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Conserved domains on  [gi|504408387|ref|WP_014595489|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Stutzerimonas]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10082 super family cl32457
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-300 4.47e-66

hypochlorite stress DNA-binding transcriptional regulator HypT;


The actual alignment was detected with superfamily member PRK10082:

Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 209.14  E-value: 4.47e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   2 NLETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVV 81
Cdd:PRK10082  10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  82 RHLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLRheglNLATRLI-ATNVGEAVHVLREGGCDLILAYYDPDaaLQLDP 160
Cdd:PRK10082  90 AELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMP----PLFTWAIeAIDVDEAVDKLREGQSDCIFSFHDED--LLEAP 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 161 elFPSLHLGRTEMLPVCAVGPDGTPLYDVDSGQtVPLLAYSAGAFLGRSVN-LLLRQRALRSTTVYETAMADSLKSMALQ 239
Cdd:PRK10082 164 --FDHIRLFESQLFPVCASDEHGEALFNLAQPH-FPLLNYSRNSYMGRLINrTLTRHSELSFSTFFVSSMSELLKQVALD 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504408387 240 GLGIAWVPRLSVEPELERGELAICGGEQWRVPLEIRLYRCSLMRKGAVRLLWRRLESRAIA 300
Cdd:PRK10082 241 GCGIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWRELRELEIV 301
 
Name Accession Description Interval E-value
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-300 4.47e-66

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 209.14  E-value: 4.47e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   2 NLETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVV 81
Cdd:PRK10082  10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  82 RHLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLRheglNLATRLI-ATNVGEAVHVLREGGCDLILAYYDPDaaLQLDP 160
Cdd:PRK10082  90 AELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMP----PLFTWAIeAIDVDEAVDKLREGQSDCIFSFHDED--LLEAP 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 161 elFPSLHLGRTEMLPVCAVGPDGTPLYDVDSGQtVPLLAYSAGAFLGRSVN-LLLRQRALRSTTVYETAMADSLKSMALQ 239
Cdd:PRK10082 164 --FDHIRLFESQLFPVCASDEHGEALFNLAQPH-FPLLNYSRNSYMGRLINrTLTRHSELSFSTFFVSSMSELLKQVALD 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504408387 240 GLGIAWVPRLSVEPELERGELAICGGEQWRVPLEIRLYRCSLMRKGAVRLLWRRLESRAIA 300
Cdd:PRK10082 241 GCGIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWRELRELEIV 301
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-298 8.24e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.01  E-value: 8.24e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   3 LETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVR 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  83 HLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDaalqlDPEL 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-----DPGL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 163 FpSLHLGRTEMLPVCavgpdgtplydvdsgqtvpllaysagaflgrSVNLLLRQRALRSTTVyetamaDSLKSMALQGLG 242
Cdd:COG0583  156 V-ARPLGEERLVLVA-------------------------------SPDHPLARRAPLVNSL------EALLAAVAAGLG 197

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 504408387 243 IAWVPRLSVEPELERGELAICGGEQWRVPLEIRL-YRCSLMRKGAVRLLWRRLESRA 298
Cdd:COG0583  198 IALLPRFLAADELAAGRLVALPLPDPPPPRPLYLvWRRRRHLSPAVRAFLDFLREAL 254
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-262 9.67e-22

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: 92.68  E-value: 9.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   1 MNLetKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEV 80
Cdd:NF040786   1 MNL--KQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  81 VRHLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDAAlqldp 160
Cdd:NF040786  79 EEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKK----- 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 161 elfpslhlgRTEMLPVC-----AVGPDGTPLY-------DVDSGQTVPLLAYSAGAFLGRSVNLLLRQRALRST---TVY 225
Cdd:NF040786 154 ---------RLVYTPFYkdrlvLITPNGTEKYrmlkeeiSISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnVVA 224

