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Conserved domains on  [gi|503994096|ref|WP_014228090|]
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MULTISPECIES: LysR family transcriptional regulator [Klebsiella]

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];
3-302 1.40e-42

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.32  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSS 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  83 QLREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVAdsWQAELDPQLRVQ 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 163 PLSPQRCFFVCHADHPLAKQGPVsiqamlrypfaapylppgvrkvlatlsqqqdftpaiqCDHIYALLATLAQTSAISFA 242
Cdd:COG0583  159 PLGEERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 243 SEDGFALCQHSHRLVKLELSDLPEEWrlmqtRFAIISPVHAAQPPLVEKLIEIILHTDRQ 302
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPR-----PLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-302 1.40e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.32  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSS 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  83 QLREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVAdsWQAELDPQLRVQ 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 163 PLSPQRCFFVCHADHPLAKQGPVsiqamlrypfaapylppgvrkvlatlsqqqdftpaiqCDHIYALLATLAQTSAISFA 242
Cdd:COG0583  159 PLGEERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 243 SEDGFALCQHSHRLVKLELSDLPEEWrlmqtRFAIISPVHAAQPPLVEKLIEIILHTDRQ 302
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPR-----PLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09791 PRK09791
LysR family transcriptional regulator;
5-283 2.69e-21

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 91.75  E-value: 2.69e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   5 FRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR-FQELNVElSSQ 83
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLiLEELRAA-QED 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  84 LREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADSWQAELDPQLRVQP 163
Cdd:PRK09791  86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEK 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 164 LSPQRCFFVCHADHPlaKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTPAIQ--CDHIYALLATLAQTSAISF 241
Cdd:PRK09791 166 LLEKQFAVFCRPGHP--AIGARSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGvvCETFSACISLVAKSDFLSI 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 503994096 242 ASEDGFALCQHSHRLVKLELSD-LPE-EWRLMQTRFAIISPVHA 283
Cdd:PRK09791 244 LPEEMGCDPLHGQGLVMLPVSEiLPKaTYYLIQRRDTRQTPLTA 287
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-297 7.39e-21

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: 88.50  E-value: 7.39e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   93 GEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVAdsWQAELDPQLRVQPLSPQRCFFV 172
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  173 CHADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTP--AIQCDHIYALLATLAQTSAISFASEDGFALC 250
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPrvVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 503994096  251 QHSHRLVKLELSDLPeewrlMQTRFAIISPVHAAQPPLVEKLIEIIL 297
Cdd:pfam03466 160 LADGRLVALPLPEPP-----LPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-129 2.98e-19

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: 86.13  E-value: 2.98e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   4 DFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSSQ 83
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 503994096  84 LREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPqaRVRFQID 129
Cdd:NF040786  82 FDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYP--NVRFKLM 125
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-296 1.14e-18

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: 82.26  E-value: 1.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  94 EVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADswQAELDPQLRVQPLSPQRCFFVC 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA--LPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 174 HADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTP--AIQCDHIYALLATLAQTSAISFASEDgFALCQ 251
Cdd:cd05466   79 PPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPniALEVDSLEAIKALVAAGLGIALLPES-AVEEL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503994096 252 HSHRLVKLELSDLPEEWRLmqtrfAIISPVHAAQPPLVEKLIEII 296
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTI-----GLVWRKGRYLSPAARAFLELL 197
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 3-102 3.11e-12

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: 65.91  E-value: 3.11e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSS 82
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100
                 ....*....|....*....|
gi 503994096  83 QLREADDAQngEVAFGCGPA 102
Cdd:NF041036  81 ELKSFKGRQ--RLSICCTPT 98
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-302 1.40e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.32  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSS 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  83 QLREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVAdsWQAELDPQLRVQ 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 163 PLSPQRCFFVCHADHPLAKQGPVsiqamlrypfaapylppgvrkvlatlsqqqdftpaiqCDHIYALLATLAQTSAISFA 242
Cdd:COG0583  159 PLGEERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 243 SEDGFALCQHSHRLVKLELSDLPEEWrlmqtRFAIISPVHAAQPPLVEKLIEIILHTDRQ 302
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPR-----PLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09791 PRK09791
LysR family transcriptional regulator;
5-283 2.69e-21

