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Conserved domains on  [gi|1567725624|ref|WP_129153301|]
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LysR family transcriptional regulator [Achromobacter aloeverae]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
13-304 2.61e-60

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 192.77  E-value: 2.61e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALR 92
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  93 HFQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTL 172
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 173 AEEPMLLVVPARHALAGQQAVTMDMilpyplmmldrykslfkrlkdeyaargapynpatiatlPTLLGMIDAGNGITLLP 252
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLVNSL--------------------------------------EALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1567725624 253 RSMAQNNGRRSR-VTLAVSDLDASRRYGSLVASKAELSAAATNFQGYLRKNFK 304
Cdd:COG0583   203 RFLAADELAAGRlVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
13-304 2.61e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 192.77  E-value: 2.61e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALR 92
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  93 HFQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTL 172
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 173 AEEPMLLVVPARHALAGQQAVTMDMilpyplmmldrykslfkrlkdeyaargapynpatiatlPTLLGMIDAGNGITLLP 252
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLVNSL--------------------------------------EALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1567725624 253 RSMAQNNGRRSR-VTLAVSDLDASRRYGSLVASKAELSAAATNFQGYLRKNFK 304
Cdd:COG0583   203 RFLAADELAAGRlVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-295 1.49e-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: 132.34  E-value: 1.49e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPA-TIATLPTLLGMIDAGNGITLLPRSMAQNNGRR 262
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIAlEVDSLEAIKALVAAGLGIALLPESAVEELADG 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1567725624 263 SRVTLAVSDLDASRRYGSLVASKAELSAAATNF 295
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAF 193
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 14-303 1.87e-36

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: 132.36  E-value: 1.87e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  14 ELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRH 93
Cdd:NF040786    2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  94 FQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAaldGTP---RGLRFQ 170
Cdd:NF040786   82 FDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT---GTKlekKRLVYT 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 171 TLAEEPMLLVVPARHALAGQQAVTMDM--ILPYPLMMldR------YKSLFKRLKdeyAARGAPYNPATIATLP---TLL 239
Cdd:NF040786  159 PFYKDRLVLITPNGTEKYRMLKEEISIseLQKEPFIM--ReegsgtRKEAEKALK---SLGISLEDLNVVASLGsteAIK 233

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567725624 240 GMIDAGNGITLLPR-SMAQNNGRRSRVTLAVSDLDASRRYgSLVASK-AELSAAATNFQGYLRKNF 303
Cdd:NF040786  234 QSVEAGLGISVISElAAEKEVERGRVLIFPIPGLPKNRDF-YLVYNKnRQLSPTAEAFLQFVKERY 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-304 2.82e-33

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: 121.24  E-value: 2.82e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 102 RNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVV 181
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 182 PARHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPA-TIATLPTLLGMIDAGNGITLLPRSMAQNNG 260
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVlEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1567725624 261 RRSR-VTLAVSDLDASRRYGSLVASKAELSAAATNFQGYLRKNFK 304
Cdd:pfam03466 161 ADGRlVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 21-208 8.94e-26

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 103.88  E-value: 8.94e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  21 FLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRHFQTASDH 100
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 101 ERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLV 180
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALV 168

                         170       180
                  ....*....|....*....|....*....
gi 1567725624 181 VPARHALAGQQ-AVTMDMILPYPLMMLDR 208
Cdd:PRK11242  169 VGRHHPLAARRkALTLDELADEPLVLLSA 197
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 18-109 3.67e-16

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 77.26  E-value: 3.67e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  18 LETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRtTRRVEATPDGERLREAAERAVAGLRDALRHFQTA 97
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLAELPGL 84

                          90
                  ....*....|..
gi 1567725624  98 SDHERNTVTVAV 109
Cdd:TIGR03298  85 APGAPTRLTIAV 96
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 13-257 1.38e-15

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: 75.54  E-value: 1.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVA---GLRD 89
Cdd:NF041036    1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDiedSLMD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  90 ALRHFQtasdhERNTVTVAVTPMLSATVMPSLIHAYTERYPDVrivlHDLPY-----DQVIREVAEGRADLAVAA-LDGT 163
Cdd:NF041036   81 ELKSFK-----GRQRLSICCTPTFGMAHLPGVLNRFMLRNADV----VDLKFlfhspAQALEGIQNKEFDLAIIEhCADL 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 164 PRGlRFQT--LAEEPMLLV-VPARHALAGQqaVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNP-ATIATLPTLL 239
Cdd:NF041036  152 DLG-RFHTypLPQDELVFVsAPSLGLPTPN--VTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLDDfRRVVVSDDLR 228

                         250       260
                  ....*....|....*....|.
gi 1567725624 240 GMID---AGNGITLLPRSMAQ 257
Cdd:NF041036  229 LTIQtvlDGGGISFVSRSLVC 249
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
26-102 5.33e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 38.73  E-value: 5.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624   26 REGSFSVA--ARKLHLSQPAVTNRVKRLEDKLHVKLLV----RTTRRVEATPDGERLREAAERAVAGLRDALrhFQTASD 99
Cdd:smart00347  21 EEGPLSVSelAKRLGVSPSTVTRVLDRLEKKGLVRREPspedRRSVLVSLTEEGRELIEQLLEARSETLAEL--LAGLTA 98


                   ...
gi 1567725624  100 HER 102
Cdd:smart00347  99 EEQ 101
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
13-304 2.61e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 192.77  E-value: 2.61e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALR 92
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  93 HFQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTL 172
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 173 AEEPMLLVVPARHALAGQQAVTMDMilpyplmmldrykslfkrlkdeyaargapynpatiatlPTLLGMIDAGNGITLLP 252
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLVNSL--------------------------------------EALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1567725624 253 RSMAQNNGRRSR-VTLAVSDLDASRRYGSLVASKAELSAAATNFQGYLRKNFK 304
Cdd:COG0583   203 RFLAADELAAGRlVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-295 1.49e-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: 132.34  E-value: 1.49e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPA-TIATLPTLLGMIDAGNGITLLPRSMAQNNGRR 262
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIAlEVDSLEAIKALVAAGLGIALLPESAVEELADG 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1567725624 263 SRVTLAVSDLDASRRYGSLVASKAELSAAATNF 295
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAF 193
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-295 1.08e-36

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: 129.95  E-value: 1.08e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPATIATLP-TLLGMIDAGNGITLLPRSMAQNNGRR 262
Cdd:cd08440    81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMsTALGMVAAGLGVAVLPALALPLADHP 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1567725624 263 SRVTLAVSDLDASRRYGSLVASKAELSAAATNF 295
Cdd:cd08440   161 GLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAF 193
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 14-303 1.87e-36

