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Conserved domains on  [gi|503972325|ref|WP_014206319|]
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MULTISPECIES: LysR family transcriptional regulator MumR [Acinetobacter]

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];
1-258 1.02e-49

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 165.42  E-value: 1.02e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELTE-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 160 CDFELSFLASPSfkggvaqmsfktlmshtiltypkitYPYKELKarmkeqgideplSITSySLATLLRLAEQGLGIAVVP 239
Cdd:COG0583  161 GEERLVLVASPD-------------------------HPLARRA------------PLVN-SLEALLAAVAAGLGIALLP 202

                        250
                 ....*....|....*....
gi 503972325 240 TLTALKEITDGRLEILNTP 258
Cdd:COG0583  203 RFLAADELAAGRLVALPLP 221
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-258 1.02e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 165.42  E-value: 1.02e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELTE-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 160 CDFELSFLASPSfkggvaqmsfktlmshtiltypkitYPYKELKarmkeqgideplSITSySLATLLRLAEQGLGIAVVP 239
Cdd:COG0583  161 GEERLVLVASPD-------------------------HPLARRA------------PLVN-SLEALLAAVAAGLGIALLP 202

                        250
                 ....*....|....*....
gi 503972325 240 TLTALKEITDGRLEILNTP 258
Cdd:COG0583  203 RFLAADELAAGRLVALPLP 221
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-274 3.94e-35

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: 128.50  E-value: 3.94e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 EL-TENQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:NF040786  81 EFdRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 160 CDFELSfLASPSFKGGVAQMSFKTLMSHtILTYPKI-------TypYKELKARMKEQGIDEP-----LSITsySLATLLR 227
Cdd:NF040786 161 YKDRLV-LITPNGTEKYRMLKEEISISE-LQKEPFImreegsgT--RKEAEKALKSLGISLEdlnvvASLG--STEAIKQ 234

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 503972325 228 LAEQGLGIAVVPTLTALKEITDGRLEILNTPIQLKTFHFTSIYIQGN 274
Cdd:NF040786 235 SVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNR 281
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-258 1.36e-28

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: 108.92  E-value: 1.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   89 TGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLA 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  169 SPSFK-GGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPTLTALKEI 247
Cdd:pfam03466  81 PPDHPlARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170
                  ....*....|.
gi 503972325  248 TDGRLEILNTP 258
Cdd:pfam03466 161 ADGRLVALPLP 171
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-255 4.94e-22

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 91.12  E-value: 4.94e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 171 SFK-GGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPTLtALKEITD 249
Cdd:cd05466   81 DHPlAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPES-AVEELAD 159


                 ....*.
gi 503972325 250 GRLEIL 255
Cdd:cd05466  160 GGLVVL 165
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-252 2.57e-20

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 88.49  E-value: 2.57e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   2 NLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSyRQLKPTHKGLTLFKYAEKFMRLETDLVAE 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLST 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  82 LTENQHLTGTIRLGVSETIVYTWLVEYIEKVQQEfPKISVEIVVDLTPNLQEGVRTGDLdMAFLLG-PTLAFECIEQALC 160
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEV-VGCVSTqPKPMRGCLAEPLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 161 DFELSFLASPSFkggVAQMSFKTLMSHTILTYPKITYPYKElkaRMKEQGIDE--PLSITSY------SLATLLRLAEQG 232
Cdd:PRK13348 160 TMRYRCVASPAF---AARYFAQGLTRHSALKAPAVAFNRKD---TLQDSFLEQlfGLPVGAYprhyvpSTHAHLAAIRHG 233

                        250       260
                 ....*....|....*....|
gi 503972325 233 LGIAVVPTLTALKEITDGRL 252
Cdd:PRK13348 234 LGYGMVPELLIGPLLAAGRL 253
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-252 6.00e-16

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 76.70  E-value: 6.00e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELtenQHLTGTIRLGVSETIvyTWLVEYIEKVQQEFPKISVEIvVDL-----TPnLQ--EGVRTGDLDMAFL-------L 146
Cdd:NF041036  81 EL---KSFKGRQRLSICCTP--TFGMAHLPGVLNRFMLRNADV-VDLkflfhSP-AQalEGIQNKEFDLAIIehcadldL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 147 GPTLAFEcieqaLCDFELSFLASPSFKGGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDepLS-----ITSYS 221
Cdd:NF041036 154 GRFHTYP-----LPQDELVFVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRD--LDdfrrvVVSDD 226

