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Conserved domains on  [gi|730267310|ref|WP_033964127|]
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MULTISPECIES: LysR family transcriptional regulator [Pseudomonadaceae]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
SCOP:  4000316

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-288 2.17e-47

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.26  E-value: 2.17e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALE 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  84 DVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEP 163
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 164 WRRDPVMAFLPARWEcpdvvtpgwLAAQPLILNDnttrlsrltsewfasdgrqptpriqlnyNDAIKSLVAAGYGATLLP 243
Cdd:COG0583  160 LGEERLVLVASPDHP---------LARRAPLVNS----------------------------LEALLAAVAAGLGIALLP 202
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 730267310 244 -HEASTPLPDTRIVMRPL-QPLLWRQLGIA-HRGGDVERPTQHVLDVL 288
Cdd:COG0583  203 rFLAADELAAGRLVALPLpDPPPPRPLYLVwRRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-288 2.17e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.26  E-value: 2.17e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALE 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  84 DVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEP 163
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 164 WRRDPVMAFLPARWEcpdvvtpgwLAAQPLILNDnttrlsrltsewfasdgrqptpriqlnyNDAIKSLVAAGYGATLLP 243
Cdd:COG0583  160 LGEERLVLVASPDHP---------LARRAPLVNS----------------------------LEALLAAVAAGLGIALLP 202
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 730267310 244 -HEASTPLPDTRIVMRPL-QPLLWRQLGIA-HRGGDVERPTQHVLDVL 288
Cdd:COG0583  203 rFLAADELAAGRLVALPLpDPPPPRPLYLVwRRRRHLSPAVRAFLDFL 250
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
95-288 4.19e-37

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: 130.80  E-value: 4.19e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAFLP 174
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDD-PGLESEPLFEEPLVLVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 A--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:cd05466   80 PdhPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELAD 159
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 730267310 253 TRIVMRPLQ-PLLWRQLGIAHRGGDVERP-TQHVLDVL 288
Cdd:cd05466  160 GGLVVLPLEdPPLSRTIGLVWRKGRYLSPaARAFLELL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
6-238 6.87e-30

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: 114.64  E-value: 6.87e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEDV 85
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  86 ERQVQGLAGRVRLGASTgAIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPqTPVKELRIEPW 164
Cdd:NF040786  83 DRYGKESKGVLRIGAST-IPGQyLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK-LEKKRLVYTPF 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 165 RRDPVMAFLPARWECPDVVTPG----WLAAQPLILNDN--TTR------LSRL---TSEW--FASdgrqptpriqLNYND 227
Cdd:NF040786 161 YKDRLVLITPNGTEKYRMLKEEisisELQKEPFIMREEgsGTRkeaekaLKSLgisLEDLnvVAS----------LGSTE 230
                        250
                 ....*....|.
gi 730267310 228 AIKSLVAAGYG 238
Cdd:NF040786 231 AIKQSVEAGLG 241
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
93-288 5.89e-27

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: 104.29  E-value: 5.89e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   93 AGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAF 172
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDD-PGLEARPLGEEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  173 LPA--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLP-HEASTP 249
Cdd:pfam03466  80 APPdhPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPrSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 730267310  250 LPDTRIVMRPLQPL-LWRQLGIAHRGGDVERP-TQHVLDVL 288
Cdd:pfam03466 160 LADGRLVALPLPEPpLPRELYLVWRKGRPLSPaVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
5-239 3.84e-26

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 104.72  E-value: 3.84e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   5 SLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAE---QA 81
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEetcRA 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  82 LEDVeRQVQGlaGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLV--ALPQTPVKEL 159
Cdd:CHL00180  86 LEDL-KNLQR--GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTELKKIL 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 160 RIEPWRRDPVMAFLPARWEcpdvvtpgwLAAQPLILNDNTTRL------SRLTSEWFAS--------DGRQPTPRIQLNY 225
Cdd:CHL00180 163 EITPYVEDELALIIPKSHP---------FAKLKKIQKEDLYRLnfitldSNSTIRKVIDniliqngiDSKRFKIEMELNS 233
                        250
                 ....*....|....
gi 730267310 226 NDAIKSLVAAGYGA 239
Cdd:CHL00180 234 IEAIKNAVQSGLGA 247
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
9-149 8.84e-13

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: 67.45  E-value: 8.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   9 LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLaDAEQALEDVERQ 88
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL-DIEDSLMDELKS 84
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 730267310  89 VQglaGRVRLG---ASTGAIAQLmPQALETLGQRHPAI-DVQVAVLTSQETLKKLAEGSLEIGLV 149
Cdd:NF041036  85 FK---GRQRLSiccTPTFGMAHL-PGVLNRFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAII 145
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-288 2.17e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.26  E-value: 2.17e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALE 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  84 DVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEP 163
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 164 WRRDPVMAFLPARWEcpdvvtpgwLAAQPLILNDnttrlsrltsewfasdgrqptpriqlnyNDAIKSLVAAGYGATLLP 243
Cdd:COG0583  160 LGEERLVLVASPDHP---------LARRAPLVNS----------------------------LEALLAAVAAGLGIALLP 202
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 730267310 244 -HEASTPLPDTRIVMRPL-QPLLWRQLGIA-HRGGDVERPTQHVLDVL 288
Cdd:COG0583  203 rFLAADELAAGRLVALPLpDPPPPRPLYLVwRRRRHLSPAVRAFLDFL 250
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
95-288 4.19e-37