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: 132.36  E-value: 1.87e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  14 ELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRH 93
Cdd:NF040786    2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  94 FQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAaldGTP---RGLRFQ 170
Cdd:NF040786   82 FDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT---GTKlekKRLVYT 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 171 TLAEEPMLLVVPARHALAGQQAVTMDM--ILPYPLMMldR------YKSLFKRLKdeyAARGAPYNPATIATLP---TLL 239
Cdd:NF040786  159 PFYKDRLVLITPNGTEKYRMLKEEISIseLQKEPFIM--ReegsgtRKEAEKALK---SLGISLEDLNVVASLGsteAIK 233

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567725624 240 GMIDAGNGITLLPR-SMAQNNGRRSRVTLAVSDLDASRRYgSLVASK-AELSAAATNFQGYLRKNF 303
Cdd:NF040786  234 QSVEAGLGISVISElAAEKEVERGRVLIFPIPGLPKNRDF-YLVYNKnRQLSPTAEAFLQFVKERY 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-304 2.82e-33

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: 121.24  E-value: 2.82e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 102 RNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVV 181
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 182 PARHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPA-TIATLPTLLGMIDAGNGITLLPRSMAQNNG 260
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVlEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1567725624 261 RRSR-VTLAVSDLDASRRYGSLVASKAELSAAATNFQGYLRKNFK 304
Cdd:pfam03466 161 ADGRlVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 104-299 3.81e-27

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: 104.93  E-value: 3.81e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08434     1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRyKSLFKRLKDEYAARgAPYNPaTIAT----LPTLLGMIDAGNGITLLPRsMAQNN 259
Cdd:cd08434    81 DHPLAGRDSVDLAELADEPFVLLSP-GFGLRPIVDELCAA-AGFTP-KIAFegeeDSTIAGLVAAGLGVAILPE-MTLLN 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1567725624 260 GRRSRVtLAVSDLDASRRYGSLVASKAELSAAATNFQGYL 299
Cdd:cd08434   157 PPGVKK-IPIKDPDAERTIGLAWLKDRYLSPAARRFKDFV 195
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 104-295 4.03e-26

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: 102.20  E-value: 4.03e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYK--SLFKRLKDEYAARGAPYNPATIAT-LPTLLGMIDAGNGITLLPRSMAqNNG 260
Cdd:cd08414    81 DHPLAARESVSLADLADEPFVLFPREPgpGLYDQILALCRRAGFTPRIVQEASdLQTLLALVAAGLGVALVPASVA-RLQ 159

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1567725624 261 RRSRVTLAVSDLDASRRYgSLVASKAELSAAATNF 295
Cdd:cd08414   160 RPGVVYRPLADPPPRSEL-ALAWRRDNASPALRAF 193
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 21-208 8.94e-26

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 103.88  E-value: 8.94e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  21 FLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRHFQTASDH 100
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 101 ERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLV 180
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALV 168

                         170       180
                  ....*....|....*....|....*....
gi 1567725624 181 VPARHALAGQQ-AVTMDMILPYPLMMLDR 208
Cdd:PRK11242  169 VGRHHPLAARRkALTLDELADEPLVLLSA 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 30-265 6.50e-25

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 101.64  E-value: 6.50e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  30 FSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAvagLRDALRHFQTASDHERNT---VT 106
Cdd:PRK11151   18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTV---LREVKVLKEMASQQGETMsgpLH 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 107 VAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHA 186
Cdd:PRK11151   95 IGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPLFDEPMLLAVYEDHP 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 187 LAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPATIAT-LPTLLGMIDAGNGITLLPRSMAQNNGRRSRV 265
Cdd:PRK11151  175 WANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATsLETLRNMVAAGSGITLLPALAVPNERKRDGV 254
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 104-277 7.88e-24

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: 96.05  E-value: 7.88e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08411     2 PLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPATIAT-LPTLLGMIDAGNGITLLPRSMAQNNGRR 262
Cdd:cd08411    82 DHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATsLETLRQMVAAGLGITLLPELAVPSEELR 161

                         170
                  ....*....|....*..
gi 1567725624 263 SR--VTLAVSDLDASRR 277
Cdd:cd08411   162 GDrlVVRPFAEPAPSRT 178
PRK09986 PRK09986
LysR family transcriptional regulator;
7-257 1.22e-23

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 97.87  E-value: 1.22e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624   7 PPSLTRLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAG 86
Cdd:PRK09986    1 MERLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  87 LRDALRHFQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAV--AALDGTP 164
Cdd:PRK09986   81 AEQSLARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 165 RGLRFQTLAEEPMLLVVPARHALAGQQAVTMDMILPYPLMMLDRYKSLF-KRLKDeyAARGAPYNPATI--ATLP-TLLG 240
Cdd:PRK09986  161 PGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWgKFLQR--VCQQAGFSPQIIrqVNEPqTVLA 238

                         250
                  ....*....|....*..
gi 1567725624 241 MIDAGNGITLLPRSMAQ 257
Cdd:PRK09986  239 MVSMGIGITLLPDSYAQ 255
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 104-251 2.86e-23

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: 94.55  E-value: 2.86e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPA-TIATLPTLLGMIDAGNGITLL 251
Cdd:cd08415    81 GHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIViETQLSHTACALVAAGLGVAIV 149
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-256 2.69e-22

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 94.45  E-value: 2.69e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGE------RLR-EAAERAVA 85
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEvflqdaRAIlEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  86 GLRDALRhfqtasdhERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPR 165
Cdd:PRK09906   81 RARKIVQ--------EDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSD 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 166 GLRFQTLAEEPMLLVVPARHALAGQQAVTM------DMILPYPlmmlDRYKSLFKRLKDEYAARGAPYNPATIAT-LPTL 238
Cdd:PRK09906  153 EIDYLELLDEPLVVVLPVDHPLAHEKEITAaqldgvNFISTDP----AYSGSLAPIIKAWFAQHNSQPNIVQVATnILVT 228

                         250
                  ....*....|....*...
gi 1567725624 239 LGMIDAGNGITLLPRSMA 256
Cdd:PRK09906  229 MNLVGMGLGCTIIPGYMN 246
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-189 3.24e-22

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 94.30  E-value: 3.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624   2 NKSSDPPSLTRLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAE 81
Cdd:PRK10086    3 LREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  82 RAVAGLRDALRHFQTASdhERNTVTVAVTPMLSATVMPSLIHAYTERYPDvrIVLHDLPYDQVIREVAEGrADLAVAALD 161
Cdd:PRK10086   83 SSLDTLNQEILDIKNQE--LSGTLTVYSRPSIAQCWLVPRLADFTRRYPS--ISLTILTGNENVNFQRAG-IDLAIYFDD 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1567725624 162 GTPRGLRFQTLAEEPMLLVVPA----RHALAG 189
Cdd:PRK10086  158 APSAQLTHHFLMDEEILPVCSPeyaeRHALTG 189
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
24-207 7.13e-22