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 91.75  E-value: 2.69e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   5 FRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR-FQELNVElSSQ 83
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLiLEELRAA-QED 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  84 LREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADSWQAELDPQLRVQP 163
Cdd:PRK09791  86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEK 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 164 LSPQRCFFVCHADHPlaKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTPAIQ--CDHIYALLATLAQTSAISF 241
Cdd:PRK09791 166 LLEKQFAVFCRPGHP--AIGARSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGvvCETFSACISLVAKSDFLSI 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 503994096 242 ASEDGFALCQHSHRLVKLELSD-LPE-EWRLMQTRFAIISPVHA 283
Cdd:PRK09791 244 LPEEMGCDPLHGQGLVMLPVSEiLPKaTYYLIQRRDTRQTPLTA 287
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-297 7.39e-21

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: 88.50  E-value: 7.39e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   93 GEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVAdsWQAELDPQLRVQPLSPQRCFFV 172
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  173 CHADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTP--AIQCDHIYALLATLAQTSAISFASEDGFALC 250
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPrvVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 503994096  251 QHSHRLVKLELSDLPeewrlMQTRFAIISPVHAAQPPLVEKLIEIIL 297
Cdd:pfam03466 160 LADGRLVALPLPEPP-----LPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-129 2.98e-19

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: 86.13  E-value: 2.98e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   4 DFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSSQ 83
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 503994096  84 LREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPqaRVRFQID 129
Cdd:NF040786  82 FDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYP--NVRFKLM 125
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-296 1.14e-18

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: 82.26  E-value: 1.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  94 EVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADswQAELDPQLRVQPLSPQRCFFVC 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA--LPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 174 HADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTP--AIQCDHIYALLATLAQTSAISFASEDgFALCQ 251
Cdd:cd05466   79 PPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPniALEVDSLEAIKALVAAGLGIALLPES-AVEEL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503994096 252 HSHRLVKLELSDLPEEWRLmqtrfAIISPVHAAQPPLVEKLIEII 296
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTI-----GLVWRKGRYLSPAARAFLELL 197
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-88 2.11e-18

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 83.92  E-value: 2.11e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   1 MHLDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVEL 80
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEA 88


                 ....*...
gi 503994096  81 SSQLREAD 88
Cdd:PRK15092  89 CSSLMYSN 96
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.18e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.50  E-value: 1.18e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096    5 FRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
3-194 1.05e-15

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 76.00  E-value: 1.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSS 82
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  83 QLREADDAQNGEVAFGCG-----PAPAARLIPAavgeFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADSWQAELDP 157
Cdd:PRK10094  82 ELQQVNDGVERQVNIVINnllynPQAVAQLLAW----LNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALAN 157

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 503994096 158 QLRVQPLSPQRCFFVCHADHPLAK-QGPVSIQAMLRYP 194
Cdd:PRK10094 158 TFSLDPLGSVQWRFVMAADHPLANvEEPLTEAQLRRFP 195
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 95-294 5.47e-15

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: 72.31  E-value: 5.47e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  95 VAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVV---ADSWQAeldPQLRVQPLSPQRCFF 171
Cdd:cd08435    2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrlADDEQP---PDLASEELADEPLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 172 VCHADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQ---QQDFTPAIQCDHIYALLATLAQTSAISFASEDgfa 248
Cdd:cd08435   79 VARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAaagLPLPRNVVETASISALLALLARSDMLAVLPRS--- 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 503994096 249 lcQHSHRLVKLELSDLPEEWRLMQTRFAIISPVHAAQPPLVEKLIE 294
Cdd:cd08435  156 --VAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
rbcR CHL00180
LysR transcriptional regulator; Provisional
 1-129 8.39e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 73.52  E-value: 8.39e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   1 MHLDF--RQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNV 78
Cdd:CHL00180   1 TDLPFtlDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 503994096  79 ELSSQLREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQID 129
Cdd:CHL00180  81 ETCRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVH 131
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-90 3.11e-14