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: 130.80  E-value: 4.19e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAFLP 174
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDD-PGLESEPLFEEPLVLVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 A--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:cd05466   80 PdhPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELAD 159
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 730267310 253 TRIVMRPLQ-PLLWRQLGIAHRGGDVERP-TQHVLDVL 288
Cdd:cd05466  160 GGLVVLPLEdPPLSRTIGLVWRKGRYLSPaARAFLELL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
6-238 6.87e-30

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: 114.64  E-value: 6.87e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEDV 85
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  86 ERQVQGLAGRVRLGASTgAIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPqTPVKELRIEPW 164
Cdd:NF040786  83 DRYGKESKGVLRIGAST-IPGQyLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK-LEKKRLVYTPF 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 165 RRDPVMAFLPARWECPDVVTPG----WLAAQPLILNDN--TTR------LSRL---TSEW--FASdgrqptpriqLNYND 227
Cdd:NF040786 161 YKDRLVLITPNGTEKYRMLKEEisisELQKEPFIMREEgsGTRkeaekaLKSLgisLEDLnvVAS----------LGSTE 230
                        250
                 ....*....|.
gi 730267310 228 AIKSLVAAGYG 238
Cdd:NF040786 231 AIKQSVEAGLG 241
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
93-288 5.89e-27

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: 104.29  E-value: 5.89e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   93 AGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAF 172
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDD-PGLEARPLGEEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  173 LPA--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLP-HEASTP 249
Cdd:pfam03466  80 APPdhPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPrSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 730267310  250 LPDTRIVMRPLQPL-LWRQLGIAHRGGDVERP-TQHVLDVL 288
Cdd:pfam03466 160 LADGRLVALPLPEPpLPRELYLVWRKGRPLSPaVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
5-239 3.84e-26

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 104.72  E-value: 3.84e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   5 SLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAE---QA 81
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEetcRA 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  82 LEDVeRQVQGlaGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLV--ALPQTPVKEL 159
Cdd:CHL00180  86 LEDL-KNLQR--GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTELKKIL 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 160 RIEPWRRDPVMAFLPARWEcpdvvtpgwLAAQPLILNDNTTRL------SRLTSEWFAS--------DGRQPTPRIQLNY 225
Cdd:CHL00180 163 EITPYVEDELALIIPKSHP---------FAKLKKIQKEDLYRLnfitldSNSTIRKVIDniliqngiDSKRFKIEMELNS 233
                        250
                 ....*....|....
gi 730267310 226 NDAIKSLVAAGYGA 239
Cdd:CHL00180 234 IEAIKNAVQSGLGA 247
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
6-288 2.00e-22

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 94.45  E-value: 2.00e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEdV 85
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL-R 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  86 ERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVAlPQTPVKELRIEPWR 165
Cdd:PRK09906  82 ARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMR-HPVYSDEIDYLELL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 166 RDPVMAFLPA--RWECPDVVTPGWLAAQPLILNDNTTR--LSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATL 241
Cdd:PRK09906 161 DEPLVVVLPVdhPLAHEKEITAAQLDGVNFISTDPAYSgsLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCTI 240
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 730267310 242 LPHEASTPLPDTrIVMRPLQ---PLLwrQLGIAHRGGDVERPTQHVLDVL 288
Cdd:PRK09906 241 IPGYMNNFNTGQ-VVFRPLAgnvPSI--ALLMAWKKGEMKPALRDFIAIV 287
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
95-288 2.83e-20

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: 86.41  E-value: 2.83e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAFLP 174
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDP-PGLASRPLLREPLVVALP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 ARWE--CPDVVTPGWLAAQPLIL--NDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPhEASTPL 250
Cdd:cd08414   80 ADHPlaARESVSLADLADEPFVLfpREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVP-ASVARL 158
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 730267310 251 PDTRIVMRPL-QPLLWRQLGIAHRGGDVERPTQHVLDVL 288
Cdd:cd08414  159 QRPGVVYRPLaDPPPRSELALAWRRDNASPALRAFLELA 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
95-273 2.97e-20

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: 86.39  E-value: 2.97e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTgAIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAFL 173
Cdd:cd08420    1 TLRIGAST-TIGEyLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDH-PDLIVEPFAEDELVLVV 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 174 PA--RWECPDVVTPGWLAAQPLILND--NTTRlsRLTSEWFAS---DGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEA 246
Cdd:cd08420   79 PPdhPLAGRKEVTAEELAAEPWILREpgSGTR--EVFERALAEaglDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLA 156
                        170       180
                 ....*....|....*....|....*....
gi 730267310 247 -STPLPDTRIVMRPLQPL-LWRQLGIAHR 273
Cdd:cd08420  157 vRKELELGRLVALPVEGLrLTRPFSLIYH 185
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-273 4.58e-20

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: 85.65  E-value: 4.58e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPqTPVKELRIEPWRRDPVMAFLP 174
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEP-EADPDLEFEPLLRDPFVLVCP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 A--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:cd08440   80 KdhPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADH 159
                        170       180
                 ....*....|....*....|..
gi 730267310 253 TRIVMRPL-QPLLWRQLGIAHR 273
Cdd:cd08440  160 PGLVARPLtEPVVTRTVGLIRR 181
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
100-275 8.44e-19

