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Conserved domains on  [gi|499257667|ref|WP_010955207|]
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MULTISPECIES: LysR family transcriptional regulator [Pseudomonas]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 13284558)

LysR family transcriptional regulator with an N-terminal DNA binding motif and a C-terminal inducer binding domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 93-281 3.02e-80

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: 240.97  E-value: 3.02e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP 172
Cdd:cd08442    4 LGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGRDRVRVHS 252
Cdd:cd08442   84 PVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSIHP 163

                        170       180
                 ....*....|....*....|....*....
gi 499257667 253 LQAPFDQAVTWLMWRQGMRGANLQAWIDL 281
Cdd:cd08442  164 LPEPFADVTTWLVWRKDSFTAALQAFLDL 192
rbcR super family cl31781
LysR transcriptional regulator; Provisional
 5-172 1.46e-32

LysR transcriptional regulator; Provisional


The actual alignment was detected with superfamily member CHL00180:

Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 121.67  E-value: 1.46e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   5 QLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDE---ALGA 81
Cdd:CHL00180   9 QLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEEtcrALED 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  82 VRGGQpAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDG--PPSLAG-LDGVPL 158
Cdd:CHL00180  89 LKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGevPTELKKiLEITPY 167

                        170
                 ....*....|....
gi 499257667 159 CDEQLVLITSPEHP 172
Cdd:CHL00180 168 VEDELALIIPKSHP 181
 
Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 93-281 3.02e-80

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: 240.97  E-value: 3.02e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP 172
Cdd:cd08442    4 LGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGRDRVRVHS 252
Cdd:cd08442   84 PVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSIHP 163

                        170       180
                 ....*....|....*....|....*....
gi 499257667 253 LQAPFDQAVTWLMWRQGMRGANLQAWIDL 281
Cdd:cd08442  164 LPEPFADVTTWLVWRKDSFTAALQAFLDL 192
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-281 9.44e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 190.85  E-value: 9.44e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDEALG 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  81 AVRG--GQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPL 158
Cdd:COG0583   81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 159 CDEQLVLITSPEHPAVltakdvagkavftfrqgcsyrmrleawyahAHTPMgrvmeIESYQSMLACVIAGAGVAMMAQSM 238
Cdd:COG0583  161 GEERLVLVASPDHPLA------------------------------RRAPL-----VNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 499257667 239 LDSLPGRDRVRVHSLQAPFDQAVTWLMWRQG-MRGANLQAWIDL 281
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRrHLSPAVRAFLDF 249
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-281 1.87e-38

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: 134.34  E-value: 1.87e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   88 AGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLIT 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  168 SPEHP----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLP 243
Cdd:pfam03466  81 PPDHPlargEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 499257667  244 GRDRVRVHSLQAPFDQAVTWLMWRQGM-RGANLQAWIDL 281
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRpLSPAVRAFIEF 199
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-172 1.46e-32

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 121.67  E-value: 1.46e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   5 QLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDE---ALGA 81
Cdd:CHL00180   9 QLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEEtcrALED 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  82 VRGGQpAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDG--PPSLAG-LDGVPL 158
Cdd:CHL00180  89 LKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGevPTELKKiLEITPY 167

                        170
                 ....*....|....
gi 499257667 159 CDEQLVLITSPEHP 172
Cdd:CHL00180 168 VEDELALIIPKSHP 181
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-281 6.86e-29

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 111.97  E-value: 6.86e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRmsALRD-EAl 79
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARR--ALQDlEA- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  80 gAVRGGQPAGDFVLGT----MYSTAATHLPA-LLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLD 154
Cdd:PRK11242  78 -GRRAIHDVADLSRGSlrlaMTPTFTAYLIGpLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 155 GVPLCDEQLVLITSPEHPA-----VLTAKDVAGKAVFTFRQGCSYRMRLEAWYA-HAHTPmgRV-MEIESYQSMLAcVIA 227
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLaarrkALTLDELADEPLVLLSAEFATREQIDRYFRrHGVTP--RVaIEANSISAVLE-IVR 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 228 GAGVAMMaqsmldsLPG-----RDRVRVHSLQAPFDQAVTWLMWRQG-MRGANLQAWIDL 281
Cdd:PRK11242 234 RGRLATL-------LPAaiareHDGLCAIPLDPPLPQRTAALLRRKGaYRSAAARAFIEL 286
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.22e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.43  E-value: 2.22e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667    3 FSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 93-281 3.02e-80

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: 240.97  E-value: 3.02e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP 172
Cdd:cd08442    4 LGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGRDRVRVHS 252
Cdd:cd08442   84 PVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSIHP 163