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 93.50  E-value: 7.13e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  24 VVREG-SFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEA-TPDGERLREAAERAVAGLRDALRHFQTASDHE 101
Cdd:PRK12684   12 AVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGlTEPGRIILASVERILQEVENLKRVGKEFAAQD 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 102 RNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAaldgTPRGLRFQTLAEEP----- 176
Cdd:PRK12684   92 QGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIA----TEAIADYKELVSLPcyqwn 167

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1567725624 177 MLLVVPARHALAGQQAVTMDMILPYPLMMLD 207
Cdd:PRK12684  168 HCVVVPPDHPLLERKPLTLEDLAQYPLITYD 198
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-299 8.66e-22

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: 90.83  E-value: 8.66e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPATIAT-LPTLLGMIDAGNGITLLPRSMAQNNGRR 262
Cdd:cd08426    81 GHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNsIETLKQLVAAGGGISLLTELAVRREIRR 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1567725624 263 SR-VTLAVSDLDASRRYGSLVA-SKAELSAAATNFQGYL 299
Cdd:cd08426   161 GQlVAVPLADPHMNHRQLELQTrAGRQLPAAASAFLQLL 199
rbcR CHL00180
LysR transcriptional regulator; Provisional
 15-188 3.63e-21

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 91.23  E-value: 3.63e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  15 LAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRHF 94
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  95 QTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVaaLDG-TPRGLR----F 169
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI--VGGeVPTELKkileI 164

                         170
                  ....*....|....*....
gi 1567725624 170 QTLAEEPMLLVVPARHALA 188
Cdd:CHL00180  165 TPYVEDELALIIPKSHPFA 183
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-299 6.78e-21

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: 88.35  E-value: 6.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTpmLSATV--MPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVV 181
Cdd:cd08421     1 HVRLLAN--TSAIVefLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 182 PARHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNP-ATIATLPTLLGMIDAGNGITLLPRSMAQNNG 260
Cdd:cd08421    79 PRDHPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLrVQVSSFDAVCRMVAAGLGIGIVPESAARRYA 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1567725624 261 RRSRVT-LAVSDLDASRRYGSLVASKAELSAAATNFQGYL 299
Cdd:cd08421   159 RALGLRvVPLDDAWARRRLLLCVRSFDALPPAARALVDHL 198
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 15-203 2.77e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 88.89  E-value: 2.77e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  15 LAELETFLWVVREG-SFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEA-TPDGERLREAAERAvagLRDALR 92
Cdd:PRK12682    3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIERI---LREVGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  93 HFQTASDHERN---TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAaldgTPRGLRF 169
Cdd:PRK12682   80 IKRIGDDFSNQdsgTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA----TESLADD 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1567725624 170 QTLAEEP-----MLLVVPARHALAGQQAVTMDMILPYPL 203
Cdd:PRK12682  156 PDLATLPcydwqHAVIVPPDHPLAQEERITLEDLAEYPL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
15-74 4.13e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.05  E-value: 4.13e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  15 LAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGE 74
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 104-299 1.11e-19

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: 85.02  E-value: 1.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAAL--DGTPRGLRFQTLAEEPMLLVV 181
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLadDEQPPDLASEELADEPLVVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 182 PARHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARG--APYNPATIATLPTLLGMIDAGNGITLLPRSMAQNN 259
Cdd:cd08435    81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGlpLPRNVVETASISALLALLARSDMLAVLPRSVAEDE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1567725624 260 GRRSRVT-LAVSDLDASRRYGSLVASKAELSAAATNFQGYL 299
Cdd:cd08435   161 LRAGVLReLPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 104-273 1.39e-19

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: 84.53  E-value: 1.39e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDeyAARGAPYNPATIA--TLPTLLG-MIDAGNGITLLPRSMAQ--N 258
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIID--ACQQAGFTPNIAArsSQWDFIAeLVAAGLGVALLPRSIAQrlD 158

                         170
                  ....*....|....*
gi 1567725624 259 NGRRSRVTLAVSDLD 273
Cdd:cd08438   159 NAGVKVIPLTDPDLR 173
PRK09791 PRK09791
LysR family transcriptional regulator;
11-255 2.55e-19

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 86.35  E-value: 2.55e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  11 TRLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDA 90
Cdd:PRK09791    3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  91 LRHFQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTP--RGLR 168
Cdd:PRK09791   83 QEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPydHEFT 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 169 FQTLAEEPMLLVVPARHALagQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARG-APYNPATIATLPTLLGMIDAGNG 247
Cdd:PRK09791  163 FEKLLEKQFAVFCRPGHPA--IGARSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAqTPQVGVVCETFSACISLVAKSDF 240


                  ....*...
gi 1567725624 248 ITLLPRSM 255
Cdd:PRK09791  241 LSILPEEM 248
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 15-256 6.00e-19

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 85.12  E-value: 6.00e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  15 LAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGE----------RLREAAERAV 84
Cdd:PRK11233    3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKilytharailRQCEQAQLAV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  85 AGLRDALrhfqtasdheRNTVTVAVTP--MLSATVMPsLIHAYTERYPDVRIVLHDlPYDQVIRE-VAEGRADLAVAALD 161
Cdd:PRK11233   83 HNVGQAL----------SGQVSIGLAPgtAASSLTMP-LLQAVRAEFPGIVLYLHE-NSGATLNEkLMNGQLDMAVIYEH 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 162 GTPRGLRFQTLAEEPMLLVVParHALAGQQ-----AVTMDMILPYPlmmldrYKSLFKRLKDEYAARGAPYN-PATIATL 235
Cdd:PRK11233  151 SPVAGLSSQPLLKEDLFLVGT--QDCPGQSvdlaaVAQMNLFLPRD------YSAVRLRVDEAFSLRRLTAKvIGEIESI 222

                         250       260
                  ....*....|....*....|.
gi 1567725624 236 PTLLGMIDAGNGITLLPRSMA 256
Cdd:PRK11233  223 ATLTAAIASGMGVTVLPESAA 243
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 104-292 3.04e-18

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: 81.10  E-value: 3.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDlPYDQVIRE-VAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVP 182
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVE-GLSGHLLEwLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 183 ARHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPAT-IATLPTLLGMIDAGNGITLLPRSMAQNNGR 261
Cdd:cd08433    80 ADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVeIDSVATLKALVAAGLGYTILPASAVAAEVA 159

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1567725624 262 RSRVTLAVSDLDASRRYGSLVASKA-ELSAAA 292
Cdd:cd08433   160 AGRLVAAPIVDPALTRTLSLATPRDrPLSPAA 191
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 24-215 3.59e-18