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: 82.22  E-value: 8.44e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 100 ASTGAIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAFLPA--R 176
Cdd:cd08415    5 AALPALALsLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDH-PGLESEPLASGRAVCVLPPghP 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 177 WECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPDTRIV 256
Cdd:cd08415   84 LARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAGAGLV 163
                        170
                 ....*....|....*....
gi 730267310 257 MRPLQPLLWRQLGIAHRGG 275
Cdd:cd08415  164 VRPFRPAIPFEFALVRPAG 182
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
6-247 1.06e-18

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 84.35  E-value: 1.06e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEDV 85
Cdd:PRK11233   3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAV 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  86 ERQVQGLAGRVRLGASTGAIAQL--MPqALETLGQRHPAIDVQVAVlTSQETL-KKLAEGSLEIGlVALPQTPVKELRIE 162
Cdd:PRK11233  83 HNVGQALSGQVSIGLAPGTAASSltMP-LLQAVRAEFPGIVLYLHE-NSGATLnEKLMNGQLDMA-VIYEHSPVAGLSSQ 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 163 PWRRDPVmaFLPARWECP-DVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRqpTPRI--QLNYNDAIKSLVAAGYGA 239
Cdd:PRK11233 160 PLLKEDL--FLVGTQDCPgQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRL--TAKVigEIESIATLTAAIASGMGV 235

                 ....*...
gi 730267310 240 TLLPHEAS 247
Cdd:PRK11233 236 TVLPESAA 243
PRK09986 PRK09986
LysR family transcriptional regulator;
4-261 8.25e-18

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 81.69  E-value: 8.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALE 83
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  84 DVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGL--VALPQTP--VKEL 159
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNpgFTSR 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 160 RIEpwrRDPVMAFLPA--RWECPDVVTPGWLAAQPLI-LNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAG 236
Cdd:PRK09986 167 RLH---ESAFAVAVPEehPLASRSSVPLKALRNEYFItLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG 243
                        250       260
                 ....*....|....*....|....*.
gi 730267310 237 YGATLLPHE-ASTPLPDtrIVMRPLQ 261
Cdd:PRK09986 244 IGITLLPDSyAQIPWPG--VVFRPLK 267
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
6-267 2.92e-17

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 80.00  E-value: 2.92e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLAD---AEQAL 82
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDleaGRRAI 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  83 EDVERQVQglaGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGL----VALPQTPVKE 158
Cdd:PRK11242  83 HDVADLSR---GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIafapVHSPEIEAQP 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 159 LRIEPWRRdpVMAFLPARWECPDVVTPGWLAAQPLIL--NDNTTRlsRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAG 236
Cdd:PRK11242 160 LFTETLAL--VVGRHHPLAARRKALTLDELADEPLVLlsAEFATR--EQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG 235
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 730267310 237 YGATLLPHEASTPLPDTRIVmrPLQP--------LLWRQ 267
Cdd:PRK11242 236 RLATLLPAAIAREHDGLCAI--PLDPplpqrtaaLLRRK 272
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-65 1.46e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.42  E-value: 1.46e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310    6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGE 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
4-273 3.64e-16

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 76.65  E-value: 3.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLadaEQALE 83
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL---EQAVE 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  84 dVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALP-QTPvkELRIE 162
Cdd:PRK10837  80 -IEQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPcHSP--ELISE 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 163 PWRRDPVMAFL-PARWECPDVVTPGWLAAQPLILNDN--TTR-------LSRLtsewfasdgrqPTPRI--QLNYNDAIK 230
Cdd:PRK10837 157 PWLEDELVVFAaPDSPLARGPVTLEQLAAAPWILRERgsGTReivdyllLSHL-----------PRFELamELGNSEAIK 225
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 730267310 231 SLVAAGYGATLLPH-------------EASTPLPdtrivmrPLQPLLWRqlgIAHR 273
Cdd:PRK10837 226 HAVRHGLGISCLSRrviadqlqagtlvEVAVPLP-------RLMRTLYR---IHHR 271
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-288 3.81e-16

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: 74.92  E-value: 3.81e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPV-KELRIEPWRRDPVMAFL 173
Cdd:cd08427    1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLpKDLVWTPLVREPLVLIA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 174 PARWECPDVVTpgWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPDT 253
Cdd:cd08427   81 PAELAGDDPRE--LLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGP 158
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 730267310 254 RIVMRPL-QPLLWRQLGIAHRGGDVERP-TQHVLDVL 288
Cdd:cd08427  159 RVRVLPLgDPAFSRRVGLLWRRSSPRSRlIQALLEAL 195
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-288 6.52e-15

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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 71.86  E-value: 6.52e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLV-ALPQTPV---KELRIEPWRRDPVM 170
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfDYPVTPPpddPGLTRVPLLDDPLD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 171 AFLPARWECPD--VVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRqpTPRIQLNYND--AIKSLVAAGYGATLLPHEA 246
Cdd:cd08423   81 LVLPADHPLAGreEVALADLADEPWIAGCPGSPCHRWLVRACRAAGF--TPRIAHEADDyaTVLALVAAGLGVALVPRLA 158
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 730267310 247 STPLPDtRIVMRPLQPLLWRQLGIAHRGGDVERPT-QHVLDVL 288
Cdd:cd08423  159 LGARPP-GVVVRPLRPPPTRRIYAAVRAGAARRPAvAAALEAL 200
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-276 4.00e-14