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 71.54  E-value: 3.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   2 HLDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRqSKLPTLTLHGQKLLPYARRFQELNVELS 81
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVALLEADLL 79


                 ....*....
gi 503994096  82 SQLREADDA 90
Cdd:PRK13348  80 STLPAERGS 88
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-230 3.80e-14

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 71.53  E-value: 3.80e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   6 RQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR-FQELnVELSSQL 84
Cdd:PRK11242   4 RHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRaLQDL-EAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  85 READDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQarVRFQIDnwlALHQAltsQLYPFVVADswqaELD-------- 156
Cdd:PRK11242  83 HDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPG--ITLTIR---EMSQE---RIEALLADD----ELDvgiafapv 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 157 --PQLRVQPLSPQRCFFVCHADHPLA-KQGPVSIQAMLRYPFAapYLPPG--VRKVLATLSQQQDFTP--AIQCDHIYAL 229
Cdd:PRK11242 151 hsPEIEAQPLFTETLALVVGRHHPLAaRRKALTLDELADEPLV--LLSAEfaTREQIDRYFRRHGVTPrvAIEANSISAV 228


                 .
gi 503994096 230 L 230
Cdd:PRK11242 229 L 229
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
2-89 4.15e-14

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 71.34  E-value: 4.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   2 HLDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRqSKLPTLTLHGQKLLPYARRFQELNVELS 81
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELL 79


                 ....*...
gi 503994096  82 SQLREADD 89
Cdd:PRK03635  80 GELPALDG 87
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-194 1.03e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 67.41  E-value: 1.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   1 MHLDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVEL 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  81 SSQLREaddaQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQAltsqlypfvVADsWQAEL----- 155
Cdd:PRK10837  81 EQLFRE----DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINA---------VLD-FRVDIglieg 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 503994096 156 ---DPQLRVQPLSPQRCFFVCHADHPLAkQGPVSIQAMLRYP 194
Cdd:PRK10837 147 pchSPELISEPWLEDELVVFAAPDSPLA-RGPVTLEQLAAAP 187
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 3-102 3.11e-12

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: 65.91  E-value: 3.11e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSS 82
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100
                 ....*....|....*....|
gi 503994096  83 QLREADDAQngEVAFGCGPA 102
Cdd:NF041036  81 ELKSFKGRQ--RLSICCTPT 98
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-296 1.72e-08

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: 53.68  E-value: 1.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  95 VAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQlypfvVAD---SWQAELDPQLRVQPLSPQRCFF 171
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSG-----EVDfgiGSEPEADPDLEFEPLLRDPFVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 172 VCHADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQ--QDFTPAIQCDHIYALLATLAQTSAISFASEDGFAL 249
Cdd:cd08440   77 VCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAagLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPL 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 503994096 250 CQHSHrLVKLELSDlPEEWRlmqtRFAIISPVHAAQPPLVEKLIEII 296
Cdd:cd08440  157 ADHPG-LVARPLTE-PVVTR----TVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 98-294 1.91e-08

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


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 53.33  E-value: 1.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  98 GCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADSwqAELDPQLRVQPLSPQRCFFVCHADH 177
Cdd:cd08415    5 AALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASL--PLDHPGLESEPLASGRAVCVLPPGH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 178 PLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTPAIQCDhiyallATLAQTsAISFASE-------DGFALC 250
Cdd:cd08415   83 PLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIE------TQLSHT-ACALVAAglgvaivDPLTAA 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503994096 251 QHS-HRLVKLELSDLPEewrlmqTRFAIISPVHAAQPPLVEKLIE 294
Cdd:cd08415  156 GYAgAGLVVRPFRPAIP------FEFALVRPAGRPLSRLAQAFID 194
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 94-296 3.79e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 52.74  E-value: 3.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  94 EVAFGCGPAPAARLIPAAVGEFHRLLPQARVRfqIDNW--LALHQALTSQLYPFVVADSWQAELDPQLRVQPLSPQRCFF 171
Cdd:cd08418    1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQIS--IYEGqlSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 172 VCHADHPLakQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTP--AIQCDHIYALLATLAQTSAISFASEDgfal 249
Cdd:cd08418   79 VARKDHPL--QGARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPrvAVRTDSIVSIINLVEKADFLTILSRD---- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 503994096 250 cQHSHRLVKLELSDLPEEWRLMQTRFAIISPVHAAQPPLVEKLIEII 296
Cdd:cd08418  153 -MGRGPLDSFRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELF 198
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-244 5.52e-08

