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Conserved domains on  [gi|15596200|ref|NP_249694|]
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transcriptional regulator MvfR [Pseudomonas aeruginosa PAO1]

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];
5-294 2.75e-25

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 101.87  E-value: 2.75e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   5 NLNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLN-YQQLIGD 83
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAeLEEAEAE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  84 IAfNLNKGPRN-LRVlldtAIPPSFCDTVSSVLLDDF---------NMVSLIRTSPADSLAtikqdNAEIDIAITIDeEL 153
Cdd:COG0583  82 LR-ALRGGPRGtLRI----GAPPSLARYLLPPLLARFrarhpgvrlELREGNSDRLVDALL-----EGELDLAIRLG-PP 150

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 154 KISRFNQCVLGYTKAFVVAHPQHPlcnaslhsiasLANYRQIslgsrsgqhsnllrpvsdkvlfVENFDDMLRLVEAGVG 233
Cdd:COG0583 151 PDPGLVARPLGEERLVLVASPDHP-----------LARRAPL----------------------VNSLEALLAAVAAGLG 197

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596200 234 WGIAPHYFVEERLRNGTLAVLsELYEPgGIDTKVYCYYNTALESERSFLRFLESARQRLRE 294
Cdd:COG0583 198 IALLPRFLAADELAAGRLVAL-PLPDP-PPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-294 2.75e-25

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 101.87  E-value: 2.75e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   5 NLNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLN-YQQLIGD 83
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAeLEEAEAE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  84 IAfNLNKGPRN-LRVlldtAIPPSFCDTVSSVLLDDF---------NMVSLIRTSPADSLAtikqdNAEIDIAITIDeEL 153
Cdd:COG0583  82 LR-ALRGGPRGtLRI----GAPPSLARYLLPPLLARFrarhpgvrlELREGNSDRLVDALL-----EGELDLAIRLG-PP 150

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 154 KISRFNQCVLGYTKAFVVAHPQHPlcnaslhsiasLANYRQIslgsrsgqhsnllrpvsdkvlfVENFDDMLRLVEAGVG 233
Cdd:COG0583 151 PDPGLVARPLGEERLVLVASPDHP-----------LARRAPL----------------------VNSLEALLAAVAAGLG 197

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596200 234 WGIAPHYFVEERLRNGTLAVLsELYEPgGIDTKVYCYYNTALESERSFLRFLESARQRLRE 294
Cdd:COG0583 198 IALLPRFLAADELAAGRLVAL-PLPDP-PPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 102-286 7.44e-14

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: 69.17  E-value: 7.44e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 102 AIPPSFCDTVSSVLLDDFN------MVSLIRTSPADSLATIKQDnaEIDIAITIDEELKiSRFNQCVLGYTKAFVVAHPQ 175
Cdd:cd05466   5 GASPSIAAYLLPPLLAAFRqrypgvELSLVEGGSSELLEALLEG--ELDLAIVALPVDD-PGLESEPLFEEPLVLVVPPD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 176 HPLCNASLHSIASLANYRQISLGSRSGQHSNLLR------PVSDKVLFVENFDDMLRLVEAGVGWGIAPHYFVEErLRNG 249
Cdd:cd05466  82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRafaeagFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE-LADG 160

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 15596200 250 TLAVLSelYEPGGIDTKVYCYYNTALESERSFLRFLE 286
Cdd:cd05466 161 GLVVLP--LEDPPLSRTIGLVWRKGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-293 7.48e-12

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: 63.46  E-value: 7.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200    95 LRVlldtAIPPSFCDTVSSVLLDDFNM------VSLIRTSPADSLATIKQDnaEIDIAITIDEELkISRFNQCVLGYTKA 168
Cdd:pfam03466   4 LRI----GAPPTLASYLLPPLLARFRErypdveLELTEGNSEELLDLLLEG--ELDLAIRRGPPD-DPGLEARPLGEEPL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   169 FVVAHPQHPLCNASLHSIASLANYRQISLGSRSGQHSNLLRPVSDK------VLFVENFDDMLRLVEAGVGWGIAPHYFV 242
Cdd:pfam03466  77 VLVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAglrprvVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15596200   243 EERLRNGTLAVLsELYEPgGIDTKVYCYYNTALESERSFLRFLESARQRLR 293
Cdd:pfam03466 157 ARELADGRLVAL-PLPEP-PLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
12-260 6.20e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 47.36  E-value: 6.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   12 FLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLnyQQLIGDIAfNLNKG 91
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLL--QQLESNLA-ELRGG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   92 P----RNLRV---------LLDTAI---PPSFCDTVSSVLLDDfnMVSLIRTSPADSLATIKqdnaeidiaitiDEELKI 155
Cdd:PRK10082  96 SdyaqRKIKIaaahslslgLLPSIIsqmPPLFTWAIEAIDVDE--AVDKLREGQSDCIFSFH------------DEDLLE 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  156 SRFNQCVLGYTKAFVV-------------AHPQHPLCNASLHS-IASLANyRQISlgsrsgQHSNLlrpvSDKVLFVENF 221
Cdd:PRK10082 162 APFDHIRLFESQLFPVcasdehgealfnlAQPHFPLLNYSRNSyMGRLIN-RTLT------RHSEL----SFSTFFVSSM 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 15596200  222 DDMLRLVeAGVGWGIA--PHYFVEERLRNGTLAVLS--ELYEP 260
Cdd:PRK10082 231 SELLKQV-ALDGCGIAwlPEYAIQQEIRSGQLVVLNrdELVIP 272
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-294 2.75e-25