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 69.47  E-value: 4.00e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPqTPVKELRIEPWRRDPVMAFLP 174
Cdd:cd08421    1 HVRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGN-VDAAGLETRPYRTDRLVVVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 A--RWECPDVVTPGWLAAQPLI-LNDNTTrLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEA-STPL 250
Cdd:cd08421   80 RdhPLAGRASVAFADTLDHDFVgLPAGSA-LHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAaRRYA 158
                        170       180
                 ....*....|....*....|....*..
gi 730267310 251 PDTRIVMRPLQ-PLLWRQLGIAHRGGD 276
Cdd:cd08421  159 RALGLRVVPLDdAWARRRLLLCVRSFD 185
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-288 4.79e-14

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: 69.17  E-value: 4.79e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPVKELRIEPWRRDPVMAFLP 174
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPLVAVVA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 A--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPheASTPLPD 252
Cdd:cd08436   81 PdhPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLP--ASVAARL 158
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 730267310 253 TRIVMRPLQPLLWRQLGIAHRGGDVERPTQHVLDVL 288
Cdd:cd08436  159 PGLAALPLEPAPRRRLYLAWSAPPPSPAARAFLELL 194
PRK12680 PRK12680
LysR family transcriptional regulator;
4-246 1.15e-13

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 70.04  E-value: 1.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIAD--LGSFAEAARVlHLAPPTVSLHIADLESRVGGKLLSRtRGRVQPSAL--GETLVERARRLLADAE 79
Cdd:PRK12680   1 MTLTQLRYLVAIADaeLNITLAAARV-HATQPGLSKQLKQLEDELGFLLFVR-KGRSLESVTpaGVEVIERARAVLSEAN 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  80 QALEDVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALP-QTPVKE 158
Cdd:PRK12680  79 NIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAgGEPSAG 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 159 LRIE--PWRR---DPVMAFLPARWECPDVVTpgwLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLV 233
Cdd:PRK12680 159 IAVPlyRWRRlvvVPRGHALDTPRRAPDMAA---LAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYV 235
                        250
                 ....*....|...
gi 730267310 234 AAGYGATLLPHEA 246
Cdd:PRK12680 236 RAGLGVGLLAEMA 248
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
9-149 8.84e-13

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: 67.45  E-value: 8.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   9 LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLaDAEQALEDVERQ 88
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL-DIEDSLMDELKS 84
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 730267310  89 VQglaGRVRLG---ASTGAIAQLmPQALETLGQRHPAI-DVQVAVLTSQETLKKLAEGSLEIGLV 149
Cdd:NF041036  85 FK---GRQRLSiccTPTFGMAHL-PGVLNRFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAII 145
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-243 4.91e-12

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: 63.48  E-value: 4.91e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLV-ALPQTPvkELRIEPWRRDPVMAFL 173
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAfSPPPEP--GIRVHSRQPAPIGAVV 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 730267310 174 P-----ARwecPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLP 243
Cdd:cd08426   79 PpghplAR---QPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLT 150
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
97-260 7.57e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 63.16  E-value: 7.57e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  97 RLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLV-ALPQTPvkELRIEPWRRDPVMAFLPA 175
Cdd:cd08450    3 TIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMrPEIQSD--GIDYQLLLKEPLIVVLPA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 176 --RWECPDVVTPGWLAAQPLILNDNTTR-LSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:cd08450   81 dhRLAGREKIPPQDLAGENFISPAPTAPvLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLLPP 160

                 ....*...
gi 730267310 253 TrIVMRPL 260
Cdd:cd08450  161 S-VVARPL 167
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
95-288 1.04e-11

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: 62.61  E-value: 1.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPqTPVKELRIEPWRRDPVMAFLP 174
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGP-PPIPGLSTEPLLEEDLFLVGP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 ARWECPDV--VTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:cd08433   80 ADAPLPRGapVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA 159
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 730267310 253 -TRIVMRPL-QPLLWRQLGIAH-RGGDVERPTQHVLDVL 288
Cdd:cd08433  160 aGRLVAAPIvDPALTRTLSLATpRDRPLSPAALAVRDLL 198
PRK09791 PRK09791
LysR family transcriptional regulator;
4-127 1.13e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 64.01  E-value: 1.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALE 83
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 730267310  84 DVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQV 127
Cdd:PRK09791  85 DIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
9-263 1.42e-11

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 63.90  E-value: 1.42e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   9 LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEDVERQ 88
Cdd:PRK11151   6 LEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQ 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  89 VQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALpqtpVKELR--IE-PWR 165
Cdd:PRK11151  86 GETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILAL----VKESEafIEvPLF 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 166 RDPVMAFLPA--RWECPDVVTPGWLAAQP-LILNDNTTRLSRLTSEWFASDGRQPTpRIQLNYNDAIKSLVAAGYGATLL 242
Cdd:PRK11151 162 DEPMLLAVYEdhPWANRDRVPMSDLAGEKlLMLEDGHCLRDQAMGFCFEAGADEDT-HFRATSLETLRNMVAAGSGITLL 240
                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 730267310 243 PH---------------EASTPLPDTRIVM--RPLQPL 263
Cdd:PRK11151 241 PAlavpnerkrdgvcylPCIKPEPRRTIGLvyRPGSPL 278
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
94-281 1.54e-11