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 52.31  E-value: 5.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  94 EVAFGCGPAPAARLIPAAVGEFHRLLPqaRVRFQIDNwlalhqALTSQlypfVVADSWQAELD----------PQLRVQP 163
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYP--GVFFTVDV------ASTAD----VLEAVLSGEADiglafspppePGIRVHS 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 164 LSPQRCFFVCHADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQD--FTPAIQCDHIYALLATLAQTSAISF 241
Cdd:cd08426   69 RQPAPIGAVVPPGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGvqLEPVLISNSIETLKQLVAAGGGISL 148


                 ...
gi 503994096 242 ASE 244
Cdd:cd08426  149 LTE 151
PRK09986 PRK09986
LysR family transcriptional regulator;
3-221 6.38e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 53.19  E-value: 6.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR-FQELNVELs 81
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRlLDNAEQSL- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  82 SQLREADDAQNGEVAFG-CGPAPAARLIPaAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADSWQAELDPQLR 160
Cdd:PRK09986  86 ARVEQIGRGEAGRIEIGiVGTALWGRLRP-AMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFT 164

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503994096 161 VQPLSPQRCFFVCHADHPLAKQGPVSIQAMLRYPFAA-PYLPPGVRKVLATLSQQQDFTPAI 221
Cdd:PRK09986 165 SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITlPFVHSDWGKFLQRVCQQAGFSPQI 226
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-127 8.00e-08

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 52.54  E-value: 8.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   8 LRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR-FQELNvELSSQLRE 86
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREiFDQLA-EATRKLRA 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 503994096  87 ADDAQNGEVAfgCGPAPAARLIPAAVGEFHRLLPQARVRFQ 127
Cdd:PRK11139  90 RSAKGALTVS--LLPSFAIQWLVPRLSSFNEAHPDIDVRLK 128
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 3-194 9.07e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.74  E-value: 9.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGsFN--RAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSK-LPTLTLHGQKLLPYARRFQeLNVE 79
Cdd:PRK12683   1 MNFQQLRIIREAVRQN-FNltEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKrLTGLTEPGKELLQIVERML-LDAE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  80 LSSQL-READDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARvrfqidnwLALHQALTSQLYPFVVADswQAEL--- 155
Cdd:PRK12683  79 NLRRLaEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVH--------LALRQGSPQEIAEMLLNG--EADIgia 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503994096 156 ------DPQLRVQPLSPQRCFFVCHADHPLAKQGPVSIQAMLRYP 194
Cdd:PRK12683 149 tealdrEPDLVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYP 193
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 6-142 1.24e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 52.34  E-value: 1.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   6 RQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR-FQELNV--ELSS 82
Cdd:PRK11151   4 RDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTvLREVKVlkEMAS 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  83 QLREaddAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARvrfqidnwLALHQALTSQL 142
Cdd:PRK11151  84 QQGE---TMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLE--------MYLHEAQTHQL 132
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
5-194 1.75e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 51.90  E-value: 1.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   5 FRQLRnFVALVEYGSFN--RAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSK-LPTLTLHGQKLLPYARRFQElnvELS 81
Cdd:PRK12684   3 LHQLR-FVREAVRQNFNltEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKrLRGLTEPGRIILASVERILQ---EVE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  82 SQLREADDAQN---GEVAFGCGPAPAARLIPAAVGEFHRLLPQARvrfqidnwLALHQALTSQLYPFVVADswQA----- 153
Cdd:PRK12684  79 NLKRVGKEFAAqdqGNLTIATTHTQARYALPAAIKEFKKRYPKVR--------LSILQGSPTQIAEMVLHG--QAdlaia 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 503994096 154 ----ELDPQLRVQP-LSPQRCFFVCHaDHPLAKQGPVSIQAMLRYP 194
Cdd:PRK12684 149 teaiADYKELVSLPcYQWNHCVVVPP-DHPLLERKPLTLEDLAQYP 193
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-201 2.03e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 51.59  E-value: 2.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   2 HLDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR-FQELNVEL 80
Cdd:PRK10082  10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHlLQQLESNL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  81 sSQLREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWL-ALHQALTSQLYPFVVADSWQAELDpQL 159
Cdd:PRK10082  90 -AELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVdKLREGQSDCIFSFHDEDLLEAPFD-HI 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 503994096 160 RvqpLSPQRCFFVCHADHplakqgpvsiQAMLRYPFAAPYLP 201
Cdd:PRK10082 168 R---LFESQLFPVCASDE----------HGEALFNLAQPHFP 196
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
20-70 2.77e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.79  E-value: 2.77e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 503994096  20 FNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYA 70
Cdd:PRK03601  18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 104-221 3.04e-07

