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Conserved domains on  [gi|446875247|ref|WP_000952503|]
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MULTISPECIES: transcriptional regulator CynR [Enterobacteriaceae]

Protein Classification

transcriptional regulator CynR( domain architecture ID 11485281)

LysR family transcriptional regulator CynR positively regulates the cynTSX operon, and negatively regulates its own transcription

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-294 4.23e-177

DNA-binding transcriptional regulator CynR; Provisional


:

Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 490.62  E-value: 4.23e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPLAVHEQ-VALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTL 239
Cdd:PRK11242 161 FTETLALVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATL 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446875247 240 LPAAIATQHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCAVVG 294
Cdd:PRK11242 241 LPAAIAREHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAEIG 295
 
Name Accession Description Interval E-value
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-294 4.23e-177

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 490.62  E-value: 4.23e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPLAVHEQ-VALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTL 239
Cdd:PRK11242 161 FTETLALVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATL 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446875247 240 LPAAIATQHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCAVVG 294
Cdd:PRK11242 241 LPAAIAREHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAEIG 295
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-286 2.76e-106

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: 307.33  E-value: 2.76e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVA 170
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPLAVHEQV-ALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHD 249
Cdd:cd08425   81 ATHPLAQRRTAlTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAREQP 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446875247 250 GLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMA 286
Cdd:cd08425  161 GLCAVALEPPLPGRTAALLRRKGAYRSAAARAFAALA 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 1.06e-67

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 211.26  E-value: 1.06e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPLAVHEQValsrlhdeklvllsaefatreqidhycekaglhpqvvieANSISAVLELIRRTSLSTLL 240
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446875247 241 PAAIATQH---DGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCA 291
Cdd:COG0583  202 PRFLAADElaaGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 1.08e-49

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: 163.61  E-value: 1.08e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   90 RGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  170 AQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQ-- 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARel 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 446875247  248 -HDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCA 291
Cdd:pfam03466 161 aDGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-289 1.20e-35

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 130.04  E-value: 1.20e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQElgaGKRAIH 83
Cdd:NF040786   4 KQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDL---WEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  84 DVADLT---RGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:NF040786  81 EFDRYGkesKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPL--AVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHP---QVVIEANSISAVLELIRR-- 233
Cdd:NF040786 161 YKDRLVLITPNGTEKyrMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLedlNVVASLGSTEAIKQSVEAgl 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446875247 234 --TSLSTL-LPAAIATQHdgLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDK 289
Cdd:NF040786 241 giSVISELaAEKEVERGR--VLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKER 297
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 4-215 1.77e-35

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 129.45  E-value: 1.77e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247    4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIH 83
Cdd:TIGR02424   6 RHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVASLS 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   84 DVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELD--VGIAFAPVHSPELEAIPLL 161
Cdd:TIGR02424  86 QLGEGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDlvVGRLGAPETMQGLSFEHLY 165

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446875247  162 TESLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHP 215
Cdd:TIGR02424 166 NEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPP 219
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-145 1.19e-14

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: 72.85  E-value: 1.19e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRAL---QELGA 77
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILdieDSLMD 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446875247  78 GKRAIHDvadltRGSLRIAVTPTFTSYFIGPLMADFYARYPSIT-LQLQEMSQEKIEDMLCRDELDVGI 145
Cdd:NF041036  81 ELKSFKG-----RQRLSICCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDLAI 144
 
Name Accession Description Interval E-value
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-294 4.23e-177

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 490.62  E-value: 4.23e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPLAVHEQ-VALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTL 239
Cdd:PRK11242 161 FTETLALVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATL 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446875247 240 LPAAIATQHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCAVVG 294
Cdd:PRK11242 241 LPAAIAREHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAEIG 295
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-286 2.76e-106

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: 307.33  E-value: 2.76e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVA 170
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPLAVHEQV-ALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHD 249
Cdd:cd08425   81 ATHPLAQRRTAlTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAREQP 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446875247 250 GLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMA 286
Cdd:cd08425  161 GLCAVALEPPLPGRTAALLRRKGAYRSAAARAFAALA 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 1.06e-67

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 211.26  E-value: 1.06e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPLAVHEQValsrlhdeklvllsaefatreqidhycekaglhpqvvieANSISAVLELIRRTSLSTLL 240
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446875247 241 PAAIATQH---DGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCA 291
Cdd:COG0583  202 PRFLAADElaaGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-286 1.03e-54

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: 176.25  E-value: 1.03e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIAT--QHD 249
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEelADG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446875247 250 GLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMA 286
Cdd:cd05466  161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 1.08e-49

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: 163.61  E-value: 1.08e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   90 RGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  170 AQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQ-- 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARel 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 446875247  248 -HDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCA 291
Cdd:pfam03466 161 aDGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-285 7.21e-38

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: 132.65  E-value: 7.21e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQH 172
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAI--ATQHDG 250
Cdd:cd08440   82 HPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALAlpLADHPG 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446875247 251 LKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHM 285
Cdd:cd08440  162 LVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDL 196
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 19-221 1.79e-37

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 135.12  E-value: 1.79e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  19 TRAASALHVSQPALSQQIRQLEESLGVPLFDRSG-RTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADLTRGSLRIAV 97
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  98 TPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPV-HSPELEAIPLLTESLALVVAQHHPLA 176
Cdd:PRK12682 100 THTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLaDDPDLATLPCYDWQHAVIVPPDHPLA 179

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446875247 177 VHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA 221
Cdd:PRK12682 180 QEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEA 224
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
19-221 3.01e-37

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 134.33  E-value: 3.01e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  19 TRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIR-LTDAGEVWRQYASRALQELGAGKRAIHDVADLTRGSLRIAV 97
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  98 TPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAF-APVHSPELEAIPLLTESLALVVAQHHPLA 176
Cdd:PRK12684 100 THTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATeAIADYKELVSLPCYQWNHCVVVPPDHPLL 179

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446875247 177 VHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA 221
Cdd:PRK12684 180 ERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEA 224
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-246 6.69e-37

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 133.36  E-value: 6.69e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRgSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQ--IDHYCEKAGLHPQVVIEANSISAVLELIRRTSLST 238
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLApiIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239