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 83.07  E-value: 3.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  24 VVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGER-LREAaeRAVAGLRDALRH-FQTASDHE 101
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWfVKEA--RSVIKKMQETRRqCQQVANGW 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 102 RNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQ--TLAEEPMLL 179
Cdd:PRK11074   91 RGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAfrDMGMLSWAC 170

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1567725624 180 VVPARHALAG-QQAVTMDMILPYP-LMMLDRYKSLFKR 215
Cdd:PRK11074  171 VVSSDHPLASmDGPLSDDELRPYPsLCLEDTSRTLPKR 208
PRK10341 PRK10341
transcriptional regulator TdcA;
18-295 1.43e-17

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 81.45  E-value: 1.43e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  18 LETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRHFQTA 97
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  98 SDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTprgLRFQTLAEEPM 177
Cdd:PRK10341   92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNE---MKLQDLHVEPL 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 178 L---LVVPARHALAGQQAVTMD------MILPYPLMmlDRYKSLFKRLKDEYAARGapyNPATIATLPTLLGMIDAGNGI 248
Cdd:PRK10341  169 FeseFVLVASKSRTCTGTTTLEslkneqWVLPQTNM--GYYSELLTTLQRNGISIE---NIVKTDSVVTIYNLVLNADFL 243

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1567725624 249 TLLPRSMAQNNGRRSRVTLAVSDLDASRRYGSLVASKAELSAAATNF 295
Cdd:PRK10341  244 TVIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVL 290
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 117-257 3.47e-17

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 78.37  E-value: 3.47e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 117 VMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLA-VAALDGTPRGLRFQTLAEEPMLLVVPARHALAGQQAVTM 195
Cdd:cd08451    15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAfVRPPVARSDGLVLELLLEEPMLVALPAGHPLARERSIPL 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567725624 196 DMILPYPLMMLDRY--KSLFKRLKDeyAARGAPYNPATIATLP---TLLGMIDAGNGITLLPRSMAQ 257
Cdd:cd08451    95 AALADEPFILFPRPvgPGLYDAIIA--ACRRAGFTPRIGQEAPqmaSAINLVAAGLGVSIVPASMRQ 159
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 104-207 5.53e-17

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: 77.58  E-value: 5.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPA 80

                          90       100
                  ....*....|....*....|....
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLD 207
Cdd:cd08412    81 DHPLAGKDEVSLADLAAEPLILLD 104
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-257 6.59e-17

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 79.47  E-value: 6.59e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  12 RLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDAL 91
Cdd:PRK10094    1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  92 RHFQTASDHERNTVTVAVTPML-SATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQ 170
Cdd:PRK10094   81 SELQQVNDGVERQVNIVINNLLyNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 171 T--LAEEPMLLVVPARHALAGQQAV-TMDMILPYPLMML-DRYKSLFKRLkdeyAARGAPYNPATIATLPTLLGMIDAGN 246
Cdd:PRK10094  161 LdpLGSVQWRFVMAADHPLANVEEPlTEAQLRRFPAVNIeDSARTLTKRV----AWRLPGQKEIIVPDMETKIAAHLAGV 236

                         250
                  ....*....|.
gi 1567725624 247 GITLLPRSMAQ 257
Cdd:PRK10094  237 GIGFLPKSLCQ 247
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 24-207 7.25e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 79.32  E-value: 7.25e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  24 VVREG-SFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEA-TPDGERLREAAERAvagLRDA--LRHF-QTAS 98
Cdd:PRK12683   12 AVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGlTEPGKELLQIVERM---LLDAenLRRLaEQFA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  99 DHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAAldgtprglrfQTLAEEPML 178
Cdd:PRK12683   89 DRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAT----------EALDREPDL 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1567725624 179 -----------LVVPARHALAGQQAVTMDMILPYPLMMLD 207
Cdd:PRK12683  159 vsfpyyswhhvVVVPKGHPLTGRENLTLEAIAEYPIITYD 198
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 13-194 1.07e-16

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 78.88  E-value: 1.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLR---- 88
Cdd:PRK11013    4 VSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDrivs 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  89 --DALRHFQTASdherntVTVAVTPMLSATVMPSLIHAYTERYPDVRivLHDLPYDQVIRE--VAEGRADLAVAALDGTP 164
Cdd:PRK11013   84 aaESLREFRQGQ------LSIACLPVFSQSLLPGLCQPFLARYPDVS--LNIVPQESPLLEewLSAQRHDLGLTETLHTP 155

                         170       180       190
                  ....*....|....*....|....*....|
gi 1567725624 165 RGLRFQTLAEEPMLLVVPARHALAGQQAVT 194
Cdd:PRK11013  156 AGTERTELLTLDEVCVLPAGHPLAAKKVLT 185
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
13-109 1.13e-16

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 78.47  E-value: 1.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRtTRRVEATPDGERLREAAERaVAGLRDALR 92
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQ-VALLEADLL 79

                          90
                  ....*....|....*..
gi 1567725624  93 HFQTASDHERNTVTVAV 109
Cdd:PRK13348   80 STLPAERGSPPTLAIAV 96
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 18-109 3.67e-16

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 77.26  E-value: 3.67e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  18 LETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRtTRRVEATPDGERLREAAERAVAGLRDALRHFQTA 97
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLAELPGL 84

                          90
                  ....*....|..
gi 1567725624  98 SDHERNTVTVAV 109
Cdd:TIGR03298  85 APGAPTRLTIAV 96
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 13-257 1.38e-15

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: 75.54  E-value: 1.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVA---GLRD 89
Cdd:NF041036    1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDiedSLMD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  90 ALRHFQtasdhERNTVTVAVTPMLSATVMPSLIHAYTERYPDVrivlHDLPY-----DQVIREVAEGRADLAVAA-LDGT 163
Cdd:NF041036   81 ELKSFK-----GRQRLSICCTPTFGMAHLPGVLNRFMLRNADV----VDLKFlfhspAQALEGIQNKEFDLAIIEhCADL 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 164 PRGlRFQT--LAEEPMLLV-VPARHALAGQqaVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNP-ATIATLPTLL 239
Cdd:NF041036  152 DLG-RFHTypLPQDELVFVsAPSLGLPTPN--VTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLDDfRRVVVSDDLR 228

                         250       260
                  ....*....|....*....|.
gi 1567725624 240 GMID---AGNGITLLPRSMAQ 257
Cdd:NF041036  229 LTIQtvlDGGGISFVSRSLVC 249
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
12-109 1.61e-14

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 72.50  E-value: 1.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  12 RLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRtTRRVEATPDGERLREAAERaVAGLRDAL 91
Cdd:PRK03635    1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQ-VRLLEAEL 78