                        170       180
                 ....*....|....*....|....*....
gi 499257667 253 LQAPFDQAVTWLMWRQGMRGANLQAWIDL 281
Cdd:cd08442  164 LPEPFADVTTWLVWRKDSFTAALQAFLDL 192
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-281 9.44e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 190.85  E-value: 9.44e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDEALG 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  81 AVRG--GQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPL 158
Cdd:COG0583   81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 159 CDEQLVLITSPEHPAVltakdvagkavftfrqgcsyrmrleawyahAHTPMgrvmeIESYQSMLACVIAGAGVAMMAQSM 238
Cdd:COG0583  161 GEERLVLVASPDHPLA------------------------------RRAPL-----VNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 499257667 239 LDSLPGRDRVRVHSLQAPFDQAVTWLMWRQG-MRGANLQAWIDL 281
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRrHLSPAVRAFLDF 249
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-281 1.87e-38

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: 134.34  E-value: 1.87e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   88 AGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLIT 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  168 SPEHP----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLP 243
Cdd:pfam03466  81 PPDHPlargEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 499257667  244 GRDRVRVHSLQAPFDQAVTWLMWRQGM-RGANLQAWIDL 281
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRpLSPAVRAFIEF 199
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-281 5.26e-37

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 130.41  E-value: 5.26e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP 172
Cdd:cd05466    4 IGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 ----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPgRDRV 248
Cdd:cd05466   84 lakrKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELA-DGGL 162

                        170       180       190
                 ....*....|....*....|....*....|....
gi 499257667 249 RVHSLQAPFDQAVTWLMWRQGMR-GANLQAWIDL 281
Cdd:cd05466  163 VVLPLEDPPLSRTIGLVWRKGRYlSPAARAFLEL 196
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-172 1.46e-32

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 121.67  E-value: 1.46e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   5 QLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDE---ALGA 81
Cdd:CHL00180   9 QLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEEtcrALED 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  82 VRGGQpAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDG--PPSLAG-LDGVPL 158
Cdd:CHL00180  89 LKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGevPTELKKiLEITPY 167

                        170
                 ....*....|....
gi 499257667 159 CDEQLVLITSPEHP 172
Cdd:CHL00180 168 VEDELALIIPKSHP 181
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-281 6.86e-29

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 111.97  E-value: 6.86e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRmsALRD-EAl 79
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARR--ALQDlEA- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  80 gAVRGGQPAGDFVLGT----MYSTAATHLPA-LLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLD 154
Cdd:PRK11242  78 -GRRAIHDVADLSRGSlrlaMTPTFTAYLIGpLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 155 GVPLCDEQLVLITSPEHPA-----VLTAKDVAGKAVFTFRQGCSYRMRLEAWYA-HAHTPmgRV-MEIESYQSMLAcVIA 227
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLaarrkALTLDELADEPLVLLSAEFATREQIDRYFRrHGVTP--RVaIEANSISAVLE-IVR 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 228 GAGVAMMaqsmldsLPG-----RDRVRVHSLQAPFDQAVTWLMWRQG-MRGANLQAWIDL 281
Cdd:PRK11242 234 RGRLATL-------LPAaiareHDGLCAIPLDPPLPQRTAALLRRKGaYRSAAARAFIEL 286
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-281 2.15e-24

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: 97.19  E-value: 2.15e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  91 FVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPE 170
Cdd:cd08414    2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 171 HP----AVLTAKDVAGKAVFTFRQ--GCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMldSLPG 244
Cdd:cd08414   82 HPlaarESVSLADLADEPFVLFPRepGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASV--ARLQ 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 499257667 245 RDRVRVHSLQAPFDQAVTWLMWRQGMRGANLQAWIDL 281
Cdd:cd08414  160 RPGVVYRPLADPPPRSELALAWRRDNASPALRAFLEL 196
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-269 5.50e-24

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 98.96  E-value: 5.50e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEG-SVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQ-LSPAGKVLLDYANRMsaLRDEA 78
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERM--LLDAE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  79 ----LGAVRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAAL----VDGPPSL 150
Cdd:PRK12683  79 nlrrLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIateaLDREPDL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 151 AGLdgvPLCDEQLVLITSPEHPAV----LTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVME------IESYQS 220
Cdd:PRK12683 159 VSF---PYYSWHHVVVVPKGHPLTgrenLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTaldadvIKTYVE 235