                 ....*...
gi 446875247 239 LLPAAIAT 246
Cdd:PRK09906 240 IIPGYMNN 247
rbcR CHL00180
LysR transcriptional regulator; Provisional
 11-243 1.66e-36

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 132.45  E-value: 1.66e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  11 AVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADLTR 90
Cdd:CHL00180  15 AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVhSPELEAI----PLLTESLA 166
Cdd:CHL00180  95 GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEV-PTELKKIleitPYVEDELA 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 167 LVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHP---QVVIEANSISAVlelirRTSLSTLLPAA 243
Cdd:CHL00180 174 LIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSkrfKIEMELNSIEAI-----KNAVQSGLGAA 248
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-289 1.20e-35

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 130.04  E-value: 1.20e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQElgaGKRAIH 83
Cdd:NF040786   4 KQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDL---WEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  84 DVADLT---RGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:NF040786  81 EFDRYGkesKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 161 LTESLALVVAQHHPL--AVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHP---QVVIEANSISAVLELIRR-- 233
Cdd:NF040786 161 YKDRLVLITPNGTEKyrMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLedlNVVASLGSTEAIKQSVEAgl 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446875247 234 --TSLSTL-LPAAIATQHdgLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDK 289
Cdd:NF040786 241 giSVISELaAEKEVERGR--VLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKER 297
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 4-215 1.77e-35

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 129.45  E-value: 1.77e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247    4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIH 83
Cdd:TIGR02424   6 RHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVASLS 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   84 DVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELD--VGIAFAPVHSPELEAIPLL 161
Cdd:TIGR02424  86 QLGEGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDlvVGRLGAPETMQGLSFEHLY 165

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446875247  162 TESLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHP 215
Cdd:TIGR02424 166 NEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPP 219
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 93-283 2.97e-35

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: 126.13  E-value: 2.97e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQH 172
Cdd:cd08438    2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHD--G 250
Cdd:cd08438   82 HPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDnaG 161

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446875247 251 LKAISLAPPLLERTAVLLRRKNSWQTAAAKAFL 283
Cdd:cd08438  162 VKVIPLTDPDLRWQLALIWRKGRYLSHAARAWL 194
PRK09986 PRK09986
LysR family transcriptional regulator;
4-245 6.37e-35

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 127.92  E-value: 6.37e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIH 83
Cdd:PRK09986  10 KLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  84 DVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGI--AFAPVHSPELEAIPLL 161
Cdd:PRK09986  90 QIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTSRRLH 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 162 TESLALVVAQHHPLAVHEQVALSRLHDEKLVLLS---AEFAtrEQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLST 238
Cdd:PRK09986 170 ESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPfvhSDWG--KFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGIT 247


                 ....*..
gi 446875247 239 LLPAAIA 245
Cdd:PRK09986 248 LLPDSYA 254
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 93-282 1.17e-34

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: 124.19  E-value: 1.17e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQH 172
Cdd:cd08434    2 VRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHDGLK 252
Cdd:cd08434   82 HPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLNPPGVK 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 446875247 253 AISLAPPLLERTAVLLRRKNSWQTAAAKAF 282
Cdd:cd08434  162 KIPIKDPDAERTIGLAWLKDRYLSPAARRF 191
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 19-270 2.25e-34

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 126.70  E-value: 2.25e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  19 TRAASALHVSQPALSQQIRQLEESLGVPLFDRSG-RTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADLTRGSLRIAV 97
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  98 TPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHS-PELEAIPLLTESLALVVAQHHPLA 176
Cdd:PRK12683 100 THTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDRePDLVSFPYYSWHHVVVVPKGHPLT 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 177 VHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVV---IEANSISAVLELirrtSLSTLLPAAIA--TQHD-G 250
Cdd:PRK12683 180 GRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVltaLDADVIKTYVEL----GMGVGIVAAMAydPQRDtG 255

                        250       260
                 ....*....|....*....|..
gi 446875247 251 LKAISlAPPLLER--TAVLLRR 270
Cdd:PRK12683 256 LVALD-TDHLFEAntTRVGLRR 276
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-273 6.54e-34

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 125.53  E-value: 6.54e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGI-AFAPVHSPELEaIP 159
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIlALVKESEAFIE-VP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 160 LLTESLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTL 239
Cdd:PRK11151 160 LFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITL 239

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 446875247 240 LPAAIAT---QHDGLKAISLAPPLLERTAVLLRRKNS 273
Cdd:PRK11151 240 LPALAVPnerKRDGVCYLPCIKPEPRRTIGLVYRPGS 276
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-286 1.69e-33

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: 121.46  E-value: 1.69e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFAT--REQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA-TQH 248
Cdd:cd08414   81 DHPLAARESVSLADLADEPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVArLQR 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446875247 249 DGLKAISLAPPLLERTAVLLRRKNSwQTAAAKAFLHMA 286
Cdd:cd08414  161 PGVVYRPLADPPPRSELALAWRRDN-ASPALRAFLELA 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-283 3.37e-33

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: 120.67  E-value: 3.37e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHP---QVVIEANSISAVLELIRR----TSLSTLlpaAI 244
Cdd:cd08420   81 DHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGldlNIVMELGSTEAIKEAVEAglgiSILSRL---AV 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446875247 245 AT--QHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFL 283
Cdd:cd08420  158 RKelELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFL 198
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 9-170 1.58e-31

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 118.79  E-value: 1.58e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   9 FLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGevwRQYASR---ALQELGAGKRAIHDV 85
Cdd:PRK11139  14 FEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG---QRYFLDireIFDQLAEATRKLRAR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  86 ADltRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQemSQEKIEDMLcRDELDVGIAFAPVHSPELEAIPLLTESL 165
Cdd:PRK11139  91 SA--KGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLK--AVDRLEDFL-RDDVDVAIRYGRGNWPGLRVEKLLDEYL 165


                 ....*
gi 446875247 166 ALVVA 170
Cdd:PRK11139 166 LPVCS 170
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-286 1.24e-27