                        250       260       270
                 ....*....|....*....|....*....|.
gi 503972325 222 LATLLRLAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:NF041036 227 LRLTIQTVLDGGGISFVSRSLVCEYLKNGQL 257
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-258 1.02e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 165.42  E-value: 1.02e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELTE-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 160 CDFELSFLASPSfkggvaqmsfktlmshtiltypkitYPYKELKarmkeqgideplSITSySLATLLRLAEQGLGIAVVP 239
Cdd:COG0583  161 GEERLVLVASPD-------------------------HPLARRA------------PLVN-SLEALLAAVAAGLGIALLP 202

                        250
                 ....*....|....*....
gi 503972325 240 TLTALKEITDGRLEILNTP 258
Cdd:COG0583  203 RFLAADELAAGRLVALPLP 221
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-274 3.94e-35

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: 128.50  E-value: 3.94e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 EL-TENQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:NF040786  81 EFdRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 160 CDFELSfLASPSFKGGVAQMSFKTLMSHtILTYPKI-------TypYKELKARMKEQGIDEP-----LSITsySLATLLR 227
Cdd:NF040786 161 YKDRLV-LITPNGTEKYRMLKEEISISE-LQKEPFImreegsgT--RKEAEKALKSLGISLEdlnvvASLG--STEAIKQ 234

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 503972325 228 LAEQGLGIAVVPTLTALKEITDGRLEILNTPIQLKTFHFTSIYIQGN 274
Cdd:NF040786 235 SVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNR 281
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-258 1.36e-28

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: 108.92  E-value: 1.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   89 TGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLA 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  169 SPSFK-GGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPTLTALKEI 247
Cdd:pfam03466  81 PPDHPlARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170
                  ....*....|.
gi 503972325  248 TDGRLEILNTP 258
Cdd:pfam03466 161 ADGRLVALPLP 171
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-255 4.94e-22

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 91.12  E-value: 4.94e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 171 SFK-GGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPTLtALKEITD 249
Cdd:cd05466   81 DHPlAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPES-AVEELAD 159


                 ....*.
gi 503972325 250 GRLEIL 255
Cdd:cd05466  160 GGLVVL 165
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-252 2.57e-20

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 88.49  E-value: 2.57e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   2 NLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSyRQLKPTHKGLTLFKYAEKFMRLETDLVAE 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLST 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  82 LTENQHLTGTIRLGVSETIVYTWLVEYIEKVQQEfPKISVEIVVDLTPNLQEGVRTGDLdMAFLLG-PTLAFECIEQALC 160
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEV-VGCVSTqPKPMRGCLAEPLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 161 DFELSFLASPSFkggVAQMSFKTLMSHTILTYPKITYPYKElkaRMKEQGIDE--PLSITSY------SLATLLRLAEQG 232
Cdd:PRK13348 160 TMRYRCVASPAF---AARYFAQGLTRHSALKAPAVAFNRKD---TLQDSFLEQlfGLPVGAYprhyvpSTHAHLAAIRHG 233

                        250       260
                 ....*....|....*....|
gi 503972325 233 LGIAVVPTLTALKEITDGRL 252
Cdd:PRK13348 234 LGYGMVPELLIGPLLAAGRL 253
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-147 3.05e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 77.37  E-value: 3.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   3 LKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRL--ETDLVa 80
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALceETCRA- 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503972325  81 eLTENQHL-TGTIRLGVSETIvYTWLV-EYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLG 147
Cdd:CHL00180  86 -LEDLKNLqRGTLIIGASQTT-GTYLMpRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGG 152
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-252 3.34e-16

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 77.12  E-value: 3.34e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSyRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVRLLEAELLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELTENQHLTGTIRLGVSETIVYTWLVEYIEKVQQEfPKISVEIVV---DLTPNLqegVRTGDLDMAFLLGPTLAFECIEQ 157
Cdd:PRK03635  81 ELPALDGTPLTLSIAVNADSLATWFLPALAPVLAR-SGVLLDLVVedqDHTAEL---LRRGEVVGAVTTEPQPVQGCRVD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 158 ALCDFELSFLASPSF-----KGGVAQmsfktlmsHTILTYPKITY-PYKELKARMKEQ--GIDEPLSITSY--SLATLLR 227
Cdd:PRK03635 157 PLGAMRYLAVASPAFaaryfPDGVTA--------EALAKAPAVVFnRKDDLQDRFLRQafGLPPGSVPCHYvpSSEAFVR 228