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 504408387 226 ETAMADSLKSMALQGLGIAWVPRLSVEPELERGELAI 262
Cdd:NF040786 225 SLGSTEAIKQSVEAGLGISVISELAAEKEVERGRVLI 261
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-298 1.40e-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: 84.65  E-value: 1.40e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   95 LQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDaalqlDPELFpSLHLGRTEML 174
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPD-----DPGLE-ARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  175 PVCAVG---PDGTPLyDVDSGQTVPLLAYSAGAFLGRSVNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAWVPRLSV 251
Cdd:pfam03466  78 LVAPPDhplARGEPV-SLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 504408387  252 EPELERGELAICGGEQWRVPLEIRLYRcslmRKG-----AVRLLWRRLESRA 298
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVW----RKGrplspAVRAFIEFLREAL 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-263 6.66e-12

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 63.39  E-value: 6.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  95 LQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYydpdaaLQLDPELFPSLHLGRTEMl 174
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA------LPVDDPGLESEPLFEEPL- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 175 pvCAVGPDGTPLYDVDSG-----QTVPLLAYSAGAFLGRSVNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAWVPRL 249
Cdd:cd05466   75 --VLVVPPDHPLAKRKSVtladlADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPES 152

                        170
                 ....*....|....
gi 504408387 250 SVEpELERGELAIC 263
Cdd:cd05466  153 AVE-ELADGGLVVL 165
 
Name Accession Description Interval E-value
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-300 4.47e-66

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 209.14  E-value: 4.47e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   2 NLETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVV 81
Cdd:PRK10082  10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  82 RHLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLRheglNLATRLI-ATNVGEAVHVLREGGCDLILAYYDPDaaLQLDP 160
Cdd:PRK10082  90 AELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMP----PLFTWAIeAIDVDEAVDKLREGQSDCIFSFHDED--LLEAP 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 161 elFPSLHLGRTEMLPVCAVGPDGTPLYDVDSGQtVPLLAYSAGAFLGRSVN-LLLRQRALRSTTVYETAMADSLKSMALQ 239
Cdd:PRK10082 164 --FDHIRLFESQLFPVCASDEHGEALFNLAQPH-FPLLNYSRNSYMGRLINrTLTRHSELSFSTFFVSSMSELLKQVALD 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504408387 240 GLGIAWVPRLSVEPELERGELAICGGEQWRVPLEIRLYRCSLMRKGAVRLLWRRLESRAIA 300
Cdd:PRK10082 241 GCGIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWRELRELEIV 301
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-298 8.24e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.01  E-value: 8.24e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   3 LETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVR 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  83 HLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDaalqlDPEL 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-----DPGL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 163 FpSLHLGRTEMLPVCavgpdgtplydvdsgqtvpllaysagaflgrSVNLLLRQRALRSTTVyetamaDSLKSMALQGLG 242
Cdd:COG0583  156 V-ARPLGEERLVLVA-------------------------------SPDHPLARRAPLVNSL------EALLAAVAAGLG 197

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 504408387 243 IAWVPRLSVEPELERGELAICGGEQWRVPLEIRL-YRCSLMRKGAVRLLWRRLESRA 298
Cdd:COG0583  198 IALLPRFLAADELAAGRLVALPLPDPPPPRPLYLvWRRRRHLSPAVRAFLDFLREAL 254
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-262 9.67e-22

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: 92.68  E-value: 9.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   1 MNLetKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEV 80
Cdd:NF040786   1 MNL--KQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  81 VRHLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDAAlqldp 160
Cdd:NF040786  79 EEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKK----- 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 161 elfpslhlgRTEMLPVC-----AVGPDGTPLY-------DVDSGQTVPLLAYSAGAFLGRSVNLLLRQRALRST---TVY 225
Cdd:NF040786 154 ---------RLVYTPFYkdrlvLITPNGTEKYrmlkeeiSISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnVVA 224