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: 106.07  E-value: 1.24e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVA 170
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPA----AIAT 246
Cdd:cd08411   81 KDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPElavpSEEL 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446875247 247 QHDGLKAISLAPPLLERTAVLLRRKNSwqtAAAKAFLHMA 286
Cdd:cd08411  161 RGDRLVVRPFAEPAPSRTIGLVWRRSS---PRAAAFEALA 197
cysB PRK12681
HTH-type transcriptional regulator CysB;
8-221 9.88e-27

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 106.52  E-value: 9.88e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   8 YFLAVAEHG-SFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTI-RLTDAGEVWRQYASRALQELGAGKRAIHDV 85
Cdd:PRK12681   8 YIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESIKSVAGEH 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  86 ADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAfapvhspeLEAIPLLTESL 165
Cdd:PRK12681  88 TWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIA--------TEALHLYDDLI 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446875247 166 AL---------VVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA 221
Cdd:PRK12681 160 MLpcyhwnrsvVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTA 224
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.51e-26

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 98.23  E-value: 2.51e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446875247    4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGE 62
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-283 1.58e-25

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: 100.37  E-value: 1.58e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQE-MSQEKIEDMLCRdELDVGIAFAPVHSPE-LEAIPLLTESLALVV 169
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQaGSDDLLAAVREG-RLDLAFVGLPERRPPgLASRELAREPLVAVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 170 AQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHD 249
Cdd:cd08436   80 APDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLP 159

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446875247 250 GLKAISLAPPLLERTAVLLRRKNSwqTAAAKAFL 283
Cdd:cd08436  160 GLAALPLEPAPRRRLYLAWSAPPP--SPAARAFL 191
cbl PRK12679
HTH-type transcriptional regulator Cbl;
11-221 1.05e-24

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 101.04  E-value: 1.05e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  11 AVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSG-RTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADLT 89
Cdd:PRK12679  12 AARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDT 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  90 RGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAP-VHSPELEAIPLLTESLALV 168
Cdd:PRK12679  92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERlSNDPQLVAFPWFRWHHSLL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446875247 169 VAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA 221
Cdd:PRK12679 172 VPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSA 224
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-267 1.69e-24

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: 97.67  E-value: 1.69e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHDGL 251
Cdd:cd08433   81 DAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAA 160

                        170
                 ....*....|....*....
gi 446875247 252 KAISLAP---PLLERTAVL 267
Cdd:cd08433  161 GRLVAAPivdPALTRTLSL 179
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-176 2.27e-24

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 100.08  E-value: 2.27e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   9 FLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEvwRQYAS--RALQELGAgkrAIHDVA 86
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK--RVFWAlkSSLDTLNQ---EILDIK 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  87 DL-TRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQeMSQEKIEdmLCRDELDVGIAFAPVHSPELEAIPLLTESL 165
Cdd:PRK10086  97 NQeLSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTIL-TGNENVN--FQRAGIDLAIYFDDAPSAQLTHHFLMDEEI 173

                        170
                 ....*....|....*
gi 446875247 166 ALVV----AQHHPLA 176
Cdd:PRK10086 174 LPVCspeyAERHALT 188
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-233 8.73e-24

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: 95.71  E-value: 8.73e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRR 233
Cdd:cd08415   81 GHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAA 142
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-245 1.92e-23

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 97.45  E-value: 1.92e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKR 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  81 AIHDVADLTRGSLRIAVTP-TFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAF--APVHSpeLEA 157
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPgTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYehSPVAG--LSS 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 158 IPLLTESLALVVAQHHPlavHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLS 237
Cdd:PRK11233 159 QPLLKEDLFLVGTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGV 235


                 ....*...
gi 446875247 238 TLLPAAIA 245
Cdd:PRK11233 236 TVLPESAA 243
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-286 4.44e-23

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: 93.76  E-value: 4.44e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQH 172
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQVALSRLHDEKLVLLSAEFaTREQIDHYCEKAGLHPQVVIEANSISAVLELIRR----TSLSTLLPAAIATQH 248
Cdd:cd08412   82 HPLAGKDEVSLADLAAEPLILLDLPH-SREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANglgySLLNDRPYRPWSYDG 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446875247 249 DGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMA 286
Cdd:cd08412  161 KRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDFA 198
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 93-286 4.93e-23

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: 93.88  E-value: 4.93e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIA-FAP-VHSPELEAIPLLTESLALVVA 170
Cdd:cd08449    2 LNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVrFADtLNDPPLASELLWREPMVVALP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPLAVHEQVALSRLHDEKLVLLS-AEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQ-H 248
Cdd:cd08449   82 EEHPLAGRKSLTLADLRDEPFVFLRlANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYARLpW 161

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446875247 249 DGLKAISLAPPLLERTAVLLRRKNswQTAAAKAFLHMA 286
Cdd:cd08449  162 PGVRFIPLKQAISADLYAVYHPDS--ATPVIQAFLALL 197
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-191 2.51e-22

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 94.24  E-value: 2.51e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  11 AVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADLTR 90
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLqemSQE---KIEDMLCRDELDVGI---AFAPVHSpELEAIPLLTES 164
Cdd:PRK11074  92 GQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELII---RQEvfnGVWDALADGRVDIAIgatRAIPVGG-RFAFRDMGMLS 167

                        170       180
                 ....*....|....*....|....*..
gi 446875247 165 LALVVAQHHPLAVHEQValsrLHDEKL 191
Cdd:PRK11074 168 WACVVSSDHPLASMDGP----LSDDEL 190
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-232 6.67e-22

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 93.13  E-value: 6.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAG-----EVWRQYASralqeLGAG 78
Cdd:PRK11013   7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlrlfeEVQRSYYG-----LDRI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  79 KRAIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLqeMSQEK--IEDMLCRDELDVGIAFAPVHSPELE 156
Cdd:PRK11013  82 VSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNI--VPQESplLEEWLSAQRHDLGLTETLHTPAGTE 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446875247 157 AIPLLTESLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIR 232
Cdd:PRK11013 160 RTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVR 235
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
4-235 9.58e-22

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 93.16  E-value: 9.58e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGagkRAIH 83
Cdd:PRK15421   5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIS---QALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  84 DVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTE 163
Cdd:PRK15421  82 ACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDY 161

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446875247 164 SLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVvieaNSISAVLELIRRTS 235
Cdd:PRK15421 162 EVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSL----KSVDNTLLLIQMVA 229
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-217 2.44e-21