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: 62.16  E-value: 1.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  94 GRVRLGAS-TgaIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPqTPVKELRIEPWRRDPVMA 171
Cdd:cd08411    1 GPLRLGVIpT--IAPyLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALP-VDEPGLEEEPLFDEPFLL 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 172 FLPA--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEA--S 247
Cdd:cd08411   78 AVPKdhPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAvpS 157
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 730267310 248 TPLPDTRIVMRPLQ-PLLWRQLGIAHRGGDVERPT 281
Cdd:cd08411  158 EELRGDRLVVRPFAePAPSRTIGLVWRRSSPRAAA 192
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
95-288 2.10e-11

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, 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, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 61.74  E-value: 2.10e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPVKELRIEPwRRDPVMAFLP 174
Cdd:cd08457    1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIET-RSLPAVVAVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 A--RWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:cd08457   80 MghPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPL 159
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 730267310 253 TRIVMRPLQPLL-WRQLGIAHRGGDVERPTQHVLDVL 288
Cdd:cd08457  160 DGIVIRPFDTFIdAGFLVVRAANGPPSTMVDRFIDEF 196
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
4-280 3.59e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 62.73  E-value: 3.59e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALE 83
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  84 DVERQVQglaGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVA--LPQTPVK---- 157
Cdd:PRK15421  82 ACNEPQQ---TRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSdiLPRSGLHyspm 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 158 ---ELRIEPWRRDPVMAflparwecPDVVTPGWLAAQPLILndNTTRLSRLT--SEWFASDGRQPTPRIQLNYNDAIKsL 232
Cdd:PRK15421 159 fdyEVRLVLAPDHPLAA--------KTRITPEDLASETLLI--YPVQRSRLDvwRHFLQPAGVSPSLKSVDNTLLLIQ-M 227
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 730267310 233 VAAGYGATLLPHEASTPLP-DTRIVMRPLQPLLWRQLGIAHRGGDVERP 280
Cdd:PRK15421 228 VAARMGIAALPHWVVESFErQGLVVTKTLGEGLWSRLYAAVRDGEQRQP 276
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
96-273 5.70e-11

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: 60.63  E-value: 5.70e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  96 VRLGA--STGAiaQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVAlPQTPVKELRIEPWRRDPVMAFL 173
Cdd:cd08434    2 VRLGFlhSLGT--SLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCS-PVPDEPDIEWIPLFTEELVLVV 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 174 PArwECP----DVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTP 249
Cdd:cd08434   79 PK--DHPlagrDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLN 156
                        170       180
                 ....*....|....*....|....*
gi 730267310 250 LPDTRIVmrPL-QPLLWRQLGIAHR 273
Cdd:cd08434  157 PPGVKKI--PIkDPDAERTIGLAWL 179
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-121 3.00e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.82  E-value: 3.00e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   9 LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLA-------DAEQA 81
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSwlesmpsELQQV 86
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 730267310  82 LEDVERQVQGLAGRVRLGAStgAIAQLmpqaLETLGQRHP 121
Cdd:PRK10094  87 NDGVERQVNIVINNLLYNPQ--AVAQL----LAWLNERYP 120
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-262 3.44e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 59.60  E-value: 3.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDR--LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRgRVQPSALGETL---VERARRLLADAEQ 80
Cdd:PRK13348   2 LDYkqLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLlrhLRQVALLEADLLS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  81 ALEDverqvqGLAGRVRLGASTGA---IAQLMPQALETLGQRHPAIDVQVavlTSQE-TLKKLAEGSLeIGLVALPQTPV 156
Cdd:PRK13348  81 TLPA------ERGSPPTLAIAVNAdslATWFLPALAAVLAGERILLELIV---DDQDhTFALLERGEV-VGCVSTQPKPM 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 157 KELRIEP-----WRRDPVMAFLpARWeCPDVVTPGWLAAQPLILNDNTTRLSrltSEWFASDGRQPTPRIQLNYNDAIKS 231
Cdd:PRK13348 151 RGCLAEPlgtmrYRCVASPAFA-ARY-FAQGLTRHSALKAPAVAFNRKDTLQ---DSFLEQLFGLPVGAYPRHYVPSTHA 225
                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 730267310 232 LVAA-----GYGatLLP-HEASTPLPDTRIVmrPLQP 262
Cdd:PRK13348 226 HLAAirhglGYG--MVPeLLIGPLLAAGRLV--DLAP 258
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
95-288 1.19e-09

