGNSDFILENIDNGLLDIGV 109
Cdd:PRK15092 124 VYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
73-222 3.69e-05

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: 43.35  E-value: 3.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  73 LIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIhFNAEEKWGILMKKNASLAKKEYITSKDLI 152
Cdd:cd08433   18 LLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTE-PLLEEDLFLVGPADAPLPRGAPVPLAELA 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 153 DLPLI----------------ASARSEAQTIfsnwygtgYEnlsfcaTSDLTTTAAiLVKNDVGYAVVVEGSI-CDAASD 215
Cdd:cd08433   97 RLPLIlpsrghglrrlvdeaaARAGLTLNVV--------VE------IDSVATLKA-LVAAGLGYTILPASAVaAEVAAG 161

                 ....*..
gi 373916477 216 ELCFRPL 222
Cdd:cd08433  162 RLVAAPI 168
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
56-111 8.03e-05

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 42.53  E-value: 8.03e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVL 111
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTY 56
PRK10341 PRK10341
transcriptional regulator TdcA;
2-120 2.21e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.77  E-value: 2.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEIIILSEKAELEVGSQSHDISGEIAIGCGVTEATQTMGKLIKKFSEIY 81
Cdd:PRK10341  44 DIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVF 123
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 373916477  82 PHVSFRIRNGNSDFILENIDNGLLD--IGVVLEPVELEKLN 120
Cdd:PRK10341 124 PKAQVSMYEAQLSSFLPAIRDGRLDfaIGTLSNEMKLQDLH 164
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
72-157 5.27e-04

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: 39.82  E-value: 5.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  72 KLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNFIHFnAEEKWGILMKKNASLAKKEYITSKDL 151
Cdd:cd08411   18 RLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPL-FDEPFLLAVPKDHPLAKRKSVTPEDL 96

                 ....*.
gi 373916477 152 IDLPLI 157
Cdd:cd08411   97 AGERLL 102
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
57-171 6.00e-04

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: 39.95  E-value: 6.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  57 IAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLD--IGVVLEPVELEKLNFIHFnAEEKWGILM 134
Cdd:cd08435    2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDlaIGRLADDEQPPDLASEEL-ADEPLVVVA 80
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 373916477 135 KKNASLAKKEYITSKDLIDLPLI-----ASARSEAQTIFSNW 171
Cdd:cd08435   81 RPGHPLARRARLTLADLADYPWVlpppgTPLRQRLEQLFAAA 122
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
55-157 6.41e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 39.57  E-value: 6.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  55 GEIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGV-----VLEPVELEKLnfihfnAEEK 129
Cdd:cd08446    1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFgrfypVEPDIAVENV------AQER 74
                         90       100
                 ....*....|....*....|....*...
gi 373916477 130 WGILMKKNASLAKKEYITSKDLIDLPLI 157
Cdd:cd08446   75 LYLAVPKSHPLAARPAVSLADLRNEPLI 102
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
73-236 1.17e-03

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 39.02  E-value: 1.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  73 LIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVELEKLNfIHFNAEEKWGILMKKNASLAKKEYITSKDLI 152
Cdd:cd08452   18 IVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALH-IETVQSSPCVLALPKQHPLASKEEITIEDLR 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477 153 DLPLIASARSEAQTIFSnwygtgyENLSFCATS--------DLTTTAAILVKNDVGYAV-VVEGSICDAASDELCFRPLY 223
Cdd:cd08452   97 DEPIITVAREAWPTLYD-------EIIQLCEQAgfrpkivqEATEYQTVIGLVSAGIGVtFVPSSAKKLFNLEVAYRKID 169
                        170
                 ....*....|....
gi 373916477 224 -PSLNSHSLFVWKK 236
Cdd:cd08452  170 qINLNAEWSIAYRK 183
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
102-157 1.54e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 38.70  E-value: 1.54e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 373916477 102 NGLLDIGVVLEPVELEKLNFIH-FNAEEKwgILMKKNASLAKKEYITSKDLIDLPLI 157
Cdd:cd08441   47 RGELDLVITSDPLPLPGIAYEPlFDYEVV--LVVAPDHPLAAKEFITPEDLADETLI 101
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
2-36 1.62e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 39.15  E-value: 1.62e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 373916477   2 QLEDELGAVLFIRGKRKMVLTEEGMVLKRRAEEII 36
Cdd:PRK11074  39 QLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
56-172 7.67e-03

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176121  Cd Length: 199  Bit Score: 36.40  E-value: 7.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373916477  56 EIAIGCGVTEATQTMGKLIKKFSEIYPHVSFRIRNGNSDFILENIDNGLLDIGVVLEPVEL-EKLNFIHFnAEEKWGILM 134
Cdd:cd08430    1 ELSLYCSVTASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLpARLAFLPL-ATSPLVFIA 79
                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 373916477 135 KKNASLAKKEYITSK-DLIDLPLIASARSEAQTIFSNWY 172
Cdd:cd08430   80 PNIACAVTQQLSQGEiDWSRLPFILPERGLARERLDQWF 118
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
3-35 8.45e-03

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 36.74  E-value: 8.45e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 373916477   3 LEDELGAVLFIRGKRKMVLTEEGmvlKRRAEEI 35
Cdd:PRK11139  44 LEDFLGLKLFRRRNRSLLLTEEG---QRYFLDI 73
 
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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