                        250       260
                 ....*....|....*....|....*
gi 503972325 228 LAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:PRK03635 229 AALAGLGWGMIPELQIEPELASGEL 253
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-252 5.79e-16

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 76.42  E-value: 5.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  17 SFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLF-KYAEKFMRLE--TDLVAELTENQHLtgTIR 93
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFlDIREIFDQLAeaTRKLRARSAKGAL--TVS 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  94 LGVSETIvyTWLVEYIEKVQQEFPKISVEIvvdLTPNLQEGVRTGDLDMAFLLG----PTLAFEcieqALCDFELSFLAS 169
Cdd:PRK11139 100 LLPSFAI--QWLVPRLSSFNEAHPDIDVRL---KAVDRLEDFLRDDVDVAIRYGrgnwPGLRVE----KLLDEYLLPVCS 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 170 PSFKGGVAQMsfKT---LMSHTIL--TYPKityPYKELKARMKEQGIDEPLSItSYSLATL-LRLAEQGLGIAVVPTLTA 243
Cdd:PRK11139 171 PALLNGGKPL--KTpedLARHTLLhdDSRE---DWRAWFRAAGLDDLNVQQGP-IFSHSSMaLQAAIHGQGVALGNRVLA 244


                 ....*....
gi 503972325 244 LKEITDGRL 252
Cdd:PRK11139 245 QPEIEAGRL 253
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-252 6.00e-16

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 76.70  E-value: 6.00e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELtenQHLTGTIRLGVSETIvyTWLVEYIEKVQQEFPKISVEIvVDL-----TPnLQ--EGVRTGDLDMAFL-------L 146
Cdd:NF041036  81 EL---KSFKGRQRLSICCTP--TFGMAHLPGVLNRFMLRNADV-VDLkflfhSP-AQalEGIQNKEFDLAIIehcadldL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 147 GPTLAFEcieqaLCDFELSFLASPSFKGGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDepLS-----ITSYS 221
Cdd:NF041036 154 GRFHTYP-----LPQDELVFVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRD--LDdfrrvVVSDD 226

                        250       260       270
                 ....*....|....*....|....*....|.
gi 503972325 222 LATLLRLAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:NF041036 227 LRLTIQTVLDGGGISFVSRSLVCEYLKNGQL 257
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-291 7.41e-16

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 76.34  E-value: 7.41e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   3 LKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKfMRLETDLVAE- 81
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRR-MLHEVQDVHEq 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  82 -LTENQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVV-----DLTPN-LQEGVRTGDLDMAFLLGPTLAfeC 154
Cdd:PRK10632  83 lYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTgipapDLIADgLDVVIRVGALQDSSLFSRRLG--A 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 155 IEQALCDFElSFLASPSFKGGVAQMSfktlmSHTILTYPkiTYPYKELKArMKEQGIDEPLS-----ITSYSLaTLLRLA 229
Cdd:PRK10632 161 MPMVVCAAK-SYLAQYGTPEKPADLS-----SHSWLEYS--VRPDNEFEL-IAPEGISTRLIpqgrfVTNDPQ-TLVRWL 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503972325 230 EQGLGIAVVPTLTALKEITDGRLEILNTPIQLKTFHFTSIYIQGNDVALK-----EKLTEVAVKVSE 291
Cdd:PRK10632 231 TAGAGIAYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKvqvciNYLTDYFVEVAK 297
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.98e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 68.57  E-value: 3.98e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 503972325    3 LKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-239 2.27e-14

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 72.02  E-value: 2.27e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMR-LETDLV 79
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRqCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  80 AELTENQHLTGTIRLGVSE-TIVYTWLVEYIEKVQQEFPkisvEIVVDLTPN----LQEGVRTGDLDMAFLLGPTLAFEC 154
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPgTAASSLTMPLLQAVRAEFP----GIVLYLHENsgatLNEKLMNGQLDMAVIYEHSPVAGL 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 155 IEQALCDFELsFLASPSFKGG-------VAQMSfktlmshtiLTYPKityPYKELKARmkeqgIDEPLSIT--SY----- 220
Cdd:PRK11233 157 SSQPLLKEDL-FLVGTQDCPGqsvdlaaVAQMN---------LFLPR---DYSAVRLR-----VDEAFSLRrlTAkvige 218