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 91.03  E-value: 2.44e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  26 HVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADLTRGSLRI--AVTptfTS 103
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcSVT---AA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 104 Y-FIGPLMADFYARYPSITLQLQ----EMSQEKIEDmlcrDELDVGIAFAPVHSPE-LEAIPLLTESLALvVAQHHPLAV 177
Cdd:PRK11716  79 YsHLPPILDRFRAEHPLVEIKLTtgdaADAVEKVQS----GEADLAIAAKPETLPAsVAFSPIDEIPLVL-IAPALPCPV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446875247 178 HEQVALSRLHDEKL-VLLSAEFATREQIDHYCEKAGLHPQV 217
Cdd:PRK11716 154 RQQLSQEKPDWSRIpFILPEHGPARRRIDLWFRRHKIKPNI 194
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-206 2.58e-21

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 91.29  E-value: 2.58e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGevwRQYASRALQELgagKRAIh 83
Cdd:PRK10837   6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHG---RLLYPRALALL---EQAV- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  84 DVADLTR---GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:PRK10837  79 EIEQLFRednGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPW 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 446875247 161 LTESLALVVAQHHPLAvHEQVALSRLHDEKLVLLSAEFATREQIDH 206
Cdd:PRK10837 159 LEDELVVFAAPDSPLA-RGPVTLEQLAAAPWILRERGSGTREIVDY 203
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-283 7.37e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 88.13  E-value: 7.37e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  94 RIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHH 173
Cdd:cd08426    3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 174 PLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRR---TSLSTLLPAAIATQHDG 250
Cdd:cd08426   83 PLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAgggISLLTELAVRREIRRGQ 162

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446875247 251 LKAISLAPP-LLERTAVLLRRKNSWQTAAAKAFL 283
Cdd:cd08426  163 LVAVPLADPhMNHRQLELQTRAGRQLPAAASAFL 196
PRK09791 PRK09791
LysR family transcriptional regulator;
6-276 1.17e-20

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 89.82  E-value: 1.17e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   6 INYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIHDV 85
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  86 ADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGI-AFAPVH-SPELEAIPLLTE 163
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTInTYYQGPyDHEFTFEKLLEK 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 164 SLALVVAQHHPLAvhEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAA 243
Cdd:PRK09791 170 QFAVFCRPGHPAI--GARSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSACISLVAKSDFLSILPEE 247

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 446875247 244 IATQ---HDGLKAISLAPPLLERTAVLLRRKNSWQT 276
Cdd:PRK09791 248 MGCDplhGQGLVMLPVSEILPKATYYLIQRRDTRQT 283
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-283 1.83e-20

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: 86.88  E-value: 1.83e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFA----PVHSPE-LEAIPLLTESLA 166
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypvtPPPDDPgLTRVPLLDDPLD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 167 LVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPA-AIA 245
Cdd:cd08423   81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRlALG 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446875247 246 TQHDGLKAISLAPPlLERTAVLLRRKNSWQTAAAKAFL 283
Cdd:cd08423  161 ARPPGVVVRPLRPP-PTRRIYAAVRAGAARRPAVAAAL 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 8-149 1.02e-19

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 86.97  E-value: 1.02e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   8 YFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIHDVAD 87
Cdd:PRK14997   9 WFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQV 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446875247  88 LTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLqEMSQEKIEdmLCRDELDVGIAFAP 149
Cdd:PRK14997  89 EPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL-EATNRRVD--VVGEGVDVAIRVRP 147
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-221 1.44e-19

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: 84.60  E-value: 1.44e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVH-SPELEAIPLLTESLALVVA 170
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDdHPDLVTLPCYRWNHCVIVP 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446875247 171 QHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA 221
Cdd:cd08413   81 PGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTA 131
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-181 3.06e-18

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 82.93  E-value: 3.06e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   6 INYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGE----------VWRQYASRALQEL 75
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEhllsqardwlSWLESMPSELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  76 GAG-KRAIHDVADltrgslriavTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVH--S 152
Cdd:PRK10094  87 NDGvERQVNIVIN----------NLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEalA 156

                        170       180
                 ....*....|....*....|....*....
gi 446875247 153 PELEAIPLLTESLALVVAQHHPLAVHEQV 181
Cdd:PRK10094 157 NTFSLDPLGSVQWRFVMAADHPLANVEEP 185
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 115-259 9.92e-18

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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. 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: 176108  Cd Length: 199  Bit Score: 79.70  E-value: 9.92e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 115 ARYPSITLQLQEMSQEKIEDMLCRDELD-VGIAF-APVHSPELEAIPLLTESLALVVAQHHPLAVHEQVALSRLHDEKLV 192
Cdd:cd08416   24 LRRPELDIELTLGSNKDLLKKLKDGELDaILVATpEGLNDPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFV 103

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446875247 193 LLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQH-DGLKAISLAPP 259
Cdd:cd08416  104 TLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVYeDKVQLIPLAEP 171
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-285 2.81e-17

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: 78.47  E-value: 2.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELD--VGIAFAPVHSPELEAIPLLTESLALVV 169
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDlaIGRLADDEQPPDLASEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 170 AQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLH-PQVVIEANSISAVLELIRRTSLSTLLPAAIAT-- 246
Cdd:cd08435   81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPlPRNVVETASISALLALLARSDMLAVLPRSVAEde 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446875247 247 -QHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHM 285
Cdd:cd08435  161 lRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDA 200
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 92-223 4.02e-17

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: 77.93  E-value: 4.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTfTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08419    1 RLRLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPP 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANS 223
Cdd:cd08419   80 DHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGS 131
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-260 8.21e-17

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: 76.87  E-value: 8.21e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  94 RIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHH 173
Cdd:cd08417    3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 174 PLAvHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA---TQHDG 250
Cdd:cd08417   83 PLA-GGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAealAERLG 161

                        170
                 ....*....|
gi 446875247 251 LKAisLAPPL 260
Cdd:cd08417  162 LRV--LPLPF 169
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-248 2.80e-16