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


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 56.80  E-value: 1.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAFLP 174
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDE-EEFDSQPLCNEPLVAVLP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 --ARWECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:cd08438   80 rgHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDN 159
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 730267310 253 TRIVMRPLQ--PLLWrQLGIA-HRGGDVERPTQHVLDVL 288
Cdd:cd08438  160 AGVKVIPLTdpDLRW-QLALIwRKGRYLSHAARAWLALL 197
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-260 1.91e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 56.12  E-value: 1.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVAlPQTPVKELRIEPWRRDPVMAFLP 174
Cdd:cd08447    1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLR-PPFARPGLETRPLVREPLVAAVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 A--RWECPDVVTPGWLAAQPLI---------LNDNTTRLsrltsewFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLP 243
Cdd:cd08447   80 AghPLAGAERLTLEDLDGQPFImysptearyFHDLVVRL-------FASAGVQPRYVQYLSQIHTMLALVRAGLGVALVP 152
                        170
                 ....*....|....*..
gi 730267310 244 HEASTPLPDtRIVMRPL 260
Cdd:cd08447  153 ASASRLRFE-GVVFRPL 168
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-134 2.96e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 56.93  E-value: 2.96e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVqpsalgeTLVERARRLLADAEQALEDV 85
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKV-------ELTEEGKRVFWALKSSLDTL 88
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 730267310  86 -----ERQVQGLAGRVRLgASTGAIAQ--LMPqALETLGQRHPAIDVQvaVLTSQE 134
Cdd:PRK10086  89 nqeilDIKNQELSGTLTV-YSRPSIAQcwLVP-RLADFTRRYPSISLT--ILTGNE 140
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
23-263 1.13e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 55.00  E-value: 1.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  23 EAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRV----QPsalGETLVERARRLLADAEQaLEDVERQVQGL-AGRVR 97
Cdd:PRK12682  21 EAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkgltEP---GKAVLDVIERILREVGN-IKRIGDDFSNQdSGTLT 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  98 LgASTGAIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPVKELRIEPWRRDPVMAFLPAR 176
Cdd:PRK12682  97 I-ATTHTQARyVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLATLPCYDWQHAVIVPPD 175
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 177 WE--CPDVVTPGWLAAQPLILNDN--TTRlSRLtSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPD 252
Cdd:PRK12682 176 HPlaQEERITLEDLAEYPLITYHPgfTGR-SRI-DRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGVGIVAEMAYRPDRD 253
                        250
                 ....*....|.
gi 730267310 253 TRIVMRPLQPL 263
Cdd:PRK12682 254 GDLVALPAGHL 264
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-98 1.22e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.78  E-value: 1.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   9 LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGrVQPSALGETLVERARRLladaeQALE-DVER 87
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQP-CRPTEAGQRLLRHARQV-----RLLEaELLG 80
                         90
                 ....*....|..
gi 730267310  88 QVQGLAG-RVRL 98
Cdd:PRK03635  81 ELPALDGtPLTL 92
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
1-128 2.53e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 54.23  E-value: 2.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   1 MREISLDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRL------ 74
Cdd:PRK11013   1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygldr 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 730267310  75 LADAEQALedveRQVQGlaGRVRLgASTGAIAQ-LMPQALETLGQRHPAIDVQVA 128
Cdd:PRK11013  81 IVSAAESL----REFRQ--GQLSI-ACLPVFSQsLLPGLCQPFLARYPDVSLNIV 128
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-243 2.58e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 53.04  E-value: 2.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAFLP 174
Cdd:cd08448    1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLP-AGLSARLLHREPFVCCLP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 ARWEcpdvvtpgwLAAQPLIlndnttRLSRLTSEWF-------------------ASDGRQPTPRIQLNYNDAIKSLVAA 235
Cdd:cd08448   80 AGHP---------LAARRRI------DLRELAGEPFvlfsrevspdyydqiialcMDAGFHPKIRHEVRHWLTVVALVAA 144

                 ....*...
gi 730267310 236 GYGATLLP 243
Cdd:cd08448  145 GMGVALVP 152
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
95-275 1.68e-07

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: 50.58  E-value: 1.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAqLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGslEIGLVALPQTPVK-ELRIEPWRRDPVMAFL 173
Cdd:cd08419    1 RLRLAVVSTAKY-FAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADN--EDDLAIMGRPPEDlDLVAEPFLDNPLVVIA 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 174 ParwecPD-------VVTPGWLAAQPLIL--NDNTTRLSrlTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLP- 243
Cdd:cd08419   78 P-----PDhplagqkRIPLERLAREPFLLrePGSGTRLA--MERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSl 150
                        170       180       190
                 ....*....|....*....|....*....|....
gi 730267310 244 HEASTPLPDTRIVMRPLQ--PLLwRQLGIAHRGG 275
Cdd:cd08419  151 HTLALELATGRLAVLDVEgfPIR-RQWYVVHRKG 183
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
95-273 1.82e-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: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGL---VALPQtpvkELRIEPWRRDPVMA 171
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALtydLDLPE----DIAFEPLARLPPYV 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 172 FLPA--RWECPDVVTPGWLAAQPLILNDNtTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLL---PHEA 246
Cdd:cd08412   77 WLPAdhPLAGKDEVSLADLAAEPLILLDL-PHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLndrPYRP 155
                        170       180
                 ....*....|....*....|....*...
gi 730267310 247 STPLPDtRIVMRPLQPLLWRQ-LGIAHR 273
Cdd:cd08412  156 WSYDGK-RLVRRPLADPVPPLrLGLAWR 182
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
6-149 2.82e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 50.80  E-value: 2.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRtRGRvqpsalGETLVERARRLLADAEQAL--- 82
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFAR-HGR------NKLLTEHGIQLLGYARKILrfn 85
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 730267310  83 ---------EDVErqvqglaGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGslEIGLV 149
Cdd:PRK15092  86 deacsslmySNLQ-------GVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQ--EVDLA 152
PRK09801 PRK09801
LysR family transcriptional regulator;
9-133 6.30e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 50.03  E-value: 6.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   9 LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEDVERQ 88
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 730267310  89 VQGLAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQ 133
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQ 135
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
12-127 1.21e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 48.83  E-value: 1.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  12 LVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEDVERQVQG 91
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 730267310  92 LAGRVRLGASTGAIAQLMPQALETLGQRHPAIDVQV 127
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
nhaR PRK11062
transcriptional activator NhaR; Provisional
19-70 2.51e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 48.08  E-value: 2.51e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 730267310  19 GSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRtRGR-VQPSALGEtLVER 70
Cdd:PRK11062  19 GSVVGAAEALFLTPQTITGQIKALEERLQGKLFKR-KGRgLEPTELGE-LVFR 69
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
9-93 4.54e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 44.16  E-value: 4.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   9 LRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADaeqaLEDVERQ 88
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKK----MQETRRQ 82