                          90
                  ....*....|....*...
gi 1567725624  92 RHFQTASDHERNTVTVAV 109
Cdd:PRK03635   79 LGELPALDGTPLTLSIAV 96
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-295 1.72e-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: 70.71  E-value: 1.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGT-PRGLRFQTLAEEPMLLVVP 182
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERrPPGLASRELAREPLVAVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 183 ARHALAGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPATIAT-LPTLLGMIDAGNGITLLPRSMAQNNGR 261
Cdd:cd08436    81 PDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSdVDLLLDLVARGLGVALLPASVAARLPG 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1567725624 262 RSRVTLAvsdlDASRRYGSLVASKAELSAAATNF 295
Cdd:cd08436   161 LAALPLE----PAPRRRLYLAWSAPPPSPAARAF 190
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 117-299 1.86e-14

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: 70.60  E-value: 1.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 117 VMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHALAGQQAVTMD 196
Cdd:cd08420    14 LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 197 MILPYPLMMLDRY----KSLFKRLKdeyAARGAPYNPATIATLPT---LLGMIDAGNGITLLPRSMAQNNGRRSR-VTLA 268
Cdd:cd08420    94 ELAAEPWILREPGsgtrEVFERALA---EAGLDGLDLNIVMELGSteaIKEAVEAGLGISILSRLAVRKELELGRlVALP 170

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1567725624 269 VSDLDASRRYgSLVASK-AELSAAATNFQGYL 299
Cdd:cd08420   171 VEGLRLTRPF-SLIYHKdKYLSPAAEAFLEFL 201
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 118-257 5.42e-14

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: 69.22  E-value: 5.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 118 MPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVA--ALDGTPRGLRFQTLAEEPMLLVVPARHALAGQQAVTM 195
Cdd:cd08449    15 LGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVrfADTLNDPPLASELLWREPMVVALPEEHPLAGRKSLTL 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567725624 196 DMILPYPLMMLDRYKSLFKRLKDEY-AARGapYNPATIATL---PTLLGMIDAGNGITLLPRSMAQ 257
Cdd:cd08449    95 ADLRDEPFVFLRLANSRFADFLINCcLQAG--FTPQITQEVvepQTLMALVAAGFGVALVPESYAR 158
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
38-200 1.18e-13

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 69.46  E-value: 1.18e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  38 HLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGlrdaLRHFQTASDHERNTVT------VAVTP 111
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQ----WQQLRHTLDQQGPSLSgelslfCSVTA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 112 MLSatVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAAL-DGTPRGLRFQTLAEEPMLLVVPARHALAGQ 190
Cdd:PRK11716   78 AYS--HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKpETLPASVAFSPIDEIPLVLIAPALPCPVRQ 155

                         170
                  ....*....|....*..
gi 1567725624 191 QAVT-------MDMILP 200
Cdd:PRK11716  156 QLSQekpdwsrIPFILP 172
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-253 4.67e-13

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: 66.85  E-value: 4.67e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVA-ALDGTP----RGLRFQTLAEEPML 178
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfDYPVTPppddPGLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 179 LVVPARHALAGQQAVTMDmilpyplmmldrykslfkRLKDE---YAARGAPYNPATIATL----------------PTLL 239
Cdd:cd08423    81 LVLPADHPLAGREEVALA------------------DLADEpwiAGCPGSPCHRWLVRACraagftpriaheaddyATVL 142

                         170
                  ....*....|....
gi 1567725624 240 GMIDAGNGITLLPR 253
Cdd:cd08423   143 ALVAAGLGVALVPR 156
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 117-254 1.34e-12

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


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 65.60  E-value: 1.34e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 117 VMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHALAGQQAVTMD 196
Cdd:cd08452    14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIE 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567725624 197 MILPYPLMMLDRykSLFKRLKDEYAA--RGAPYNPATI--AT-LPTLLGMIDAGNGITLLPRS 254
Cdd:cd08452    94 DLRDEPIITVAR--EAWPTLYDEIIQlcEQAGFRPKIVqeATeYQTVIGLVSAGIGVTFVPSS 154
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 117-257 1.34e-12

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: 65.46  E-value: 1.34e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 117 VMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAV---AALDGTPRGLRFQTLAEEPMLLVVPARHALAGQQAV 193
Cdd:cd08453    14 VLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIvipPPGASAPPALAYRPLLSEPLVLAVPAAWAAEGGAPL 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567725624 194 TMDMILPYPLMMLDRY--KSLFKRLKDEYAARGAPYNPATIA-TLPTLLGMIDAGNGITLLPRSMAQ 257
Cdd:cd08453    94 ALAAVAAEPLVIFPRRiaPAFHDAVTGYYRAAGQTPRIAQEAiQMQTIISLVSAGMGVALVPASLRN 160
PRK12680 PRK12680
LysR family transcriptional regulator;
27-251 2.23e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 66.57  E-value: 2.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  27 EGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEA-TPDGerlREAAERAVAGLRDALRHFQTASDHERNT- 104
Cdd:PRK12680   16 ELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESvTPAG---VEVIERARAVLSEANNIRTYAANQRRESq 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 105 --VTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGT-PRGLRFQTLAEEPMLLVV 181
Cdd:PRK12680   93 gqLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGePSAGIAVPLYRWRRLVVV 172

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567725624 182 PARHAL-AGQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPATIATLPTLLGM-IDAGNGITLL 251
Cdd:PRK12680  173 PRGHALdTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTyVRAGLGVGLL 244
cysB PRK12681
HTH-type transcriptional regulator CysB;
31-203 7.58e-12

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 64.92  E-value: 7.58e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  31 SVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRV-EATPDGERLREAAeRAVAGLRDALRhfQTASDH---ERNTVT 106
Cdd:PRK12681   20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIA-REILSKVESIK--SVAGEHtwpDKGSLY 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 107 VAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVA--ALDgtprglRFQTLAeepML------ 178
Cdd:PRK12681   97 IATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIAteALH------LYDDLI---MLpcyhwn 167

                         170       180
                  ....*....|....*....|....*..
gi 1567725624 179 --LVVPARHALAGQQAVTMDMILPYPL 203
Cdd:PRK12681  168 rsVVVPPDHPLAKKKKLTIEELAQYPL 194
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 104-267 2.21e-11

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 61.85  E-value: 2.21e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAgQQAVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYNPAtiATLP---TLLGMIDAGNGITLLPRSMAQNNG 260
Cdd:cd08417    81 DHPLA-GGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVA--LTVPhflAAPALVAGTDLIATVPRRLAEALA 157


                  ....*..
gi 1567725624 261 RRSRVTL 267
Cdd:cd08417   158 ERLGLRV 164
cbl PRK12679
HTH-type transcriptional regulator Cbl;
34-204 2.39e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 63.29  E-value: 2.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  34 ARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEA-TPDGERLREAAERAVAGLRDALRHFQTASDHERNTVTVAVTPM 112
Cdd:PRK12679   23 ANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGmTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHT 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 113 LSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAAldgtprglrfQTLAEEPML-----------LVV 181
Cdd:PRK12679  103 QARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAS----------ERLSNDPQLvafpwfrwhhsLLV 172