                        250       260
                 ....*....|....*....|.
gi 503972325 221 --SLATLLRLAEQGLGIAVVP 239
Cdd:PRK11233 219 ieSIATLTAAIASGMGVTVLP 239
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-143 4.53e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 71.19  E-value: 4.53e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   3 LKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRletDLVAEL 82
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD---TLNQEI 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503972325  83 TE--NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIvvdLTPNLQEGVRTGDLDMA 143
Cdd:PRK10086  93 LDikNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTI---LTGNENVNFQRAGIDLA 152
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-145 8.66e-13

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 67.36  E-value: 8.66e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEafyWVVTL---KSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRlETD 77
Cdd:PRK11151   1 MNIRDLE---YLVALaehRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLR-EVK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  78 LVAELTENQ--HLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFL 145
Cdd:PRK11151  77 VLKEMASQQgeTMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIL 146
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-143 1.33e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 66.98  E-value: 1.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   6 LEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVAELTEN 85
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYS 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503972325  86 QhLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMA 143
Cdd:PRK15092  96 N-LQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLA 152
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-171 1.34e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 63.94  E-value: 1.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   3 LKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAekfmrleTDLVAEL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRA-------LALLEQA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  83 TENQHL----TGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQA 158
Cdd:PRK10837  78 VEIEQLfredNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEP 157

                        170
                 ....*....|...
gi 503972325 159 LCDFELSFLASPS 171
Cdd:PRK10837 158 WLEDELVVFAAPD 170
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-255 3.98e-11

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: 60.92  E-value: 3.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  90 GTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIV-----VDLtpnLQEGVrtgdlDMAFLLGPTLAFECIEQALCDFEL 164
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVlsdrlVDL---VEEGF-----DLAIRIGELPDSSLVARRLGPVRR 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 165 SFLASPSF--KGGVAQmSFKTLMSHTILTYpkiTYPYKELKARMKEQGIDEPLSITSY----SLATLLRLAEQGLGIAVV 238
Cdd:cd08422   73 VLVASPAYlaRHGTPQ-TPEDLARHRCLGY---RLPGRPLRWRFRRGGGEVEVRVRGRlvvnDGEALRAAALAGLGIALL 148

                        170
                 ....*....|....*..
gi 503972325 239 PTLTALKEITDGRLEIL 255
Cdd:cd08422  149 PDFLVAEDLASGRLVRV 165
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-123 6.12e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.90  E-value: 6.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMR-LET--- 76
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQdLEAgrr 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 503972325  77 ---DlVAELTenqhlTGTIRLGVSETIVyTWLV-EYIEKVQQEFPKISVEI 123
Cdd:PRK11242  81 aihD-VADLS-----RGSLRLAMTPTFT-AYLIgPLIDAFHARYPGITLTI 124
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-239 7.92e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 61.96  E-value: 7.92e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELTENQHLtgTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAfLLGPTLAFECIEQA-L 159
Cdd:PRK15421  82 ACNEPQQT--RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLV-MTSDILPRSGLHYSpM 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 160 CDFELSFLASPSFK-GGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSITSYSLaTLLRLAEQGLGIAVV 238
Cdd:PRK15421 159 FDYEVRLVLAPDHPlAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTL-LLIQMVAARMGIAAL 237


                 .
gi 503972325 239 P 239
Cdd:PRK15421 238 P 238
PRK10341 PRK10341
transcriptional regulator TdcA;
4-270 8.04e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 61.80  E-value: 8.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   4 KNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVAELT 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  84 EnqhLTGT----IRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAF--LLGPTLAFECIEQ 157
Cdd:PRK10341  90 G---MSSEavvdVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 158 ALCDFELSFLASPSFKGGVAqmsfKTLMShtiLTYPKITYP------YKELKARMKEQGIDEPLSITSYSLATLLRLAEQ 231
Cdd:PRK10341 167 PLFESEFVLVASKSRTCTGT----TTLES---LKNEQWVLPqtnmgyYSELLTTLQRNGISIENIVKTDSVVTIYNLVLN 239