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: 75.38  E-value: 2.80e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEM-SQEKIEDMLCRdELDVGIAFAPVHSPELEAIPLLTESLALVVA 170
Cdd:cd08447    1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMvTTDQIEALESG-RIDLGLLRPPFARPGLETRPLVREPLVAAVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPLAVHEQVALSRLHDEKLVLLSAEFAT--REQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQH 248
Cdd:cd08447   80 AGHPLAGAERLTLEDLDGQPFIMYSPTEARyfHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRLR 159
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-286 3.45e-16

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: 75.38  E-value: 3.45e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 109 LMADFYARYPSITLQLQEM-SQEKIEDMLcRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAVHEQVALSRLH 187
Cdd:cd08448   18 ILRAFRAEYPGIEVALHEMsSAEQIEALL-RGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDLRELA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 188 DEKLVLLSAEFAT--REQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA-TQHDGLKAISLAPPLLERT 264
Cdd:cd08448   97 GEPFVLFSREVSPdyYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRSLArAGLAGVRFLPLKGATQRSE 176

                        170       180
                 ....*....|....*....|..
gi 446875247 265 AVLLRRKNSwQTAAAKAFLHMA 286
Cdd:cd08448  177 LYAAWKASA-PNPALQAFLAAL 197
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-116 1.49e-15

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 75.39  E-value: 1.49e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   9 FLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRsGRTIRLTDAGEVWRQYAsRALQELGAGKRAIHDVADL 88
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHL-RQVALLEADLLSTLPAERG 87

                         90       100
                 ....*....|....*....|....*....
gi 446875247  89 TRGSLRIAVTP-TFTSYFIgPLMADFYAR 116
Cdd:PRK13348  88 SPPTLAIAVNAdSLATWFL-PALAAVLAG 115
PRK12680 PRK12680
LysR family transcriptional regulator;
1-221 1.52e-15

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 75.81  E-value: 1.52e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHG-SFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIR-LTDAGEVWRQYASRALQELGAG 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  79 KRAIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELE-A 157
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGiA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446875247 158 IPLLTESLALVVAQHHPLAvHEQVALSRLHDEKLVLLSAEFATR--EQIDHYCEKAGLHPQVVIEA 221
Cdd:PRK12680 161 VPLYRWRRLVVVPRGHALD-TPRRAPDMAALAEHPLISYESSTRpgSSLQRAFAQLGLEPSIALTA 225
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-283 1.82e-15

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: 73.22  E-value: 1.82e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQH 172
Cdd:cd08456    2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRR-TSLSTLLP-AAIATQHDG 250
Cdd:cd08456   82 HRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAgVGVSVVNPlTALDYAAAG 161

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446875247 251 LKAISLAPPlLERTAVLLRRKNSWQTAAAKAFL 283
Cdd:cd08456  162 LVVRRFSPA-VPFEVSLIRPKHRPSSALVAAFS 193
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 105-286 2.70e-15

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: 72.92  E-value: 2.70e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 105 FIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAVHEQVALS 184
Cdd:cd08452   14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIE 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 185 RLHDEKLVLLSAEF--ATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLP-AAIATQHDGLKAISLAPPLL 261
Cdd:cd08452   94 DLRDEPIITVAREAwpTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPsSAKKLFNLEVAYRKIDQINL 173

                        170       180
                 ....*....|....*....|....*
gi 446875247 262 ERTAVLLRRKNSwQTAAAKAFLHMA 286
Cdd:cd08452  174 NAEWSIAYRKDN-HNPLLKHFIHIS 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
4-124 3.56e-15

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 74.41  E-value: 3.56e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIH 83
Cdd:PRK10632   5 KRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLY 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446875247  84 DVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQL 124
Cdd:PRK10632  85 AFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL 125
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-283 3.91e-15

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 72.17  E-value: 3.91e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQH 172
Cdd:cd08421    2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA---TQHD 249
Cdd:cd08421   82 HPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAArryARAL 161

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446875247 250 GLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFL 283
Cdd:cd08421  162 GLRVVPLDDAWARRRLLLCVRSFDALPPAARALV 195
leuO PRK09508
leucine transcriptional activator; Reviewed
 9-280 5.42e-15

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 73.90  E-value: 5.42e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   9 FLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTdagevwrqyaSRALQELGAGKRAIHDVADL 88
Cdd:PRK09508  30 FDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPT----------ARARQLFGPVRQALQLVQNE 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  89 TRGS----------LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAI 158
Cdd:PRK09508 100 LPGSgfepesservFNLCICSPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTSV 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 159 PLLTESLALVVAQHHPlAVHEQVALSRLHDEKLVLLS----AEFAtreqiDHYCEKAGLHPQVVIEANSISAVLELIRRT 234
Cdd:PRK09508 180 PLFKDELVLVASKNHP-RIKGPITEEQLYNEQHAVVSldrfASFS-----QPWYDTVDKQASIAYQGTALSSVLNVVSQT 253

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 446875247 235 SLSTLLPAAIATQH---DGLKAISLAPPLLERTAVLlrrknSWQTAAAK 280
Cdd:PRK09508 254 HLVAIAPRWLAEEFaesLELQILPLPLKNNSRTCYL-----SWHESAGR 297
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 92-249 6.94e-15

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: 71.83  E-value: 6.94e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHS-PELEAIPLLTESLALVVA 170
Cdd:cd08443    1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDyDDLITLPCYHWNRCVVVK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446875247 171 QHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEAnSISAVLELIRRTSLSTLLPAAIATQHD 249
Cdd:cd08443   81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTA-TDADVIKTYVRLGLGVGVIASMAYDPV 158
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 105-286 8.87e-15

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: 71.44  E-value: 8.87e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 105 FIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPV-HSPELEAIPLLTESLALVVAQHHPLAVHEQVAL 183
Cdd:cd08451   15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVaRSDGLVLELLLEEPMLVALPAGHPLARERSIPL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 184 SRLHDEKLVLLSAEFAT--REQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQH-DGLKAISLAPPL 260
Cdd:cd08451   95 AALADEPFILFPRPVGPglYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASMRQLQaPGVVYRPLAGAP 174

                        170       180
                 ....*....|....*....|....*.
gi 446875247 261 LeRTAVLLRRKNSWQTAAAKAFLHMA 286
Cdd:cd08451  175 L-TAPLALAYRRGERSPAVRNFIALV 199
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-145 1.19e-14