                         170       180
                  ....*....|....*....|...
gi 1567725624 182 PARHALAGQQAVTMDMILPYPLM 204
Cdd:PRK12679  173 PHDHPLTQITPLTLESIAKWPLI 195
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-257 2.64e-11

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: 61.51  E-value: 2.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 109 VTPMLsATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHALA 188
Cdd:cd08448     7 VGSML-YRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 189 GQQAVTM------DMILPYPLMMLDRYKSLFKRLKD-------EYAARgapyNPATIATlptllgMIDAGNGITLLPRSM 255
Cdd:cd08448    86 ARRRIDLrelagePFVLFSREVSPDYYDQIIALCMDagfhpkiRHEVR----HWLTVVA------LVAAGMGVALVPRSL 155


                  ..
gi 1567725624 256 AQ 257
Cdd:cd08448   156 AR 157
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
13-281 5.47e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 62.34  E-value: 5.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALr 92
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  93 hfQTASDHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHD-LPYDQViREVAEGRADLAVAAlDGTPR-GLRFQ 170
Cdd:PRK15421   81 --QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSgVTFDPQ-PALQQGELDLVMTS-DILPRsGLHYS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 171 TLAEEPMLLVVPARHALAGQQAVT-----MDMILPYPLM--MLDRYKSLFKrlkdeyAARGAPYNPATIATLpTLLGMID 243
Cdd:PRK15421  157 PMFDYEVRLVLAPDHPLAAKTRITpedlaSETLLIYPVQrsRLDVWRHFLQ------PAGVSPSLKSVDNTL-LLIQMVA 229

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1567725624 244 AGNGITLLPRSMAQNNGRRSR-VTLAVSDLDASRRYGSL 281
Cdd:PRK15421  230 ARMGIAALPHWVVESFERQGLvVTKTLGEGLWSRLYAAV 268
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-254 7.51e-11

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: 60.35  E-value: 7.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08447     1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMML---------DRYKSLFKRlkdeyaARGAPYNPATIATLPTLLGMIDAGNGITLLPRS 254
Cdd:cd08447    81 GHPLAGAERLTLEDLDGQPFIMYsptearyfhDLVVRLFAS------AGVQPRYVQYLSQIHTMLALVRAGLGVALVPAS 154
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 110-256 2.08e-10

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: 59.22  E-value: 2.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 110 TPMLsaTVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHALAG 189
Cdd:cd08446    10 SAIL--DTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVPKSHPLAA 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567725624 190 QQAVTMDMILPYPLMML---------DRYKSLFKRlkdeyaARGAPYNPATIATLPTLLGMIDAGNGITLLPRSMA 256
Cdd:cd08446    88 RPAVSLADLRNEPLILFprggrpsfaDEVLGLFRR------AGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVA 157
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 29-180 2.60e-10

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 60.24  E-value: 2.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  29 SFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRHFQTASDheRNTVTVA 108
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSA--KGALTVS 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567725624 109 VTPMLSAT-VMPSLiHAYTERYP--DVRIVLHDLPYDQVIREVaegraDLAVAALDGTPRGLRFQTLAEEPMLLV 180
Cdd:PRK11139  100 LLPSFAIQwLVPRL-SSFNEAHPdiDVRLKAVDRLEDFLRDDV-----DVAIRYGRGNWPGLRVEKLLDEYLLPV 168
PRK11482 PRK11482
DNA-binding transcriptional regulator;
33-244 5.86e-10

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 59.35  E-value: 5.86e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  33 AARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRDALRhfQTASDHERNTVTVAVTPM 112
Cdd:PRK11482   49 AAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGALD--ITGSYDKQRTITIATTPS 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 113 LSATVMPSLIHAYTERYPdvRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARH-ALAGQQ 191
Cdd:PRK11482  127 VGALVMPVIYQAIKTHYP--QLLLRNIPISDAENQLSQFQTDLIIDTHSCSNRTIQHHVLFTDNVVLVCRQGHpLLSLED 204

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567725624 192 AVTMDMILPYPLMMLD--RYKSLFKRLKDEYAARG---APYNPATIATL---PTLLGMIDA 244
Cdd:PRK11482  205 DEETLDNAEHTLLLPEgqNFSGLRQRLQEMFPDRQisfSSYNILTIAALiasSDMLGIMPS 265
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 104-251 6.62e-10

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: 57.88  E-value: 6.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08457     1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPM 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567725624 184 RHALAGQQAVTMDMILPYPLMMLDrYKSLFkRLKDEYAARGAPYNPATIATL---PTLLGMIDAGNGITLL 251
Cdd:cd08457    81 GHPLAQLDVVSPQDLAGERIITLE-NGYLF-RMRVEVALGKIGVKRRPIIEVnlsHTALSLVREGLGIAII 149
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 106-203 9.55e-10

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 57.25  E-value: 9.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 106 TVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVA--ALDGTPRGLRFqtlaeePM-----L 178
Cdd:cd08413     3 TIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAteALDDHPDLVTL------PCyrwnhC 76

                          90       100
                  ....*....|....*....|....*
gi 1567725624 179 LVVPARHALAGQQAVTMDMILPYPL 203
Cdd:cd08413    77 VIVPPGHPLADLGPLTLEDLAQYPL 101
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 104-196 1.04e-09

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: 57.04  E-value: 1.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08456     1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPP 80

                          90
                  ....*....|...
gi 1567725624 184 RHALAGQQAVTMD 196
Cdd:cd08456    81 GHRLAVKKVLTPS 93
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 115-265 6.60e-09

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: 54.54  E-value: 6.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 115 ATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHALAGQQAVT 194
Cdd:cd08442    12 AVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHPPVSRAEDL 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567725624 195 MDMilpyPLMMLDRYKSLFKRLKDEYAARGAPynPATI---ATLPTLLGMIDAGNGITLLPRSMAQNNGRRSRV 265
Cdd:cd08442    92 AGS----TLLAFRAGCSYRRRLEDWLAEEGVS--PGKImefGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSV 159
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 117-205 7.27e-09

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: 54.82  E-value: 7.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 117 VMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAV-----AALDgtprgLRFQTLAEEPMLLVVPARHALAGQQ 191
Cdd:cd08419    13 FAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAImgrppEDLD-----LVAEPFLDNPLVVIAPPDHPLAGQK 87