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 503972325 232 GLGIAVVPTLTAlKEITDGRLEILNTPIQLKTFHFTSIY 270
Cdd:PRK10341 240 ADFLTVIPCDMT-SPFGSNQFITIPIEETLPVAQYAAVW 277
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 90-253 2.16e-10

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 59.08  E-value: 2.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  90 GTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELsFLAS 169
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPF-LLAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 170 PSfkggvaqmsfktlmSHTILTYPKITypYKELKAR----------MKEQ--------GIDEPLSITSYSLATLLRLAEQ 231
Cdd:cd08411   80 PK--------------DHPLAKRKSVT--PEDLAGErlllleeghcLRDQalelcrlaGAREQTDFEATSLETLRQMVAA 143

                        170       180
                 ....*....|....*....|..
gi 503972325 232 GLGIAVVPTLTALKEITDGRLE 253
Cdd:cd08411  144 GLGITLLPELAVPSEELRGDRL 165
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-123 2.44e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 60.39  E-value: 2.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEaFYWVVTLKSFN--KAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKP-THKGLTLFKYAEKFMRLETD 77
Cdd:PRK12682   1 MNLQQLR-FVREAVRRNLNltEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIERILREVGN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 503972325  78 L--VAELTENQHlTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEI 123
Cdd:PRK12682  80 IkrIGDDFSNQD-SGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSL 126
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 91-259 6.06e-10

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 57.67  E-value: 6.06e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAF-LLGPTLAFECIE-QALCDFELSFLA 168
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgRLADDEQPPDLAsEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 169 S---PSFKGgvAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSIT-SYSLATLLRLAEQGLGIAVVPTLTAL 244
Cdd:cd08435   81 RpghPLARR--ARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVeTASISALLALLARSDMLAVLPRSVAE 158

                        170
                 ....*....|....*
gi 503972325 245 KEITDGRLEILNTPI 259
Cdd:cd08435  159 DELRAGVLRELPLPL 173
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 2-65 1.15e-09

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 58.08  E-value: 1.15e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503972325   2 NLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLF 65
Cdd:PRK11013   5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLF 68
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-252 1.23e-09

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: 56.87  E-value: 1.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  93 RLGVSETIVYTWLVEYIEKVQQEFPKISVEI-----VVDLtpnLQEG----VRTGDLD----MAFLLGPtlafecieqal 159
Cdd:cd08476    2 RLRVSLPLVGGLLLPVLAAFMQRYPEIELDLdfsdrLVDV---IDEGfdavIRTGELPdsrlMSRRLGS----------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 160 cdFELSFLASPSF--KGGVAQmSFKTLMSHTILTYpkiTYPYK------ELKARMKEQGIDEPLSITSYSLATLLRLAEQ 231
Cdd:cd08476   68 --FRMVLVASPDYlaRHGTPE-TPADLAEHACLRY---RFPTTgklepwPLRGDGGDPELRLPTALVCNNIEALIEFALQ 141

                        170       180
                 ....*....|....*....|.
gi 503972325 232 GLGIAVVPTLTALKEITDGRL 252
Cdd:cd08476  142 GLGIACLPDFSVREALADGRL 162
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-167 4.74e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 56.32  E-value: 4.74e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVA 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELTENQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALC 160
Cdd:PRK09906  81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELL 160


                 ....*..
gi 503972325 161 DFELSFL 167
Cdd:PRK09906 161 DEPLVVV 167
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
3-260 2.76e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 53.90  E-value: 2.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   3 LKNLEA--FYWVVTL---KSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFM-RLET 76
Cdd:PRK10082   8 LHNIETkwLYDFLTLekcRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLqQLES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  77 DLvAELTENQHLT---------GTIRLGVSETIV------YTWLVEYIEkvqqefpkisVEIVVDLtpnlqegVRTGDLD 141
Cdd:PRK10082  88 NL-AELRGGSDYAqrkikiaaaHSLSLGLLPSIIsqmpplFTWAIEAID----------VDEAVDK-------LREGQSD 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 142 MAFllgpTLAFECIEQALCD----FElSFLASPSFKGGVAQMSFKTLMSHtiltYPKITYPYKELKARMKEQGIDE--PL 215
Cdd:PRK10082 150 CIF----SFHDEDLLEAPFDhirlFE-SQLFPVCASDEHGEALFNLAQPH----FPLLNYSRNSYMGRLINRTLTRhsEL 220