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 504408387 226 ETAMADSLKSMALQGLGIAWVPRLSVEPELERGELAI 262
Cdd:NF040786 225 SLGSTEAIKQSVEAGLGISVISELAAEKEVERGRVLI 261
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-298 1.40e-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: 84.65  E-value: 1.40e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   95 LQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDaalqlDPELFpSLHLGRTEML 174
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPD-----DPGLE-ARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  175 PVCAVG---PDGTPLyDVDSGQTVPLLAYSAGAFLGRSVNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAWVPRLSV 251
Cdd:pfam03466  78 LVAPPDhplARGEPV-SLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 504408387  252 EPELERGELAICGGEQWRVPLEIRLYRcslmRKG-----AVRLLWRRLESRA 298
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVW----RKGrplspAVRAFIEFLREAL 204
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 3.92e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.65  E-value: 3.92e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 504408387    6 KWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQ 64
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 3-145 8.21e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 73.27  E-value: 8.21e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   3 LETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVR 82
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504408387  83 HLHHVeGQQGEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDL 145
Cdd:PRK09906  81 RARKI-VQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDV 142
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-88 1.33e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 69.60  E-value: 1.33e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504408387  11 FVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLHHVE 88
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVA 86
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-96 6.31e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 67.69  E-value: 6.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   2 NLETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRtPIELTEAGQlflvsarnmveqlgEVV 81
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQ--------------RLL 65

                         90
                 ....*....|....*
gi 504408387  82 RHLHHVEGQQGEVLQ 96
Cdd:PRK13348  66 RHLRQVALLEADLLS 80
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
3-272 5.58e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.79  E-value: 5.58e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   3 LETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRtPIELTEAGQLFLVSARnMVEQL-GEVV 81
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRLLRHAR-QVRLLeAELL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  82 RHLHHVEGQQgEVLQISA-AHSLALGFFPAwIAGLrheglnLATRLIATNV---GEAV--HVLREGgcdlilayyDPDAA 155
Cdd:PRK03635  80 GELPALDGTP-LTLSIAVnADSLATWFLPA-LAPV------LARSGVLLDLvveDQDHtaELLRRG---------EVVGA 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 156 LQLDPELFP---SLHLGRTEMLPVCAVG------PDGTplyDVDSGQTVPLLAYSA-----GAFLGRSVNL---LLRQRA 218
Cdd:PRK03635 143 VTTEPQPVQgcrVDPLGAMRYLAVASPAfaaryfPDGV---TAEALAKAPAVVFNRkddlqDRFLRQAFGLppgSVPCHY 219

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 504408387 219 LRSTtvyetamaDSLKSMALQGLGIAWVPRLSVEPELERGELA-ICGGEQWRVPL 272
Cdd:PRK03635 220 VPSS--------EAFVRAALAGLGWGMIPELQIEPELASGELVdLTPGRPLDVPL 266
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-263 6.66e-12

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 63.39  E-value: 6.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  95 LQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYydpdaaLQLDPELFPSLHLGRTEMl 174
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA------LPVDDPGLESEPLFEEPL- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 175 pvCAVGPDGTPLYDVDSG-----QTVPLLAYSAGAFLGRSVNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAWVPRL 249
Cdd:cd05466   75 --VLVVPPDHPLAKRKSVtladlADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPES 152

                        170
                 ....*....|....
gi 504408387 250 SVEpELERGELAIC 263
Cdd:cd05466  153 AVE-ELADGGLVVL 165
rbcR CHL00180
LysR transcriptional regulator; Provisional
 13-131 1.01e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 64.27  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  13 ALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLHHVEGQQG 92
Cdd:CHL00180  15 AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQR 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 504408387  93 EVLQISAAHSLALGFFPAWIAGLRHEGLNLA-------TRLIATNV 131
Cdd:CHL00180  95 GTLIIGASQTTGTYLMPRLIGLFRQRYPQINvqlqvhsTRRIAWNV 140
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
3-129 4.18e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 62.34  E-value: 4.18e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   3 LETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVE--QLG-- 78
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNtwQAAkk 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504408387  79 EVVRHLHHVEgqqgevLQISAAHSLALGFFPAWIAGL--RHEGLNLATRlIAT 129
Cdd:PRK03601  81 EVAHTSQHNE------LSIGASASLWECMLTPWLGRLyqNQEALQFEAR-IAQ 126
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 15-104 4.71e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 62.17  E-value: 4.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  15 AATR--SFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLhhVEGQQG 92
Cdd:PRK11139  16 AAARhlSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAK 93