                          90
                  ....*....|....
gi 1567725624 192 AVTMDMILPYPLMM 205
Cdd:cd08419    88 RIPLERLAREPFLL 101
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 117-255 8.20e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 54.54  E-value: 8.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 117 VMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHALAGQQA-VTM 195
Cdd:cd08445    15 LLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRIVLREEPLVVALPAGHPLAQEKApLTL 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567725624 196 DMILPYPLM---------MLDRYKSLFkrlkdeyAARGapYNPATIA---TLPTLLGMIDAGNGITLLPRSM 255
Cdd:cd08445    95 AQLADEPLIlypasprpsFADQVLSLF-------RDHG--LRPRVIQevrELQTALGLVAAGEGVTLVPASV 157
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 105-300 1.06e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 54.28  E-value: 1.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 105 VTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAAL--DGTPRGLRFQTLAEEPMLLVV- 181
Cdd:cd08418     2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLpdEMYLKELISEPLFESDFVVVAr 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 182 ---PARHALAGQQAVTMDMILPYPLMmlDRYKSLFKRLKDeyaARGAPYNPATIATLPTLLGMIDAGNGITLLPRSMAQN 258
Cdd:cd08418    82 kdhPLQGARSLEELLDASWVLPGTRM--GYYNNLLEALRR---LGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRG 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1567725624 259 NGRRSR-VTLAVSDLDASRRYGSLVASKAELSAAATNFQGYLR 300
Cdd:cd08418   157 PLDSFRlITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFR 199
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 107-208 1.09e-08

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: 54.26  E-value: 1.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 107 VAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHA 186
Cdd:cd08425     5 LAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHP 84

                          90       100
                  ....*....|....*....|...
gi 1567725624 187 LAGQ-QAVTMDMILPYPLMMLDR 208
Cdd:cd08425    85 LAQRrTALTLDDLAAEPLALLSP 107
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
14-73 1.34e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 55.15  E-value: 1.34e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  14 ELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDG 73
Cdd:PRK10632    3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAG 62
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 111-252 1.40e-08

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: 53.92  E-value: 1.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 111 PMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHALAGQ 190
Cdd:cd08450     8 PGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGR 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567725624 191 QAVTMDMILPYPLMMLDRYKSLFKRLKDEYAAR-GAPYNPATIA-TLPTLLGMIDAGNGITLLP 252
Cdd:cd08450    88 EKIPPQDLAGENFISPAPTAPVLQQVIENYAAQhNIQPNIIQEAdNLLSAMSLVASTLGCALLP 151
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 12-155 6.27e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 53.15  E-value: 6.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  12 RLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLreaAERAVAGLRDAL 91
Cdd:PRK10837    2 HITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLL---YPRALALLEQAV 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567725624  92 ---RHFQtasdHERNTVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADL 155
Cdd:PRK10837   79 eieQLFR----EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDI 141
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-261 8.77e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 51.51  E-value: 8.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08461     1 TLVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 184 RHALAgQQAVTMDMI--LPYPLMMLDRYKslFKRLKDE-YAARGAPYNPATIAT----LPTLLGMIDAgngITLLPRSMA 256
Cdd:cd08461    81 GHPLL-QGPLSLDQFcaLDHIVVSPSGGG--FAGSTDEaLAALGLTRNVVLSVPsflvVPEILAATDM---VAFVPSRLV 154


                  ....*
gi 1567725624 257 QNNGR 261
Cdd:cd08461   155 PNLEG 159
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 17-136 1.30e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.30  E-value: 1.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  17 ELETFLW---VVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERL----------REAAERA 83
Cdd:PRK14997    3 DLNDFAWfvhVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFyehckamlveAQAAQDA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1567725624  84 VAGLRDALRHFQtasdhernTVTVAVTpMLSATVMPSLIHaYTERYPDVRIVL 136
Cdd:PRK14997   83 IAALQVEPRGIV--------KLTCPVT-LLHVHIGPMLAK-FMARYPDVSLQL 125
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 118-200 1.57e-07

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: 50.66  E-value: 1.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 118 MPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAAL-DGTPRGLRFQTLAEEPMLLVVPARHALAGQQAVTMD 196
Cdd:cd08430    15 LPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARpDKLPARLAFLPLATSPLVFIAPNIACAVTQQLSQGE 94

                          90
                  ....*....|.
gi 1567725624 197 -------MILP 200
Cdd:cd08430    95 idwsrlpFILP 105
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
10-154 2.81e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 51.21  E-value: 2.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  10 LTRLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAERAVAGLRD 89
Cdd:PRK10082    8 LHNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLES 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567725624  90 ALRHFQTASDHERNTVTVAVTPMLSATVMPSLIhayTERYPDVRIVLHDLPYDQVIREVAEGRAD 154
Cdd:PRK10082   88 NLAELRGGSDYAQRKIKIAAAHSLSLGLLPSII---SQMPPLFTWAIEAIDVDEAVDKLREGQSD 149
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
18-81 3.54e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.79  E-value: 3.54e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567725624  18 LETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAAE 81
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAE 69
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 107-256 1.08e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176158  Cd Length: 221  Bit Score: 48.56  E-value: 1.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 107 VAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPARHA 186
Cdd:cd08469     4 IAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIFEQIPPRFRRRTLFDEDEVWVMRKDHP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 187 LAGqQAVTMDMILPYPLMM-------------------LDRYKSLFKRLKDEYAARGAPYNPATIATLPTLLG---MIDA 244
Cdd:cd08469    84 AAR-GALTIETLARYPHIVvslggeeegavsgfisergLARQTEMFDRRALEEAFRESGLVPRVAVTVPHALAvppLLAD 162

                         170
                  ....*....|..
gi 1567725624 245 GNGITLLPRSMA 256
Cdd:cd08469   163 SDMLALLPRSLA 174
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 105-204 1.74e-06

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176134  Cd Length: 198  Bit Score: 47.94  E-value: 1.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 105 VTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVA--ALDgtprglRFQTLAEEP-----M 177
Cdd:cd08443     2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIAteALH------DYDDLITLPcyhwnR 75

                          90       100
                  ....*....|....*....|....*..
gi 1567725624 178 LLVVPARHALAGQQAVTMDMILPYPLM 204
Cdd:cd08443    76 CVVVKRDHPLADKQSISIEELATYPIV 102
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 105-257 4.14e-06

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 46.66  E-value: 4.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 105 VTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPAR 184
Cdd:cd08467     2 FTLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRHG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567725624 185 HALAGQQaVTMDMILPYPLMMLDRYKSLFKRLKDEYAARGAPYN-PATIATLPTLLGMIDAGNGITLLPRSMAQ 257
Cdd:cd08467    82 HPALAQE-WTLDDFATLRHVAIAPPGRLFGGIYKRLENLGLKRNvAIAVSSFLTAAATVAATDLIATVPRRVAT 154
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 105-204 4.67e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl 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 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: 176135  Cd Length: 198  Bit Score: 46.34  E-value: 4.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 105 VTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVA--ALDGTPRGLRFQTLAEEPMLLvVP 182
Cdd:cd08444     2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIAteALENHPELVSFPYYDWHHHII-VP 80