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: 72.85  E-value: 1.19e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   1 MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRAL---QELGA 77
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILdieDSLMD 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446875247  78 GKRAIHDvadltRGSLRIAVTPTFTSYFIGPLMADFYARYPSIT-LQLQEMSQEKIEDMLCRDELDVGI 145
Cdd:NF041036  81 ELKSFKG-----RQRLSICCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDLAI 144
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
4-97 4.59e-14

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 70.96  E-value: 4.59e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   4 RHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRsGRTIRLTDAGEVWRQYASR-------ALQELG 76
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQvrlleaeLLGELP 83

                         90       100
                 ....*....|....*....|.
gi 446875247  77 AGkraihdvaDLTRGSLRIAV 97
Cdd:PRK03635  84 AL--------DGTPLTLSIAV 96
PRK10341 PRK10341
transcriptional regulator TdcA;
3-246 1.69e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 69.51  E-value: 1.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   3 SRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELgagKRAI 82
Cdd:PRK10341   9 TQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREM---KNMV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  83 HDVADLTrGSLRIAVTPTFTSY----FIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELD--VGIAFAPVHSPELE 156
Cdd:PRK10341  86 NEINGMS-SEAVVDVSFGFPSLigftFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDfaIGTLSNEMKLQDLH 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 157 AIPLLTESLALVVAQHHPLAvhEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSL 236
Cdd:PRK10341 165 VEPLFESEFVLVASKSRTCT--GTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADF 242

                        250
                 ....*....|
gi 446875247 237 STLLPAAIAT 246
Cdd:PRK10341 243 LTVIPCDMTS 252
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 93-283 2.06e-13

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. 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: 176128  Cd Length: 198  Bit Score: 67.74  E-value: 2.06e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVG--IAFAPVHSPELEAIPLLTESLALVVA 170
Cdd:cd08437    2 LRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIAllGSLTPLENSALHSKIIKTQHFMIIVS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRT-SLSTLLPAAIaTQHD 249
Cdd:cd08437   82 KDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENvGIGFLTDIAV-KPDD 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446875247 250 GLKAISLA---PPLLERTavLLRRKNSWQTAAAKAFL 283
Cdd:cd08437  161 HLVAIPLLdneQPTFYIS--LAHRKDQLLTPAQKKLL 195
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 92-286 2.17e-11

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: 61.85  E-value: 2.17e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQE-MSQEKIEDMLCRdELDVGIAFAPVHSPELEAIPLLTESLALVVA 170
Cdd:cd08442    1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTgTTGALIQAVLEG-RLDGAFVAGPVEHPRLEQEPVFQEELVLVSP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPLAvheqVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHDG 250
Cdd:cd08442   80 KGHPPV----SRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQG 155

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446875247 251 LKAIS---LAPPLLERTAVLLRRKNsWQTAAAKAFLHMA 286
Cdd:cd08442  156 RGSVSihpLPEPFADVTTWLVWRKD-SFTAALQAFLDLL 193
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 9-145 5.90e-11

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 61.97  E-value: 5.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   9 FLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQelgagkraIHDVADL 88
Cdd:PRK15092  19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR--------FNDEACS 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446875247  89 T------RGSLRIAVtPTFTSYFIGP-LMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGI 145
Cdd:PRK15092  91 SlmysnlQGVLTIGA-SDDTADTILPfLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK09801 PRK09801
LysR family transcriptional regulator;
2-145 1.11e-10

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 61.20  E-value: 1.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   2 LSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEvwRQYaSRALQELGAGKRA 81
Cdd:PRK09801   7 LAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQ--RCY-EHALEILTQYQRL 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446875247  82 IHDVADL-TR--GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLqEMSQEKIEdmLCRDELDVGI 145
Cdd:PRK09801  84 VDDVTQIkTRpeGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF-ELFDRQID--LVQDNIDLDI 147
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-68 1.75e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 60.42  E-value: 1.75e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   9 FLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYA 68
Cdd:PRK03601   9 FLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-160 3.08e-10

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 60.07  E-value: 3.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247   9 FLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADL 88
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446875247  89 TRGSLRIAVTPTFTsyfIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFapvHSPELEAIPL 160
Cdd:PRK10082  99 AQRKIKIAAAHSLS---LGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGQSDCIFSF---HDEDLLEAPF 164
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-260 9.71e-10

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: 57.29  E-value: 9.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFaPVHSPE-LEAIPLLTESLALVVAQ 171
Cdd:cd08461    2 LVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTT-PEYAPDgLRSRPLFEERYVCVTRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 172 HHPLAVHEqvalsrlhdeklvLLSAEFATREQI-------------DHYCEKAGLHPQVVIEANSISAVLELIRRTSLST 238
Cdd:cd08461   81 GHPLLQGP-------------LSLDQFCALDHIvvspsgggfagstDEALAALGLTRNVVLSVPSFLVVPEILAATDMVA 147

                        170       180
                 ....*....|....*....|..
gi 446875247 239 LLPAAIATQHDGLKAIslAPPL 260
Cdd:cd08461  148 FVPSRLVPNLEGLQEV--ELPL 167
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-70 1.27e-09

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 58.10  E-value: 1.27e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446875247   5 HINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASR 70
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADK 73
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 93-221 1.71e-09

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: 56.36  E-value: 1.71e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAF-APVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08444    2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATeALENHPELVSFPYYDWHHHIIVPV 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA 221
Cdd:cd08444   82 GHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSA 131
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-283 3.50e-09

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: 55.27  E-value: 3.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPV--HSPELEAIPLLTESLALVVA 170
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPfpLPKDLVWTPLVREPLVLIAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHPlavheqvalsrlHDEKLVLLSAE---------FATReQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLP 241
Cdd:cd08427   82 AELA------------GDDPRELLATQpfirydrsaWGGR-LVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVP 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 446875247 242 AAIATQHDG--LKAISLAPPLLERTAVLLRRKNSWQTAAAKAFL 283
Cdd:cd08427  149 DIAVPLPAGprVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALL 192
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 92-221 3.84e-09