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503972325 216 SITSY---SLATLLR-LAEQGLGIAVVPTLTALKEITDGRLEILN-----TPIQ 260
Cdd:PRK10082 221 SFSTFfvsSMSELLKqVALDGCGIAWLPEYAIQQEIRSGQLVVLNrdelvIPIQ 274
PRK09986 PRK09986
LysR family transcriptional regulator;
1-239 1.72e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 51.65  E-value: 1.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKyaekfmrlETDLVA 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILME--------ESRRLL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  81 ELTEN---------QHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVeIVVDLTPNLQ-EGVRTGDLDMAF----LL 146
Cdd:PRK09986  79 DNAEQslarveqigRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEW-LLRELSPSMQmAALERRELDAGIwrmaDL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 147 GPTLAFECIEQAlcdfELSFLASPSFKGGVAQ---MSFKTLMSHTILTYPKITYPY-KELKARMKEQG--------IDEP 214
Cdd:PRK09986 158 EPNPGFTSRRLH----ESAFAVAVPEEHPLASrssVPLKALRNEYFITLPFVHSDWgKFLQRVCQQAGfspqiirqVNEP 233

                        250       260
                 ....*....|....*....|....*
gi 503972325 215 lsitsyslATLLRLAEQGLGIAVVP 239
Cdd:PRK09986 234 --------QTVLAMVSMGIGITLLP 250
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 91-158 1.80e-07

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 50.62  E-value: 1.80e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFL----LGPTLAFECIEQA 158
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydldLPEDIAFEPLARL 72
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 89-253 2.08e-07

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: 50.54  E-value: 2.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  89 TGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVD--LTPNLQE----GVRTGDL---DM-AFLLGPTLAFECIeqa 158
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDdgLVDIVAEgfdaGIRLGESvekDMvAVPLGPPLRMAVV--- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 159 lcdfelsflASPSFkggvaqmsfktLMSHTILTYPK-------ITY-------PYK-ELKARMKEQGIDEPLSITSYSLA 223
Cdd:cd08474   79 ---------ASPAY-----------LARHGTPEHPRdllnhrcIRYrfptsgaLYRwEFERGGRELEVDVEGPLILNDSD 138

                        170       180       190
                 ....*....|....*....|....*....|
gi 503972325 224 TLLRLAEQGLGIAVVPTLTALKEITDGRLE 253
Cdd:cd08474  139 LMLDAALDGLGIAYLFEDLVAEHLASGRLV 168
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 109-254 2.12e-07

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 50.29  E-value: 2.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 109 IEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPT--LAFECieQALCDFELSFLASPSF-KGGVAQMSFKTLm 185
Cdd:cd08433   19 LRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPpiPGLST--EPLLEEDLFLVGPADApLPRGAPVPLAEL- 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503972325 186 shtiLTYPKI-TYPYKELKARMKE--QGIDEPLSITSY--SLATLLRLAEQGLGIAVVPTLTALKEITDGRLEI 254
Cdd:cd08433   96 ----ARLPLIlPSRGHGLRRLVDEaaARAGLTLNVVVEidSVATLKALVAAGLGYTILPASAVAAEVAAGRLVA 165
PRK09801 PRK09801
LysR family transcriptional regulator;
4-121 3.02e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 50.80  E-value: 3.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   4 KNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVAELT 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 503972325  84 E-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISV 121
Cdd:PRK09801  89 QiKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV 127
PRK09791 PRK09791
LysR family transcriptional regulator;
3-141 7.83e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 49.76  E-value: 7.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   3 LKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSyrqlkptHKGLTLFKYAEKFMRLETDLVAEL 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRR-------SKGVTLTDAGESFYQHASLILEEL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503972325  83 TENQ--------HLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIV----VDLTPNLqegvRTGDLD 141
Cdd:PRK09791  80 RAAQedirqrqgQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMegqlVSMINEL----RQGELD 146
PRK12680 PRK12680
LysR family transcriptional regulator;
21-259 7.16e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 46.92  E-value: 7.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  21 AATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKP-THKGLTLFKYAeKFMRLETDLVAELTENQHL--TGTIRLGVS 97
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESvTPAGVEVIERA-RAVLSEANNIRTYAANQRResQGQLTLTTT 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  98 ETIVYTWLVEYIEKVQQEFPKISVeivvdltpNLQEGVRTGDLDmafLLGPTLAFECIEQALCDFELSFLASPSF----- 172
Cdd:PRK12680 101 HTQARFVLPPAVAQIKQAYPQVSV--------HLQQAAESAALD---LLGQGDADIAIVSTAGGEPSAGIAVPLYrwrrl 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 173 ----KGGVAQMSFKTLMSHTILTYPKITY-----PYKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPTLTA 243
Cdd:PRK12680 170 vvvpRGHALDTPRRAPDMAALAEHPLISYesstrPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLGVGLLAEMAV 249