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 49.84  E-value: 3.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 104 AARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADSwqAELDPQLRVQPLSPQRCFFVCHADHPLAKQG 183
Cdd:cd08434   11 GTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSP--VPDEPDIEWIPLFTEELVLVVPKDHPLAGRD 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 503994096 184 PVSIQAMLRYPFAapYLPP--GVRKVLATLSQQQDFTPAI 221
Cdd:cd08434   89 SVDLAELADEPFV--LLSPgfGLRPIVDELCAAAGFTPKI 126
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 23-194 3.43e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 50.76  E-value: 3.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  23 AAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSK-LPTLTLHGQKLLPYARR-FQELNvELSSQLREADDAQNGEVAFGCG 100
Cdd:PRK12682  22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGKrLKGLTEPGKAVLDVIERiLREVG-NIKRIGDDFSNQDSGTLTIATT 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 101 PAPAARLIPAAVGEFHRLLPQARvrfqidnwLALHQALTSQLYPFV---VAD----SWQAELDPQLRVQPlspqrCFFVC 173
Cdd:PRK12682 101 HTQARYVLPRVVAAFRKRYPKVN--------LSLHQGSPDEIARMVisgEADigiaTESLADDPDLATLP-----CYDWQ 167

                        170       180
                 ....*....|....*....|....*.
gi 503994096 174 HA-----DHPLAKQGPVSIQAMLRYP 194
Cdd:PRK12682 168 HAvivppDHPLAQEERITLEDLAEYP 193
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-80 4.89e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 50.39  E-value: 4.89e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503994096   8 LRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLL-PYARRFQELNVEL 80
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFwALKSSLDTLNQEI 92
PRK10341 PRK10341
transcriptional regulator TdcA;
6-124 5.44e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 50.25  E-value: 5.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   6 RQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVELSSQLR 85
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 503994096  86 EADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARV 124
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQV 128
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-72 8.98e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.43  E-value: 8.98e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 503994096  29 LSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARR 72
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQ 46
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 103-296 1.14e-06

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 48.26  E-value: 1.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 103 PAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQlypfvvadswQAEL--------DPQLRVQPLSPQRCFFVCH 174
Cdd:cd08420   10 IGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDG----------EIDLglvegpvdHPDLIVEPFAEDELVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 175 ADHPLAKQGPVSIQAMLRYPFAApyLPPG------VRKVLATLSQQQ-DFTPAIQCDHIYALLATLAQTSAISFAS---- 243
Cdd:cd08420   80 PDHPLAGRKEVTAEELAAEPWIL--REPGsgtrevFERALAEAGLDGlDLNIVMELGSTEAIKEAVEAGLGISILSrlav 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 503994096 244 ----EDGfalcqhshRLVKLELSDLPeewrlMQTRFAIISPVHAAQPPLVEKLIEII 296
Cdd:cd08420  158 rkelELG--------RLVALPVEGLR-----LTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 94-296 4.66e-06