                 ....*
gi 730267310  89 VQGLA 93
Cdd:PRK11074  83 CQQVA 87
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-125 6.42e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 43.60  E-value: 6.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   6 LDRLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLADAEQALEDV 85
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 730267310  86 ERQVQGLAGRVRLGASTgAIAQ--LMPQALETLgQRHPAIDV 125
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSS-TMAQnvLAGLTAKML-KEYPGLSV 123
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
95-243 6.44e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 42.98  E-value: 6.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGA--STGAIAqlMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPvKELRIEPWRRDPVMAF 172
Cdd:cd08442    1 PLRLGSmeTTAAVR--LPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEH-PRLEQEPVFQEELVLV 77
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 730267310 173 LPArwECPDVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLP 243
Cdd:cd08442   78 SPK--GHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLP 146
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
95-169 1.44e-04

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 41.87  E-value: 1.44e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVAL-PQTPVKELRIEPWRRDPV 169
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLaDDEQPPDLASEELADEPL 76
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
95-288 3.36e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 40.72  E-value: 3.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPV-KELRIEPWRRDPVMAFL 173
Cdd:cd08449    1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNdPPLASELLWREPMVVAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 174 P-----ARWECpdvVTPGWLAAQPLI-LNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEAS 247
Cdd:cd08449   81 PeehplAGRKS---LTLADLRDEPFVfLRLANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYA 157
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 730267310 248 TpLPDTRIVMRPLQPLLWRQLGIAHRGGDVERPTQHVLDVL 288
Cdd:cd08449  158 R-LPWPGVRFIPLKQAISADLYAVYHPDSATPVIQAFLALL 197
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
94-260 3.40e-04

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 40.73  E-value: 3.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  94 GRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVAL-PQTPvkELRIEPWRRDPVMAF 172
Cdd:cd08446    1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFyPVEP--DIAVENVAQERLYLA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 173 LPARW--ECPDVVTPGWLAAQPLILNDNTTRLSrLTSE---WFASDGRQptPRIQLNYNDAIK--SLVAAGYGATLLPHE 245
Cdd:cd08446   79 VPKSHplAARPAVSLADLRNEPLILFPRGGRPS-FADEvlgLFRRAGVE--PRVAQEVEDVVAalALVAAGFGVCIVPES 155
                        170
                 ....*....|....*.
gi 730267310 246 AST-PLPDtrIVMRPL 260
Cdd:cd08446  156 VAAlRWPG--VVFRPL 169
PRK10341 PRK10341
transcriptional regulator TdcA;
1-163 3.59e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.39  E-value: 3.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   1 MREISLDRLRTLVAIADL---GSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERARRLLAD 77
Cdd:PRK10341   1 MSTILLPKTQHLVVFQEVirsGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  78 AEQALEDVERQVQGLAGRVRLGASTGAIAQLMPQALETLGQRHPaiDVQVAVLTSQ--ETLKKLAEGSLE--IGLVALPQ 153
Cdd:PRK10341  81 MKNMVNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFP--KAQVSMYEAQlsSFLPAIRDGRLDfaIGTLSNEM 158
                        170
                 ....*....|
gi 730267310 154 TPvKELRIEP 163
Cdd:PRK10341 159 KL-QDLHVEP 167
cbl PRK12679
HTH-type transcriptional regulator Cbl;
23-256 7.06e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.56  E-value: 7.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  23 EAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVqpsaLGETlvERARRLLADAEQALEDVERqVQGLA--------G 94
Cdd:PRK12679  21 EVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRL----LGMT--EPGKALLVIAERILNEASN-VRRLAdlftndtsG 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPVKELRIEPWRRDPVMAFLP 174
Cdd:PRK12679  94 VLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWHHSLLVP 173
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 175 ARWECPDV--VTPGWLAAQPLI-LNDNTTRLSRLtSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLP 251
Cdd:PRK12679 174 HDHPLTQItpLTLESIAKWPLItYRQGITGRSRI-DDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQE 252

                 ....*
gi 730267310 252 DTRIV 256
Cdd:PRK12679 253 ESNLI 257
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
104-262 1.17e-03

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 39.32  E-value: 1.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 104 AIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPVKeLRIEPWRRDPVMAFLPA--RWECP 180
Cdd:cd08456    9 ALSQsFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPG-IERERLLRIDGVCVLPPghRLAVK 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 181 DVVTPGWLAAQPLILNDNTTRLSRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEASTPLPDTRIVMRPL 260
Cdd:cd08456   88 KVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAAAGLVVRRF 167