                        250
                 ....*....|....*.
gi 503972325 244 LKEITDGRLEILNTPI 259
Cdd:PRK12680 250 NANDEDLRAWPAPAPI 265
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-243 1.01e-05

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 45.28  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFL-LGPTLAFECIEQALCDFELSFLAS 169
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVgLPERRPPGLASRELAREPLVAVVA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503972325 170 PSFK-GGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGI--DEPLSITsySLATLLRLAEQGLGIAVVPTLTA 243
Cdd:cd08436   81 PDHPlAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVrrRVAFEVS--DVDLLLDLVARGLGVALLPASVA 155
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-255 1.50e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 44.87  E-value: 1.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  92 IRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAF--ECIEQALCDFELSFLAS 169
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLpkDLVWTPLVREPLVLIAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 170 PSFKGGvaqmSFKTLMShtilTYPKITYPYKELKARM-----KEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPtLTAL 244
Cdd:cd08427   82 AELAGD----DPRELLA----TQPFIRYDRSAWGGRLvdrflRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVP-DIAV 152

                        170
                 ....*....|.
gi 503972325 245 KEITDGRLEIL 255
Cdd:cd08427  153 PLPAGPRVRVL 163
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-241 1.82e-05

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 44.82  E-value: 1.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMA--FLLG--PTLAFECIeqalcdFELSF 166
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGigSEPEadPDLEFEPL------LRDPF 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 167 LA-----SPSFKGgvAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPTL 241
Cdd:cd08440   75 VLvcpkdHPLARR--RSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPAL 152
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-123 2.73e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 44.81  E-value: 2.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  31 AVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRLETDLVAELTENQH-LTGTIRLGVSETIVYTWLVEYI 109
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPsLSGELSLFCSVTAAYSHLPPIL 86

                         90
                 ....*....|....
gi 503972325 110 EKVQQEFPKisVEI 123
Cdd:PRK11716  87 DRFRAEHPL--VEI 98
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-73 5.49e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 44.20  E-value: 5.49e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503972325   1 MNLKNLEAFYWVVTlKSFN--KAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKP-THKGLTLFKYAEKFMR 73
Cdd:PRK12684   1 MNLHQLRFVREAVR-QNFNltEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGlTEPGRIILASVERILQ 75
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-72 5.69e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 43.85  E-value: 5.69e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503972325   1 MNLKNLEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFM 72
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLM 72
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-239 6.23e-05

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


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 42.88  E-value: 6.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFL----LGPTLAFECIEQ-----ALCD 161
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVrpppDPPGLASRPLLReplvvALPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 162 felsflASPsfKGGVAQMSFKTLMSHTILTYPKITYP--YKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVP 239
Cdd:cd08414   81 ------DHP--LAARESVSLADLADEPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVP 152
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 90-279 1.31e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 42.33  E-value: 1.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  90 GTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEI-----VVDLtpnLQEgvRTgdlDMAFLLGPTLAFECIEQALCDFEL 164
Cdd:cd08478    3 GLLRVDAATPFVLHLLAPLIAKFRERYPDIELELvsnegIIDL---IER--KT---DVAIRIGELTDSTLHARPLGKSRL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 165 SFLASPSF--KGGVAQmSFKTLMSHTIL--TYPKI--TYPYKelkaRMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVV 238
Cdd:cd08478   75 RILASPDYlaRHGTPQ-SIEDLAQHQLLgfTEPASlnTWPIK----DADGNLLKIQPTITASSGETLRQLALSGCGIACL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 503972325 239 PTLTALKEITDGRLEILNTPIQLK-TFHFTSIYIQGNDVALK 279
Cdd:cd08478  150 SDFMTDKDIAEGRLIPLFAEQTSDvRQPINAVYYRNTALSLR 191
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-252 2.14e-04