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: 55.45  E-value: 3.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTfTSYFIGP-LMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPV---HSPELEAIPLLTESLAL 167
Cdd:cd08453    1 RLSLAFVST-ADYSVLPeLVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPgasAPPALAYRPLLSEPLVL 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446875247 168 VVAQHHPLAVHEQVALSRLHDEKLVLLSAEFAT--REQIDHYCEKAGLHPQVVIEA 221
Cdd:cd08453   80 AVPAAWAAEGGAPLALAAVAAEPLVIFPRRIAPafHDAVTGYYRAAGQTPRIAQEA 135
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 93-232 4.75e-09

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: 55.19  E-value: 4.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQH 172
Cdd:cd08457    2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMG 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIR 232
Cdd:cd08457   82 HPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVR 141
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 109-242 2.42e-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: 53.15  E-value: 2.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 109 LMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAVHEQVALSRLHD 188
Cdd:cd08450   18 VLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPPQDLAG 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446875247 189 EKLVLLSAEFAT-REQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPA 242
Cdd:cd08450   98 ENFISPAPTAPVlQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPL 152
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-189 2.60e-08

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


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 52.97  E-value: 2.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQemSQEKIEDMLcRDELDVGIAFAPVHSPELEAIPLLTESLALV---- 168
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLS--TSDRLVDFA-REGIDLAIRYGDGDWPGLEAERLMDEELVPVcspa 78

                         90       100
                 ....*....|....*....|..
gi 446875247 169 -VAQHHPLAVHEQVALSRLHDE 189
Cdd:cd08432   79 lLAGLPLLSPADLARHTLLHDA 100
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-246 5.47e-08

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: 51.90  E-value: 5.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMS-QEKIEDMLCRdELDVGIA-FAPVHsPELEAIPLLTESLALV 168
Cdd:cd08446    1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTkDEQIEALRAG-RIHIGFGrFYPVE-PDIAVENVAQERLYLA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 169 VAQHHPLAVHEQVALSRLHDEKLVLLSAE----FATrEQIDhYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAI 244
Cdd:cd08446   79 VPKSHPLAARPAVSLADLRNEPLILFPRGgrpsFAD-EVLG-LFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESV 156


                 ..
gi 446875247 245 AT 246
Cdd:cd08446  157 AA 158
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 94-282 1.08e-07

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: 51.20  E-value: 1.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  94 RIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSP--ELEAIPLLTESLALVVAQ 171
Cdd:cd08418    3 SIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYlkELISEPLFESDFVVVARK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 172 HHPLAVHEqvALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA-TQHDG 250
Cdd:cd08418   83 DHPLQGAR--SLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGrGPLDS 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446875247 251 LKAISLAP--PLLERTAVLLRRKNSWQTAAAKAF 282
Cdd:cd08418  161 FRLITIPVeePLPSADYYLIYRKKSRLTPLAEQL 194
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-260 6.67e-07

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: 48.77  E-value: 6.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  94 RIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVV-AQH 172
Cdd:cd08464    3 RIGLSDDVESWLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFdPQQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPL--AVHEQVALSRLHdeklVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA---TQ 247
Cdd:cd08464   83 LSLsaPLTLEDYVARPH----VLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGTPLIATVPARLArawAA 158

                        170
                 ....*....|...
gi 446875247 248 HDGLKAisLAPPL 260
Cdd:cd08464  159 ALGLRA--SPPPL 169
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 93-170 7.80e-07

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 48.50  E-value: 7.80e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLqeMSQEKIEDmLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVA 170
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSL--LPSADLVD-LRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAA 76
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-284 1.14e-06

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: 48.38  E-value: 1.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 109 LMADFYARYPSITLQLQEM-SQEKIEdMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAVH-EQVALSRL 186
Cdd:cd08445   19 LIRRFRQAAPDVEIELIEMtTVQQIE-ALKEGRIDVGFGRLRIEDPAIRRIVLREEPLVVALPAGHPLAQEkAPLTLAQL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 187 HDEKLVLLSAE----FATreQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIatQHDGLKAISLApPLLE 262
Cdd:cd08445   98 ADEPLILYPASprpsFAD--QVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASV--QRLRRDDVVYR-PLLD 172

                        170       180
                 ....*....|....*....|....*...
gi 446875247 263 RTAV----LLRRKN--SWQTAAAKAFLH 284
Cdd:cd08445  173 PDATspiiMSVRAGdeSPYIALILQLIR 200
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-168 1.21e-06

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 48.21  E-value: 1.21e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQeMSQEKIeDMLcRDELDVGIAFAPVHSPELEAIPLLTESLALV 168
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELV-LSDRLV-DLV-EEGFDLAIRIGELPDSSLVARRLGPVRRVLV 75
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 94-264 2.97e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 46.86  E-value: 2.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  94 RIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHH 173
Cdd:cd08466    3 NIAANETLDLLLLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 174 PLAVHEqVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQ-HDGLK 252
Cdd:cd08466   83 PRIQGS-LSLEQYLAEKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQyAEQLN 161

                        170
                 ....*....|..
gi 446875247 253 AISLAPPLLERT 264
Cdd:cd08466  162 LQILPLPFKTKP 173
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 104-260 4.96e-06

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: 46.42  E-value: 4.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 104 YFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAvHEQVAL 183
Cdd:cd08459   13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRI-GSTLTL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 184 SRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA---TQHDGLKAISLAPPL 260
Cdd:cd08459   92 EQFLAARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQTDLVATVPERLArlfARAGGLRIVPLPFPL 171
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 92-170 6.31e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 46.13  E-value: 6.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLqlqemsqekieDMLCRDE--------LDVGIAFAPVHSPELEAIPLLTE 163
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITV-----------NLVTRDEpfdfsqgsFDAAIHFGDPVWPGAESEYLMDE 69


                 ....*..
gi 446875247 164 SLALVVA 170
Cdd:cd08481   70 EVVPVCS 76
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 89-170 1.04e-05

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 45.41  E-value: 1.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  89 TRGSLRI-AVTPtFTSYFIGPLMADFYARYPSITLQLQemSQEKIEDMLCRdELDVGIAFAPVHSPELEAIPLLTESLAL 167
Cdd:cd08478    1 PSGLLRVdAATP-FVLHLLAPLIAKFRERYPDIELELV--SNEGIIDLIER-KTDVAIRIGELTDSTLHARPLGKSRLRI 76