                 ..
gi 730267310 261 QP 262
Cdd:cd08456  168 SP 169
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
94-267 1.51e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR 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 (PBP2). The PBP2 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: 176116  Cd Length: 197  Bit Score: 38.85  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  94 GRVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGL----VALPQTPVKELRIEPWRrdpV 169
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIafapVRSPDIDAQPLFDERLA---L 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 170 MAFLPARWEC-PDVVTPGWLAAQPLIL--NDNTTRlsRLTSEWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPHEA 246
Cdd:cd08425   78 VVGATHPLAQrRTALTLDDLAAEPLALlsPDFATR--QHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAI 155
                        170       180
                 ....*....|....*....|....*....
gi 730267310 247 STPLPDTRIVmrPLQP--------LLWRQ 267
Cdd:cd08425  156 AREQPGLCAV--ALEPplpgrtaaLLRRK 182
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
95-288 3.74e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 37.73  E-value: 3.74e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  95 RVRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPVKELRIEPWR--RDPVMAF 172
Cdd:cd08453    1 RLSLAFVSTADYSVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPALAYRPllSEPLVLA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 173 LPARW--ECPDVVTPGWLAAQPLILNDNTT--RLSRLTSEWFASDGRQPTPR---IQLNyndAIKSLVAAGYGATLLPhE 245
Cdd:cd08453   81 VPAAWaaEGGAPLALAAVAAEPLVIFPRRIapAFHDAVTGYYRAAGQTPRIAqeaIQMQ---TIISLVSAGMGVALVP-A 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 730267310 246 ASTPLPDTRIVMRPLQ---PLLwrQLGIAHRGGDVERPTQHVLDVL 288
Cdd:cd08453  157 SLRNLARPGVVYRELAdpaPVL--ETGLVWRRDDASPVLARFLDLV 200
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
8-72 6.05e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 37.73  E-value: 6.05e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 730267310   8 RLRTLVAIADLGSFAEAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQPSALGETLVERAR 72
Cdd:PRK15243   8 KLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVK 72
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
4-84 6.18e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.49  E-value: 6.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310   4 ISLDRLRTLVAIADLG--SFAEAARVLHLAPPTVSLHIADLESRvggKLLSRTRG-------RVQPSALGETLVERARRL 74
Cdd:COG1846   36 LTPAQFRVLAALAEAGglTQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPDpedrravLVRLTEKGRALLEEARPA 112
                         90
                 ....*....|
gi 730267310  75 LADAEQALED 84
Cdd:COG1846  113 LEALLAELLA 122
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
23-256 6.77e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 37.33  E-value: 6.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  23 EAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRV----QPsalGETLVERARRLLADAEQALEDVERQVQGLAGRVRL 98
Cdd:PRK12683  21 EVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLtgltEP---GKELLQIVERMLLDAENLRRLAEQFADRDSGHLTV 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  99 gASTGAIAQ-LMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVAlpqtpvkelriEPWRRDPVMAFLPA-R 176
Cdd:PRK12683  98 -ATTHTQARyALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAT-----------EALDREPDLVSFPYyS 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 177 WECPDVVTPG--WLAAQPLILND-----------NTTRLSRLTSewfASDGRQPTPRIQLNYNDA--IKSLVAAGYGATL 241
Cdd:PRK12683 166 WHHVVVVPKGhpLTGRENLTLEAiaeypiitydqGFTGRSRIDQ---AFAEAGLVPDIVLTALDAdvIKTYVELGMGVGI 242
                        250
                 ....*....|....*
gi 730267310 242 LPHEASTPLPDTRIV 256
Cdd:PRK12683 243 VAAMAYDPQRDTGLV 257
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
23-259 8.55e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 37.26  E-value: 8.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  23 EAARVLHLAPPTVSLHIADLESRVGGKLLSRTRGRVQpsalgeTLVERARRLLADAEQALEDVE--RQVQGLAGRVRLG- 99
Cdd:PRK12684  21 EAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLR------GLTEPGRIILASVERILQEVEnlKRVGKEFAAQDQGn 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 100 ---ASTGAIAQ-LMPQALETLGQRHPAID--------VQVA--VLTSQETLKKLAEG-SLEIGLVALP--Qtpvkelrie 162
Cdd:PRK12684  95 ltiATTHTQARyALPAAIKEFKKRYPKVRlsilqgspTQIAemVLHGQADLAIATEAiADYKELVSLPcyQ--------- 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 163 pWRRdpvMAFLPARWECPDV--VTPGWLAAQPLILNDNTTRLSRLTSEWFASdgRQPTPRIQLNYNDA--IKSLVAAGYG 238
Cdd:PRK12684 166 -WNH---CVVVPPDHPLLERkpLTLEDLAQYPLITYDFAFAGRSKINKAFAL--RGLKPDIVLEAIDAdvIKTYVELGLG 239
                        250       260
                 ....*....|....*....|.
gi 730267310 239 ATLLPHEASTPLPDTRIVMRP 259
Cdd:PRK12684 240 VGIVADMAFDPERDRNLRAID 260
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
96-264 8.90e-03

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


Pssm-ID: 176121  Cd Length: 199  Bit Score: 36.40  E-value: 8.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310  96 VRLGASTGAIAQLMPQALETLGQRHPAIDVQVAVLTSQETLKKLAEGSLEIGLVALPQTPVKELRIEPWRRDPVMAFLPA 175
Cdd:cd08430    2 LSLYCSVTASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAFLPLATSPLVFIAPN 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730267310 176 RWeCP--DVVTPGWLAAQ--PLILNDNTTRLSRLTSeWFASDGRQPTPRIQLNYNDAIKSLVAAGYGATLLPH---EASt 248
Cdd:cd08430   82 IA-CAvtQQLSQGEIDWSrlPFILPERGLARERLDQ-WFRRRGIKPNIYAQVAGHEAIVSMVALGCGVGIVPElvlDNS- 158
                        170
                 ....*....|....*.
gi 730267310 249 PLPDtRIVMRPLQPLL 264
Cdd:cd08430  159 PLKD-KVRILEVQPEL 173
 
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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