                         90
                 ....*....|..
gi 504408387  93 EVLQISAAHSLA 104
Cdd:PRK11139  94 GALTVSLLPSFA 105
PRK09791 PRK09791
LysR family transcriptional regulator;
8-162 1.24e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 60.93  E-value: 1.24e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   8 LEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLHHV 87
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504408387  88 EGQQGEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDAalqLDPEL 162
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGP---YDHEF 161
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-109 3.80e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 59.66  E-value: 3.80e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   1 MNLETkwLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQlgev 80
Cdd:PRK11151   1 MNIRD--LEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLRE---- 74

                         90       100
                 ....*....|....*....|....*....
gi 504408387  81 VRHLHHVEGQQGEVLqisaAHSLALGFFP 109
Cdd:PRK11151  75 VKVLKEMASQQGETM----SGPLHIGLIP 99
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
3-77 4.32e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.43  E-value: 4.32e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504408387   3 LETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQL 77
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWL 76
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-177 2.14e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 57.32  E-value: 2.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   8 LEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQ-LFLVSARNMvEQLGEVVRHLHH 86
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKrVFWALKSSL-DTLNQEILDIKN 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  87 VE--GQqgevLQISAAHSLALGFFPAWIAGL--RHEGLNLATRliatnVGEAVHVLREGGCDLILaYYD--PDAALQldp 160
Cdd:PRK10086  98 QElsGT----LTVYSRPSIAQCWLVPRLADFtrRYPSISLTIL-----TGNENVNFQRAGIDLAI-YFDdaPSAQLT--- 164

                        170
                 ....*....|....*..
gi 504408387 161 elfpSLHLGRTEMLPVC 177
Cdd:PRK10086 165 ----HHFLMDEEILPVC 177
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
11-262 8.36e-09

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 55.75  E-value: 8.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  11 FVALAATRSF--SQAAQRRFVTQPAFSRRIRSLEEALGLQLINR-SRTPIELTEAGQLFLVSARNM---VEQLGEVVRHL 84
Cdd:PRK12684   8 FVREAVRQNFnlTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERIlqeVENLKRVGKEF 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  85 HHVEgqQGEvLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAyydpDAALQLDPELfp 164
Cdd:PRK12684  88 AAQD--QGN-LTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIA----TEAIADYKEL-- 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 165 slhlgrtEMLPV-----CAVGPDGTPLYD-----VDSGQTVPLLAYSAgAFLGRS-VNLLLRQRALRSTTVYETAMADSL 233
Cdd:PRK12684 159 -------VSLPCyqwnhCVVVPPDHPLLErkpltLEDLAQYPLITYDF-AFAGRSkINKAFALRGLKPDIVLEAIDADVI 230

                        250       260
                 ....*....|....*....|....*....
gi 504408387 234 KSMALQGLGIAWVPRLSVEPELERGELAI 262
Cdd:PRK12684 231 KTYVELGLGVGIVADMAFDPERDRNLRAI 259
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
19-262 7.73e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.84  E-value: 7.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  19 SFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLHHVEGQQGEVLQIS 98
Cdd:PRK10632  18 SFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRIG 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  99 AAHSLALGFFPAWIAGLRHE--GL--NLATRLIATNvgeavhvLREGGCDLILAYydpdAALQlDPELFpSLHLGRTEML 174
Cdd:PRK10632  98 CSSTMAQNVLAGLTAKMLKEypGLsvNLVTGIPAPD-------LIADGLDVVIRV----GALQ-DSSLF-SRRLGAMPMV 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 175 pVCA----VGPDGTPLYDVDSGqTVPLLAYSAG--------AFLGRSVNLLLRQRalrsttvYETAMADSLKSMALQGLG 242
Cdd:PRK10632 165 -VCAaksyLAQYGTPEKPADLS-SHSWLEYSVRpdnefeliAPEGISTRLIPQGR-------FVTNDPQTLVRWLTAGAG 235

                        250       260
                 ....*....|....*....|
gi 504408387 243 IAWVPRLSVEPELERGELAI 262
Cdd:PRK10632 236 IAYVPLMWVIDEINRGELEI 255
cbl PRK12679
HTH-type transcriptional regulator Cbl;
15-258 1.00e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 52.50  E-value: 1.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  15 AATRSF--SQAAQRRFVTQPAFSRRIRSLEEALGLQL-INRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLHHVEGQQ 91
Cdd:PRK12679  12 AARQDYnlTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDT 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  92 GEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAyydpDAALQLDPEL--FPSLHLG 169
Cdd:PRK12679  92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIA----SERLSNDPQLvaFPWFRWH 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 170 RTEMLPVCAVGPDGTPLyDVDSGQTVPLLAYSAGaFLGRS-VNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAWVPR 248
Cdd:PRK12679 168 HSLLVPHDHPLTQITPL-TLESIAKWPLITYRQG-ITGRSrIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAE 245