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: 41.53  E-value: 2.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPtLAFECIEQ-ALCDFELSFLAS 169
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSP-PPEPGIRVhSRQPAPIGAVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 170 PSFK-GGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGID-EPLSITSySLATLLRLAEQGLGIAVVPTLTALKEI 247
Cdd:cd08426   80 PGHPlARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQlEPVLISN-SIETLKQLVAAGGGISLLTELAVRREI 158


                 ....*
gi 503972325 248 TDGRL 252
Cdd:cd08426  159 RRGQL 163
nhaR PRK11062
transcriptional activator NhaR; Provisional
 9-74 3.43e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 41.53  E-value: 3.43e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503972325   9 FYWVVTLK-SFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFMRL 74
Cdd:PRK11062  11 YFWMVCKEgSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTL 77
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 91-255 6.08e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 39.97  E-value: 6.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLqegVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFD---FSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 171 SFK-----GGVAQMSFKTLMSHTilTYPKITYPYKElkarmkEQGIDEPLSITS-----YSLATllRLAEQGLGIAVVPT 240
Cdd:cd08481   78 ALLagralAAPADLAHLPLLQQT--TRPEAWRDWFE------EVGLEVPTAYRGmrfeqFSMLA--QAAVAGLGVALLPR 147

                        170
                 ....*....|....*
gi 503972325 241 LTALKEITDGRLEIL 255
Cdd:cd08481  148 FLIEEELARGRLVVP 162
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-143 1.05e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 40.03  E-value: 1.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325   1 MNLKNLEAFYWVVTlKSFN--KAATKLQTTQPAVSQKITSLENELGFKVLDRS-YRQLKPTHKGLTLFKYAEKfMRLETD 77
Cdd:PRK12683   1 MNFQQLRIIREAVR-QNFNltEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVER-MLLDAE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503972325  78 LVAELTE--NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEFPKISVEivvdltpnLQEG--------VRTGDLDMA 143
Cdd:PRK12683  79 NLRRLAEqfADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLA--------LRQGspqeiaemLLNGEADIG 146
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 91-266 1.23e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 39.12  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 171 SFKGGVAQMSFKTLMS--HTILTYPKITYPYkeLKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVPTLTALKEIT 248
Cdd:cd08417   81 DHPLAGGPLTLEDYLAapHVLVSPRGRGHGL--VDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAE 158

                        170
                 ....*....|....*...
gi 503972325 249 DGRLEILNTPIQLKTFHF 266
Cdd:cd08417  159 RLGLRVLPLPFELPPFTV 176
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 91-252 2.62e-03

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


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 38.33  E-value: 2.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  91 TIRLGVSETIVYTWLVEYIEKVQQEFPKISVEI-----VVDLtpnlqegvRTGDLDMA--FLLGPTLAFECIEqaLCDFE 163
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLstsdrLVDF--------AREGIDLAirYGDGDWPGLEAER--LMDEE 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325 164 LSFLASPSFKGGVAQMSFKTLMSHTILTYPKITYPYKELKARMKEQGIDEPLSIT--SYSLAtlLRLAEQGLGIAVVPTL 241
Cdd:cd08432   71 LVPVCSPALLAGLPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRfdDSSLA--LQAAVAGLGVALAPRA 148

                        170
                 ....*....|.
gi 503972325 242 TALKEITDGRL 252
Cdd:cd08432  149 LVADDLAAGRL 159
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 94-239 5.58e-03

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


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 37.10  E-value: 5.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503972325  94 LGVSETIVYTWLVEYIEKVQQEFPKISVEIVVDLTPNLQEGVRTGDLDMAFLLGP----TLAFECIEQALCDFELSF--- 166
Cdd:cd08452    4 IGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPiqhtALHIETVQSSPCVLALPKqhp 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503972325 167 LASPsfkggvAQMSFKTLMSHTILTYPKITYP--YKELKARMKEQGIDEPLSITSYSLATLLRLAEQGLGIAVVP 239
Cdd:cd08452   84 LASK------EEITIEDLRDEPIITVAREAWPtlYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVP 152
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-72 7.88e-03

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 37.48  E-value: 7.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503972325   6 LEAFYWVVTLKSFNKAATKLQTTQPAVSQKITSLENELGFKVLDRSYRQLKPTHKGLTLFKYAEKFM 72
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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