                 ...
gi 446875247 168 VVA 170
Cdd:cd08478   77 LAS 79
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-162 2.46e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 41.43  E-value: 2.46e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKiedMLCRDELDVGIAFAPVHSPELEAIPLLT 162
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPV---DLVEEGFDLDIRVGDLPDSSLIARKLAP 69
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 94-262 4.09e-04

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: 40.50  E-value: 4.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  94 RIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHH 173
Cdd:cd08467    3 TLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRHGH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 174 PLAVHEqvaLSRLHDEKL--VLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHDGL 251
Cdd:cd08467   83 PALAQE---WTLDDFATLrhVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAM 159

                        170
                 ....*....|.
gi 446875247 252 KAISLAPPLLE 262
Cdd:cd08467  160 LPLRVVPPPVD 170
PBP2_DntR_like_1 cd08460
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-245 8.16e-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: 176149 [Multi-domain]  Cd Length: 200  Bit Score: 39.88  E-value: 8.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 101 FTSYFIGPLMADFYARYPSITLQ-LQEmsQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAVHE 179
Cdd:cd08460   10 FVAAFGPALLAAVAAEAPGVRLRfVPE--SDKDVDALREGRIDLEIGVLGPTGPEIRVQTLFRDRFVGVVRAGHPLARGP 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446875247 180 qVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIA 245
Cdd:cd08460   88 -ITPERYAAAPHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGSDLIALVPERVT 152
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-160 8.60e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176166  Cd Length: 197  Bit Score: 39.52  E-value: 8.60e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLqEMSQEKIEdmLCRDELDVGIAFAPVHSPELEAIPL 160
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDL-VLSDRLVD--LVEEGFDAAFRIGELADSSLVARPL 67
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 108-231 1.23e-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: 39.09  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 108 PLMADFYARYPSITLQL-QEMSQEKIeDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAVHEQVALSRL 186
Cdd:cd08441   17 PVLDQFRERWPDVELDLsSGFHFDPL-PALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDL 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446875247 187 HDEKLVLLSAEfatREQID---HYCEKAGLHPQVVIEANSISAVLELI 231
Cdd:cd08441   96 ADETLITYPVE---RERLDvfrHFLQPAGIEPKRRRTVELTLMILQLV 140
PBP2_CbnR cd08486
The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved ...
 91-245 2.95e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of LysR-type regulator CbnR which is 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. 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: 176175  Cd Length: 198  Bit Score: 38.15  E-value: 2.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  91 GSLRIAV--TPTFTSYFIgpLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIA-FAPVHsPELEAIPLLTESLAL 167
Cdd:cd08486    1 GELSVAYfgTPIYRSLPL--LLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSrFFPRH-PGIEIVNIAQEDLYL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 168 VVAQHHPLAVHEQVALSRLHDEKLVLL----SAEFAtrEQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAA 243
Cdd:cd08486   78 AVHRSQSGKFGKTCKLADLRAVELTLFprggRPSFA--DEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPAS 155


                 ..
gi 446875247 244 IA 245
Cdd:cd08486  156 VA 157
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 93-285 3.66e-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: 37.70  E-value: 3.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPvhSPELEAIPLLTESLALVVAQH 172
Cdd:cd08439    2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHP--PPGASATILRRSPTVWYCAAG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 173 HPLAVHEQValsrlhdeKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAA-------IA 245
Cdd:cd08439   80 YILAPGEPL--------PLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEmvppdlrIL 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446875247 246 TQHDGLkaislaPPLLERTAVLLRRKNSWQTAAAKAFLHM 285
Cdd:cd08439  152 GESEGL------PPLPDTGYTLCLDPNRPSELAQAFFEAL 185
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 92-216 4.10e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI 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: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 37.77  E-value: 4.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEkiEDMLcRDELDVGIAFAPVHSPE-LEAIPLLTESLALVVA 170
Cdd:cd08482    1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGP--VDSL-RDGIDAAIRFNDAPWPAgMQVIELFPERVGPVCS 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446875247 171 QHHPLAVHE-QVALSRLHDEKLVllsaEFATREQI-DHYCEKAGLHPQ 216
Cdd:cd08482   78 PSLAPTVPLrQAPAAALLGAPLL----HTRSRPQAwPDWAAAQGLAPE 121
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 92-246 4.39e-03

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: 37.77  E-value: 4.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGI-AFAPVhSPELEAIPLLTESLALVVA 170
Cdd:cd08469    1 SFVIAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIgIFEQI-PPRFRRRTLFDEDEVWVMR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247 171 QHHP----------LAVHEQVALSRLHDEKLVL----------LSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLEL 230
Cdd:cd08469   80 KDHPaargaltietLARYPHIVVSLGGEEEGAVsgfiserglaRQTEMFDRRALEEAFRESGLVPRVAVTVPHALAVPPL 159

                        170
                 ....*....|....*.
gi 446875247 231 IRRTSLSTLLPAAIAT 246
Cdd:cd08469  160 LADSDMLALLPRSLAR 175
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-124 4.66e-03

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


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 37.44  E-value: 4.66e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446875247  90 RGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQL 124
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLEL 36
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
 92-213 5.98e-03

The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. 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, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147  Cd Length: 196  Bit Score: 37.00  E-value: 5.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  92 SLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08458    1 SLRVACYTAPALSFMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISILAGDYPGLTTEPVPSFRAVCLLPP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446875247 172 HHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGL 213
Cdd:cd08458   81 GHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSCGV 122
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 93-180 7.01e-03

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: 36.86  E-value: 7.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446875247  93 LRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAP-VHSPELEAIPLLTESLALVVAQ 171
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGeLPPGGVKTRPLGEVEFVFAVAP 81


                 ....*....
gi 446875247 172 HHPLAVHEQ 180
Cdd:cd08431   82 NHPLAKLDG 90
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-124 9.94e-03

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


Pssm-ID: 176161  Cd Length: 202  Bit Score: 36.34  E-value: 9.94e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 446875247  91 GSLRIAVTPTFTSYFIGPLMADFYARYPSITLQL 124
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDL 34
 
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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