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 101.87  E-value: 2.75e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   5 NLNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLN-YQQLIGD 83
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAeLEEAEAE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  84 IAfNLNKGPRN-LRVlldtAIPPSFCDTVSSVLLDDF---------NMVSLIRTSPADSLAtikqdNAEIDIAITIDeEL 153
Cdd:COG0583  82 LR-ALRGGPRGtLRI----GAPPSLARYLLPPLLARFrarhpgvrlELREGNSDRLVDALL-----EGELDLAIRLG-PP 150

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 154 KISRFNQCVLGYTKAFVVAHPQHPlcnaslhsiasLANYRQIslgsrsgqhsnllrpvsdkvlfVENFDDMLRLVEAGVG 233
Cdd:COG0583 151 PDPGLVARPLGEERLVLVASPDHP-----------LARRAPL----------------------VNSLEALLAAVAAGLG 197

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596200 234 WGIAPHYFVEERLRNGTLAVLsELYEPgGIDTKVYCYYNTALESERSFLRFLESARQRLRE 294
Cdd:COG0583 198 IALLPRFLAADELAAGRLVAL-PLPDP-PPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 102-286 7.44e-14

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: 69.17  E-value: 7.44e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 102 AIPPSFCDTVSSVLLDDFN------MVSLIRTSPADSLATIKQDnaEIDIAITIDEELKiSRFNQCVLGYTKAFVVAHPQ 175
Cdd:cd05466   5 GASPSIAAYLLPPLLAAFRqrypgvELSLVEGGSSELLEALLEG--ELDLAIVALPVDD-PGLESEPLFEEPLVLVVPPD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 176 HPLCNASLHSIASLANYRQISLGSRSGQHSNLLR------PVSDKVLFVENFDDMLRLVEAGVGWGIAPHYFVEErLRNG 249
Cdd:cd05466  82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRafaeagFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE-LADG 160

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 15596200 250 TLAVLSelYEPGGIDTKVYCYYNTALESERSFLRFLE 286
Cdd:cd05466 161 GLVVLP--LEDPPLSRTIGLVWRKGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-293 7.48e-12

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: 63.46  E-value: 7.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200    95 LRVlldtAIPPSFCDTVSSVLLDDFNM------VSLIRTSPADSLATIKQDnaEIDIAITIDEELkISRFNQCVLGYTKA 168
Cdd:pfam03466   4 LRI----GAPPTLASYLLPPLLARFRErypdveLELTEGNSEELLDLLLEG--ELDLAIRRGPPD-DPGLEARPLGEEPL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   169 FVVAHPQHPLCNASLHSIASLANYRQISLGSRSGQHSNLLRPVSDK------VLFVENFDDMLRLVEAGVGWGIAPHYFV 242
Cdd:pfam03466  77 VLVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAglrprvVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15596200   243 EERLRNGTLAVLsELYEPgGIDTKVYCYYNTALESERSFLRFLESARQRLR 293
Cdd:pfam03466 157 ARELADGRLVAL-PLPEP-PLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 2.88e-09

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 52.39  E-value: 2.88e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15596200     6 LNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQA 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
12-260 6.20e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 47.36  E-value: 6.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   12 FLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLnyQQLIGDIAfNLNKG 91
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLL--QQLESNLA-ELRGG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   92 P----RNLRV---------LLDTAI---PPSFCDTVSSVLLDDfnMVSLIRTSPADSLATIKqdnaeidiaitiDEELKI 155
Cdd:PRK10082  96 SdyaqRKIKIaaahslslgLLPSIIsqmPPLFTWAIEAIDVDE--AVDKLREGQSDCIFSFH------------DEDLLE 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  156 SRFNQCVLGYTKAFVV-------------AHPQHPLCNASLHS-IASLANyRQISlgsrsgQHSNLlrpvSDKVLFVENF 221
Cdd:PRK10082 162 APFDHIRLFESQLFPVcasdehgealfnlAQPHFPLLNYSRNSyMGRLIN-RTLT------RHSEL----SFSTFFVSSM 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 15596200  222 DDMLRLVeAGVGWGIA--PHYFVEERLRNGTLAVLS--ELYEP 260
Cdd:PRK10082 231 SELLKQV-ALDGCGIAwlPEYAIQQEIRSGQLVVLNrdELVIP 272
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-308 7.84e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 46.93  E-value: 7.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200    6 LNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRdgykvepTEQALRLIPYMRSLLNY-QQLIGDI 84
Cdd:PRK15421   4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVR-------KSQPLRFTPQGEILLQLaNQVLPQI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   85 AFNLNKGPRNLRVLLDTAIPPSFCDTVSSVLLDDFN----MVSLIRTSPA--DSLATIKQDnaEIDIAITIDEELKISRF 158
Cdd:PRK15421  77 SQALQACNEPQQTRLRIAIECHSCIQWLTPALENFHknwpQVEMDFKSGVtfDPQPALQQG--ELDLVMTSDILPRSGLH 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  159 NQCVLGYTKAFVVAhPQHPLCNASLHSIASLANYRQISLG---SRSGQHSNLLRP--VSDKVLFVENFDDMLRLVEAGVG 233
Cdd:PRK15421 155 YSPMFDYEVRLVLA-PDHPLAAKTRITPEDLASETLLIYPvqrSRLDVWRHFLQPagVSPSLKSVDNTLLLIQMVAARMG 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  234 WGIAPHYFVEERLRNGtLAVLSELYEpgGIDTKVYCYYNTALESERSFLRFLESARQR-------LRELGRQRFdDAPAW 306
Cdd:PRK15421 234 IAALPHWVVESFERQG-LVVTKTLGE--GLWSRLYAAVRDGEQRQPVTEAFIRSARNHacdhlpfVKSAERPTY-DAPTV 309