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: 46.35  E-value: 4.66e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  94 EVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQ------LYPFVvadswqaeLDPQLRVQPLSPQ 167
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGrldvgfVRPPP--------DPPGLASRPLLRE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 168 RCFFVCHADHPLAKQGPVSIQAMLRYPF--AAPYLPPGVRKVLATLSQQQDFTPAI--QCDHIYALLAtLAqtsaisfAS 243
Cdd:cd08414   73 PLVVALPADHPLAARESVSLADLADEPFvlFPREPGPGLYDQILALCRRAGFTPRIvqEASDLQTLLA-LV-------AA 144

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 503994096 244 EDGFALCQHSHR------LVKLELSDLPEEWRLmqtrfAIISPvHAAQPPLVEKLIEII 296
Cdd:cd08414  145 GLGVALVPASVArlqrpgVVYRPLADPPPRSEL-----ALAWR-RDNASPALRAFLELA 197
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-203 6.83e-06

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 46.06  E-value: 6.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  95 VAFGCGPAPAARLIPAAVGEFHRLLPQARVRfqidnwlaLHQALTSQLYPFVVAD-------SWQAELDPQLRVQPLSPQ 167
Cdd:cd08436    2 LAIGTITSLAAVDLPELLARFHRRHPGVDIR--------LRQAGSDDLLAAVREGrldlafvGLPERRPPGLASRELARE 73

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 503994096 168 RCFFVCHADHPLAKQGPVSIQAMLRYPFAApyLPPG 203
Cdd:cd08436   74 PLVAVVAPDHPLAGRRRVALADLADEPFVD--FPPG 107
cbl PRK12679
HTH-type transcriptional regulator Cbl;
30-194 7.21e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 46.73  E-value: 7.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  30 SQSAFSRSIQALEQSVGHPLFDRQSK-LPTLTLHGQKLLPYARRFqeLNvELSSQLREADDAQN---GEVAFGCGPAPAA 105
Cdd:PRK12679  29 SQSGVSRHIRELEDELGIEIFIRRGKrLLGMTEPGKALLVIAERI--LN-EASNVRRLADLFTNdtsGVLTIATTHTQAR 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 106 RLIPAAVGEFHRLLPQARvrfqidnwLALHQALTSQLYPFVV---AD----SWQAELDPQLRVQP-LSPQRCFFVCHaDH 177
Cdd:PRK12679 106 YSLPEVIKAFRELFPEVR--------LELIQGTPQEIATLLQngeADigiaSERLSNDPQLVAFPwFRWHHSLLVPH-DH 176

                        170
                 ....*....|....*..
gi 503994096 178 PLAKQGPVSIQAMLRYP 194
Cdd:PRK12679 177 PLTQITPLTLESIAKWP 193
PRK09801 PRK09801
LysR family transcriptional regulator;
6-128 7.79e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 46.95  E-value: 7.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   6 RQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYA----RRFQELnVELS 81
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHAleilTQYQRL-VDDV 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 503994096  82 SQLREADDaqnGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQI 128
Cdd:PRK09801  88 TQIKTRPE---GMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFEL 131
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 3-71 1.16e-05

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 46.30  E-value: 1.16e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYAR 71
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAR 69
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-194 1.69e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 45.78  E-value: 1.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYArrfQELNVELSS 82
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLA---NQVLPQISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  83 QLREADDAQNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQ----IDNWLALHQ-----ALTSQLYPfvvadswqa 153
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKsgvtFDPQPALQQgeldlVMTSDILP--------- 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 503994096 154 elDPQLRVQPLSPQRCFFVCHADHPLAKQGPVS-----IQAMLRYP 194
Cdd:PRK15421 150 --RSGLHYSPMFDYEVRLVLAPDHPLAAKTRITpedlaSETLLIYP 193
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 3-105 2.97e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 45.06  E-value: 2.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   3 LDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFqelnvelss 82
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAI--------- 71

                         90       100       110
                 ....*....|....*....|....*....|...
gi 503994096  83 qLREADDAQ----------NGEVAFGCGPAPAA 105
Cdd:PRK11233  72 -LRQCEQAQlavhnvgqalSGQVSIGLAPGTAA 103
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 104-265 5.63e-05