                        250
                 ....*....|
gi 504408387 249 LSVEPELERG 258
Cdd:PRK12679 246 QSSGEQEESN 255
PRK10341 PRK10341
transcriptional regulator TdcA;
4-107 2.28e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.40  E-value: 2.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   4 ETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRH 83
Cdd:PRK10341   8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNE 87

                         90       100
                 ....*....|....*....|....
gi 504408387  84 LHHVEGQqgEVLQISAAHSLALGF 107
Cdd:PRK10341  88 INGMSSE--AVVDVSFGFPSLIGF 109
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-82 2.87e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 51.10  E-value: 2.87e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  13 ALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVR 82
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
PRK12680 PRK12680
LysR family transcriptional regulator;
8-251 5.39e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 50.39  E-value: 5.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   8 LEDFVALA-ATRSFSQAAQRRFVTQPAFSRRIRSLEEALG-LQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLH 85
Cdd:PRK12680   6 LRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGfLLFVRKGRSLESVTPAGVEVIERARAVLSEANNIRTYAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  86 HVEGQQGEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLIL---AYYDPDAALqldpel 162
Cdd:PRK12680  86 NQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvstAGGEPSAGI------ 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 163 fpSLHLGRTEMLPVCavgPDGTPL------YDVDSGQTVPLLAYSAGAFLGRSVNLLLRQRALRSTTVYETAMADSLKSM 236
Cdd:PRK12680 160 --AVPLYRWRRLVVV---PRGHALdtprraPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTY 234

                        250
                 ....*....|....*
gi 504408387 237 ALQGLGIAWVPRLSV 251
Cdd:PRK12680 235 VRAGLGVGLLAEMAV 249
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-261 1.43e-06

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 48.07  E-value: 1.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 102 SLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDaalqlDPELfpslhlgRTEML---PVCA 178
Cdd:cd08426    9 GLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPP-----EPGI-------RVHSRqpaPIGA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 179 VGPDGTPLydvdSGQTVPLLAYSAGAFLG---------RSVNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAWVPRL 249
Cdd:cd08426   77 VVPPGHPL----ARQPSVTLAQLAGYPLAlpppsfslrQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTEL 152

                        170
                 ....*....|..
gi 504408387 250 SVEPELERGELA 261
Cdd:cd08426  153 AVRREIRRGQLV 164
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-118 3.32e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 47.76  E-value: 3.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   1 MNLETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEV 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 504408387  81 VRHLHHVEGqqgeVLQISAAHSLALGFFPAWIAGLRHE 118
Cdd:PRK10837  81 EQLFREDNG----ALRIYASSTIGNYILPAMIARYRRD 114
PRK09986 PRK09986
LysR family transcriptional regulator;
6-78 4.37e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 47.41  E-value: 4.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   6 KWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSAR----------NMVE 75
Cdd:PRK09986  10 KLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRrlldnaeqslARVE 89


                 ...
gi 504408387  76 QLG 78
Cdd:PRK09986  90 QIG 92
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 95-252 1.26e-05

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 45.25  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  95 LQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAYYDPDAAlQLDPELFPSLHLgrteml 174
Cdd:cd08415    2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHP-GLESEPLASGRA------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 175 pVCAVgPDGTPLydvdSGQTV---------PLLAYSAGAFLGRSVNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAW 245
Cdd:cd08415   75 -VCVL-PPGHPL----ARKDVvtpadlagePLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAI 148