                 ..
gi 15596200  307 QP 308
Cdd:PRK15421 310 RP 311
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 170-260 6.06e-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: 176113  Cd Length: 198  Bit Score: 43.28  E-value: 6.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 170 VVAHPQHPLCNASLHSIASLANYRQISLGSRSGQHSNLL-------RPVSDKVLfVENFDDMLRLVEAGVGWGIAPHYFV 242
Cdd:cd08421  76 VVVPRDHPLAGRASVAFADTLDHDFVGLPAGSALHTFLReaaarlgRRLRLRVQ-VSSFDAVCRMVAAGLGIGIVPESAA 154

                        90
                ....*....|....*...
gi 15596200 243 EERLRNGTLAVLsELYEP 260
Cdd:cd08421 155 RRYARALGLRVV-PLDDA 171
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-68 1.60e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 42.67  E-value: 1.60e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15596200    1 MPIHNLNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLI 68
Cdd:PRK11013   1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLF 68
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-260 2.98e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 41.85  E-value: 2.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   13 LQVIAS----GSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLNYQQLIGDIAFNL 88
Cdd:PRK11074   7 LEVVDAvartGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200   89 NKGPR-NLRVLLDTAIPPSFCdtvsSVLLDDF-----NMVSLIR----TSPADSLATikqdnAEIDIAITIDEELKI-SR 157
Cdd:PRK11074  87 ANGWRgQLSIAVDNIVRPDRT----RQLIVDFyrhfdDVELIIRqevfNGVWDALAD-----GRVDIAIGATRAIPVgGR 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200  158 FNQCVLGYTK-AFVVAhPQHPLCN-ASLHSIASLANYRQISL--GSRS--GQHSNLLRpvSDKVLFVENFDDMLRLVEAG 231
Cdd:PRK11074 158 FAFRDMGMLSwACVVS-SDHPLASmDGPLSDDELRPYPSLCLedTSRTlpKRITWLLD--NQRRLVVPDWESAINCLSAG 234

                        250       260
                 ....*....|....*....|....*....
gi 15596200  232 VGWGIAPHYFVEERLRNGTLAVLsELYEP 260
Cdd:PRK11074 235 LCVGMVPTHFAKPLINSGKLVEL-TLENP 262
PRK10341 PRK10341
transcriptional regulator TdcA;
8-76 3.60e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.77  E-value: 3.60e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15596200    8 HVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLN 76
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITR 79
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-75 4.81e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 41.21  E-value: 4.81e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200    6 LNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLL 75
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL 74
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-62 2.79e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.97  E-value: 2.79e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596200    6 LNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTE 62
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTE 60
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 170-254 5.24e-03

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: 37.47  E-value: 5.24e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596200 170 VVAHPQHPLCNASLHSIASLANYRQISL--GS-----------RSGQHSNLLRPVsdkvLFVENFDDMLRLVEAGVGWGI 236
Cdd:cd08420  76 LVVPPDHPLAGRKEVTAEELAAEPWILRepGSgtrevferalaEAGLDGLDLNIV----MELGSTEAIKEAVEAGLGISI 151

                        90
                ....*....|....*...
gi 15596200 237 APHYFVEERLRNGTLAVL 254
Cdd:cd08420 152 LSRLAVRKELELGRLVAL 169
leuO PRK09508
leucine transcriptional activator; Reviewed
 6-81 6.55e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 37.69  E-value: 6.55e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596200    6 LNHVNMFLQVIASGSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPYMRSLLnyqQLI 81
Cdd:PRK09508  24 LNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQAL---QLV 96
rbcR CHL00180
LysR transcriptional regulator; Provisional
 13-70 9.27e-03

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 37.31  E-value: 9.27e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15596200   13 LQVIAS-GSISSAARILRKSHTAVSSAVSNLEIDLCVELVRRDGYKVEPTEQALRLIPY 70
Cdd:CHL00180  13 LKAIATeGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRY 71
 
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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