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: 43.36  E-value: 5.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 104 AARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVadSWQAELDPQLRVQPLSPQRcfFVC--HADHPLAk 181
Cdd:cd08417   11 EALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAI--GVFPELPPGLRSQPLFEDR--FVCvaRKDHPLA- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 182 QGPVSIQAMLRYPFAAPYLPPGVRKVLATLSQQQDFTP--AIQCDHIYALLATLAQTSAISFASEDgfaLCQHSHRLVKL 259
Cdd:cd08417   86 GGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRrvALTVPHFLAAPALVAGTDLIATVPRR---LAEALAERLGL 162


                 ....*.
gi 503994096 260 ELSDLP 265
Cdd:cd08417  163 RVLPLP 168
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 94-208 5.76e-05

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 43.35  E-value: 5.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  94 EVAFGCGPAPAARLIPAAVGEFHRLLPQARVRF------QIDNWLALHQALTSQLYpfvvadswQAELDPQLRVQPLSPQ 167
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIveglsgHLLEWLLNGRLDLALLY--------GPPPIPGLSTEPLLEE 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 503994096 168 RCFFVCHADHPLAKQGPVSIQAMLRYPFAAPYLPPGVRKVL 208
Cdd:cd08433   73 DLFLVGPADAPLPRGAPVPLAELARLPLILPSRGHGLRRLV 113
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 104-197 1.04e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. 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: 176158  Cd Length: 221  Bit Score: 42.78  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 104 AARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVAdsWQAELDPQLRVQPLSPQRCFFVCHADHPLAKqG 183
Cdd:cd08469   11 TAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIG--IFEQIPPRFRRRTLFDEDEVWVMRKDHPAAR-G 87

                         90
                 ....*....|....
gi 503994096 184 PVSIQAMLRYPFAA 197
Cdd:cd08469   88 ALTIETLARYPHIV 101
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 107-195 1.04e-04

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


Pssm-ID: 176111  Cd Length: 197  Bit Score: 42.49  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096 107 LIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPFVVADswQAELDPQLRVQPLSPQRCFFVCHADHPLAKQGPVS 186
Cdd:cd08419   13 FAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMG--RPPEDLDLVAEPFLDNPLVVIAPPDHPLAGQKRIP 90


                 ....*....
gi 503994096 187 IQAMLRYPF 195
Cdd:cd08419   91 LERLAREPF 99
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 94-195 1.35e-04

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 42.15  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  94 EVAFGCGPAPAARLIPAAVGEFHRLLPQARVRFQIDNWLALHQALTSQLYPfvVADSWQAELDPQLRVQPLSPQRCFFVC 173
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELD--LALTYDLDLPEDIAFEPLARLPPYVWL 78

                         90       100
                 ....*....|....*....|..
gi 503994096 174 HADHPLAKQGPVSIQAMLRYPF 195
Cdd:cd08412   79 PADHPLAGKDEVSLADLAAEPL 100
nhaR PRK11062
transcriptional activator NhaR; Provisional
 2-80 8.74e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 40.38  E-value: 8.74e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503994096   2 HLDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARRFQELNVEL 80
Cdd:PRK11062   3 HINYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEM 81
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 11-107 2.61e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 38.82  E-value: 2.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096  11 FVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRQSKLPTLTLHGQKLLPYARrfqelnvelsSQLREADDA 90
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCK----------AMLVEAQAA 79

                         90
                 ....*....|....*..
gi 503994096  91 QNGEVAFGCGPAPAARL 107
Cdd:PRK14997  80 QDAIAALQVEPRGIVKL 96
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-124 2.70e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.82  E-value: 2.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994096   1 MHLDFRQLRNFVALVEYGSFNRAAEAVCLSQSAFSRSIQALEQSVGHPLFDRqsklptltLHGqKLLPYA---RRFQELN 77
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER--------VRG-RLHPTVqglRLFEEVQ 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 503994096  78 ---VELSSQLREADDA---QNGEVAFGCGPAPAARLIPAAVGEFHRLLPQARV 124
Cdd:PRK11013  73 rsyYGLDRIVSAAESLrefRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSL 125
 
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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