                 ....*..
gi 504408387 246 VPRLSVE 252
Cdd:cd08415  149 VDPLTAA 155
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-76 1.72e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 45.44  E-value: 1.72e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504408387   1 MNLetKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQ 76
Cdd:PRK11233   1 MNF--RRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQ 74
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-254 1.99e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 45.37  E-value: 1.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   1 MNLetKWLEdFVALAATRSF--SQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIE-LTEAGQLFLVSARNMVEQL 77
Cdd:PRK12682   1 MNL--QQLR-FVREAVRRNLnlTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  78 GEVVRHLHHVEGQQGEVLQISAAHSLALGFFPAWIAGLR--HEGLNLAtrLIATNVGEAVHVLREGGCDLILAyydpDAA 155
Cdd:PRK12682  78 GNIKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRkrYPKVNLS--LHQGSPDEIARMVISGEADIGIA----TES 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 156 LQLDPELfpslhlgRTemLPV-----CAVGPDGTPL-----YDVDSGQTVPLLAYSaGAFLGRS-VNLLLRQRALRSTTV 224
Cdd:PRK12682 152 LADDPDL-------AT--LPCydwqhAVIVPPDHPLaqeerITLEDLAEYPLITYH-PGFTGRSrIDRAFAAAGLQPDIV 221

                        250       260       270
                 ....*....|....*....|....*....|
gi 504408387 225 YETAMADSLKSMALQGLGIAWVPRLSVEPE 254
Cdd:PRK12682 222 LEAIDSDVIKTYVRLGLGVGIVAEMAYRPD 251
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 138-276 5.60e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 43.03  E-value: 5.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 138 LREGGCDLILAyydpdAALQLDPELFPSLHLGRTEMlpVCAVGPDgTPLYDVDSG-QTVPLLAY-------SAGAFLGRS 209
Cdd:cd08431   45 LASGRADLVIG-----ATGELPPGGVKTRPLGEVEF--VFAVAPN-HPLAKLDGPlDASAIKQYpaivvadTSRNLPPRS 116

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504408387 210 VNLLLRQRALRSTTvyetaMADSLKSMALqGLGIAWVPRLSVEPELERGELAICGGEQWRVPLEIRL 276
Cdd:cd08431  117 SGLLEGQDRIRVPT-----MQAKIDAQVL-GLGVGYLPRHLAKPELASGELVEKALEDPRPPQELFL 177
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-110 1.10e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 43.08  E-value: 1.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   3 LETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVR 82
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100
                 ....*....|....*....|....*...
gi 504408387  83 HLHhvEGQQGEVLQISAAHSLALGFFPA 110
Cdd:PRK15421  82 ACN--EPQQTRLRIAIECHSCIQWLTPA 107
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-262 1.16e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.96  E-value: 1.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  21 SQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPI-ELTEAGQLFLVSARnmvEQLGEV--VRHL--HHVEGQQGeVL 95
Cdd:PRK12681  20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAR---EILSKVesIKSVagEHTWPDKG-SL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  96 QISAAHSLALGFFPAWIAGLR----------HEG-------------LNLAtrlIATnvgEAVHVLReggcDLIlayydp 152
Cdd:PRK12681  96 YIATTHTQARYALPPVIKGFIeryprvslhmHQGsptqiaeaaakgnADFA---IAT---EALHLYD----DLI------ 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 153 daalqldpeLFPSLHLGRtemlpvCAVGPDGTPLYDVdSGQTV------PLLAYSAGaFLGRS-VNLLLRQRALRSTTVY 225
Cdd:PRK12681 160 ---------MLPCYHWNR------SVVVPPDHPLAKK-KKLTIeelaqyPLVTYVFG-FTGRSeLDTAFNRAGLTPRIVF 222

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 504408387 226 ETAMADSLKSMALQGLGIAWVPRLSVEPELERGELAI 262
Cdd:PRK12681 223 TATDADVIKTYVRLGLGVGVIASMAVDPVADPDLVAI 259
PRK09801 PRK09801
LysR family transcriptional regulator;
6-113 1.43e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 42.71  E-value: 1.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387   6 KWLEDFVALAATRSFSQAAQRRFVTqPAF-SRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHL 84
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQT-PAFvTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDV 87

                         90       100
                 ....*....|....*....|....*....
gi 504408387  85 HHVEGQQGEVLQISAahslALGFFPAWIA 113
Cdd:PRK09801  88 TQIKTRPEGMIRIGC----SFGFGRSHIA 112
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 230-260 2.03e-04