                          90       100
                  ....*....|....*....|..
gi 1567725624 183 ARHALAGQQAVTMDMILPYPLM 204
Cdd:cd08444    81 VGHPLESITPLTIETIAKWPII 102
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-299 1.31e-05

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 45.26  E-value: 1.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 108 AVTPMLSaTVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAA--LDGTPRGLRFQTLAEEPMLLVVPARH 185
Cdd:cd08427     6 AIATVLT-GLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVepPFPLPKDLVWTPLVREPLVLIAPAEL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 186 ALAGQQAVTMDmilpYPLMMLDRyKSLFKRLKDEY--AARGAPYNPATIATLPTLLGMIDAGNGITLLPRSMAQNNGRRS 263
Cdd:cd08427    85 AGDDPRELLAT----QPFIRYDR-SAWGGRLVDRFlrRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGPR 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1567725624 264 RVTLAVSDLDASRRYGSLVASKAELSAAATNFQGYL 299
Cdd:cd08427   160 VRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PRK09801 PRK09801
LysR family transcriptional regulator;
17-80 2.14e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 45.41  E-value: 2.14e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567725624  17 ELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGERLREAA 80
Cdd:PRK09801   10 DLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHA 73
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 104-191 2.24e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 44.49  E-value: 2.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08459     1 TFRIAMSDIGEMYFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRK 80


                  ....*...
gi 1567725624 184 RHALAGQQ 191
Cdd:cd08459    81 DHPRIGST 88
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-196 3.28e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 43.84  E-value: 3.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLP--YDQViREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVV 181
Cdd:cd08463     1 TFRIAAPDYLNALFLPELVARFRREAPGARLEIHPLGpdFDYE-RALASGELDLVIGNWPEPPEHLHLSPLFSDEIVCLM 79

                          90
                  ....*....|....*
gi 1567725624 182 PARHALAGQQAVTMD 196
Cdd:cd08463    80 RADHPLARRGLMTLD 94
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
13-115 1.28e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 41.49  E-value: 1.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  13 LELAELETFLWVVREGSFSVA--ARKLHLSQPAVTNRVKRLEDKlhvKLLVRTT-------RRVEATPDGERLREAAERA 83
Cdd:COG1846    36 LTPAQFRVLAALAEAGGLTQSelAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEARPA 112

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1567725624  84 VAGLRDALrhFQTASDHERNTVTVAVTPMLSA 115
Cdd:COG1846   113 LEALLAEL--LAGLSEEELEALLRLLRRLAEN 142
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
26-102 5.33e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 38.73  E-value: 5.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624   26 REGSFSVA--ARKLHLSQPAVTNRVKRLEDKLHVKLLV----RTTRRVEATPDGERLREAAERAVAGLRDALrhFQTASD 99
Cdd:smart00347  21 EEGPLSVSelAKRLGVSPSTVTRVLDRLEKKGLVRREPspedRRSVLVSLTEEGRELIEQLLEARSETLAEL--LAGLTA 98


                   ...
gi 1567725624  100 HER 102
Cdd:smart00347  99 EEQ 101
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
9-165 5.36e-04

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 40.96  E-value: 5.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624   9 SLTRLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPdgerLREAAERAVAG-- 86
Cdd:PRK10216    4 SLTTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTP----LMVSMEQNLAEwm 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624  87 -----LRDAlRHFQTASDHErntVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQvIREVAEGRADLAVAALD 161
Cdd:PRK10216   80 qmgnqLLDK-PHHQTPRGLK---FELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDYDS-LDAITRGEVDIGFTGRE 154


                  ....
gi 1567725624 162 GTPR 165
Cdd:PRK10216  155 SHPR 158
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 104-202 6.37e-04

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


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 39.94  E-value: 6.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHdlpydqviREV--------AEGRADLAVAALDGTPRG-LRFQTLAE 174
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLS--------EEVlggtwdalASGRADLVIGATGELPPGgVKTRPLGE 72

                          90       100
                  ....*....|....*....|....*....
gi 1567725624 175 EPMLLVVPARHALAG-QQAVTMDMILPYP 202
Cdd:cd08431    73 VEFVFAVAPNHPLAKlDGPLDASAIKQYP 101
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-196 8.27e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 39.91  E-value: 8.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 104 TVTVAVTPMLSATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAALDGTPRGLRFQTLAEEPMLLVVPA 183
Cdd:cd08464     1 TFRIGLSDDVESWLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFDP 80

                          90
                  ....*....|...
gi 1567725624 184 RHaLAGQQAVTMD 196
Cdd:cd08464    81 QQ-LSLSAPLTLE 92
nhaR PRK11062
transcriptional activator NhaR; Provisional
 21-74 9.24e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 40.38  E-value: 9.24e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1567725624  21 FLWVV-REGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEATPDGE 74
Cdd:PRK11062   11 YFWMVcKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGE 65
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 115-255 1.93e-03

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 38.47  E-value: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 115 ATVMPSLIHAYTERYPDVRIVLHDLPYDQVIREVAEGRADLAVAAldGTPRGLRFQTLAEEPMLLVVPARHALAGQQavt 194
Cdd:cd08439    12 DTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALIT--HPPPGASATILRRSPTVWYCAAGYILAPGE--- 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567725624 195 mdmilPYPLMMLDRyKSLFKRL-KDEYAARGAPYNPATIA-TLPTLLGMIDAGNGITLLPRSM 255
Cdd:cd08439    87 -----PLPLALLDE-PTLDRRAaLAALDAAGIPWRIAYAAsSLSGLRAAVRAGLGITARTQEM 143
leuO PRK09508
leucine transcriptional activator; Reviewed
 2-70 4.84e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 38.08  E-value: 4.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1567725624   2 NKSSDPPSLTRLELAELETFLWVVREGSFSVAARKLHLSQPAVTNRVKRLEDKLHVKLLVRTTRRVEAT 70
Cdd:PRK09508   11 TKESSEPQLRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPT 79
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 118-253 7.49e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 36.78  E-value: 7.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567725624 118 MPSLiHAYTERYPDVrivlhDLPYDQV-----IREVAEGRADLAVAAlDGTPR-GLRFQTLAEEPMLLVVPARHALAGQQ 191
Cdd:cd08441    16 MPVL-DQFRERWPDV-----ELDLSSGfhfdpLPALLRGELDLVITS-DPLPLpGIAYEPLFDYEVVLVVAPDHPLAAKE 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1567725624 192 AVT----MDMIL---PYPLMMLDRYKSLFKRLKDEYAARgapynpATIATLPTLLGMIDAGNGITLLPR 253
Cdd:cd08441    89 FITpedlADETLityPVERERLDVFRHFLQPAGIEPKRR------RTVELTLMILQLVASGRGVAALPN 151
 
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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