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 41.66  E-value: 2.03e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 504408387 230 ADSLKSMALQGLGIAWVPRLSVEPELERGEL 260
Cdd:cd08422  132 GEALRAAALAGLGIALLPDFLVAEDLASGRL 162
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-71 3.34e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.55  E-value: 3.34e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504408387   1 MNLETKWLEDFVALAATRSFSQAAQRRFVTQPAFSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSAR 71
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYAR 79
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-94 3.62e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 41.34  E-value: 3.62e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504408387  28 FVTQPAFSRRIRSLEEALGLQLI---NRSrtpIELTEAGQLFLVSARNMVEQLGEVVRHLHHVEGQ-QGEV 94
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFvrdNRS---VTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSlSGEL 69
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 15-262 4.68e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 41.18  E-value: 4.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  15 AATRSF--SQAAQRRFVTQPAFSRRIRSLEEALGLQL-INRSRTPIELTEAGQLFLVSARNMVEQLGEVVRHLHHVEGQQ 91
Cdd:PRK12683  12 AVRQNFnlTEVANALYTSQSGVSKQIKDLEDELGVEIfIRRGKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRD 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  92 GEVLQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGGCDLILAyydpDAALQLDPEL--FPSL--- 166
Cdd:PRK12683  92 SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIA----TEALDREPDLvsFPYYswh 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 167 HlgrtemlpvCAVGPDGTPLY-----DVDSGQTVPLLAYSAGaFLGRSVNLLLRQRALRSTTVYETAM-ADSLKSMALQG 240
Cdd:PRK12683 168 H---------VVVVPKGHPLTgrenlTLEAIAEYPIITYDQG-FTGRSRIDQAFAEAGLVPDIVLTALdADVIKTYVELG 237

                        250       260
                 ....*....|....*....|..
gi 504408387 241 LGIAWVPRLSVEPELERGELAI 262
Cdd:PRK12683 238 MGVGIVAAMAYDPQRDTGLVAL 259
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 230-260 1.06e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176161  Cd Length: 202  Bit Score: 39.42  E-value: 1.06e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 504408387 230 ADSLKSMALQGLGIAWVPRLSVEPELERGEL 260
Cdd:cd08472  134 SEAYLAAALAGLGIIQVPRFMVRPHLASGRL 164
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 23-74 1.55e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 39.59  E-value: 1.55e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 504408387  23 AAQRRFVTQPA--FSRRIRSLEEALGLQLINRSRTPIELTEAGQLFLVSARNMV 74
Cdd:PRK14997  20 AAAGRALDEPKskLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAML 73
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-254 2.50e-03

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 38.32  E-value: 2.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387  95 LQISAAHSLALGFFPAWIAGLRHEGLNLATRLIATNVGEAVHVLREGgcdlilayyDPDAALQLDPELFPSLHLGRTEML 174
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAG---------ELDAAIVVEPPFPLPKDLVWTPLV 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504408387 175 --PVCAVGPDGTPLYDVDSG-QTVPLLAYSAGAFLGRSVNLLLRQRALRSTTVYETAMADSLKSMALQGLGIAWVPRLSV 251
Cdd:cd08427   73 rePLVLIAPAELAGDDPRELlATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAV 152


                 ...
gi 504408387 252 EPE 254
Cdd:cd08427  153 PLP 155
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 232-278 2.79e-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: 38.24  E-value: 2.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 504408387 232 SLKSMALQGLGIAWVPRLSVEPELERGELAIcggeqwrVPLE-IRLYR 278
Cdd:cd08420  138 AIKEAVEAGLGISILSRLAVRKELELGRLVA-------LPVEgLRLTR 178
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 230-260 5.00e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 37.44  E-value: 5.00e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 504408387 230 ADSLKSMALQGLGIAWVPRLSVEPELERGEL 260
Cdd:cd08474  137 SDLMLDAALDGLGIAYLFEDLVAEHLASGRL 167
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 231-260 5.67e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 37.22  E-value: 5.67e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 504408387 231 DSLKSMALQGLGIAWVPRLSVEPELERGEL 260
Cdd:cd08476  133 EALIEFALQGLGIACLPDFSVREALADGRL 162
 
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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