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 499257667 221 MlacviaGAGVAMMAQSMLDslPGRD-RVRVHSLQAPFDQAVTWLMWRQG 269
Cdd:PRK12683 236 L------GMGVGIVAAMAYD--PQRDtGLVALDTDHLFEANTTRVGLRRG 277
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-276 6.00e-23

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 96.21  E-value: 6.00e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEG-SVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQ-LSPAGKVLLDYANRMsaLRD-- 76
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERI--LREvg 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  77 --EALGAVRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALV----DGPPSL 150
Cdd:PRK12682  79 niKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAteslADDPDL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 151 AGLdgvPLCDEQLVLITSPEHP----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVME------IESYqs 220
Cdd:PRK12682 159 ATL---PCYDWQHAVIVPPDHPlaqeERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEaidsdvIKTY-- 233

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499257667 221 mlacVIAGAGVAMMAQSMLDSLPGRDRVRVhSLQAPFDQAVTWLMWRqgmRGANLQ 276
Cdd:PRK12682 234 ----VRLGLGVGIVAEMAYRPDRDGDLVAL-PAGHLFGPNTAWVALK---RGAYLR 281
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 98-234 2.51e-21

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: 89.09  E-value: 2.51e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  98 STAATH-LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP---- 172
Cdd:cd08420    8 TTIGEYlLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPlagr 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499257667 173 AVLTAKDVAGkAVFTFR-QGCSYRMRLEAWYAHAHTPMGR---VMEIESYQSMLACVIAGAGVAMM 234
Cdd:cd08420   88 KEVTAEELAA-EPWILRePGSGTREVFERALAEAGLDGLDlniVMELGSTEAIKEAVEAGLGISIL 152
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-251 1.16e-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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 87.27  E-value: 1.16e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPS-LAGLDGVPLCDEQLVLITSPEH 171
Cdd:cd08436    4 IGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERrPPGLASRELAREPLVAVVAPDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 172 P----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGRDR 247
Cdd:cd08436   84 PlagrRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLAA 163


                 ....
gi 499257667 248 VRVH 251
Cdd:cd08436  164 LPLE 167
PRK09986 PRK09986
LysR family transcriptional regulator;
6-238 1.58e-20

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 89.01  E-value: 1.58e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   6 LRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDEALGAVR-- 83
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEqi 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  84 GGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAAL--VDGPPSLAGLDGVPLCDE 161
Cdd:PRK09986  92 GRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTSRRLHES 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 162 QLVLITSPEHPAV----LTAKDVAGK--AVFTFRQGCSYRMRLEAWYAHAHTPMGrVMEIESYQSMLACVIAGAGVAMMA 235
Cdd:PRK09986 172 AFAVAVPEEHPLAsrssVPLKALRNEyfITLPFVHSDWGKFLQRVCQQAGFSPQI-IRQVNEPQTVLAMVSMGIGITLLP 250


                 ...
gi 499257667 236 QSM 238
Cdd:PRK09986 251 DSY 253
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.22e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.43  E-value: 2.22e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667    3 FSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-269 1.07e-19

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 86.95  E-value: 1.07e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEG-SVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQ-LSPAGKVLLDYANRMsaLRD-E 77
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERI--LQEvE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  78 AL---GAVRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAAL----VDGPPSL 150
Cdd:PRK12684  79 NLkrvGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIateaIADYKEL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 151 AGLdgvPLCDEQLVLITSPEHPAV----LTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVME------IESYQS 220
Cdd:PRK12684 159 VSL---PCYQWNHCVVVPPDHPLLerkpLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEaidadvIKTYVE 235

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 499257667 221 MlacviaGAGVAMMAQSMLDslPGRDR-VRVHSLQAPFDQAVTWLMWRQG 269
Cdd:PRK12684 236 L------GLGVGIVADMAFD--PERDRnLRAIDAGHLFGSSTTRLGLRRG 277
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-172 1.46e-19

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 86.78  E-value: 1.46e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   6 LRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLL----DYANRMSALRDEALGA 81
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLsqarDWLSWLESMPSELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  82 VRGGQPAGDFVLGT-MYSTAAThlPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAAL-VDGPPSLA-GLDGVPL 158
Cdd:PRK10094  87 NDGVERQVNIVINNlLYNPQAV--AQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIgVTGTEALAnTFSLDPL 164

                        170
                 ....*....|....
gi 499257667 159 CDEQLVLITSPEHP 172
Cdd:PRK10094 165 GSVQWRFVMAADHP 178
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-242 4.40e-19

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 85.45  E-value: 4.40e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDEALG 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  81 AVRGGQPAGDFVLGTMYSTAATHLPAlLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCD 160
Cdd:PRK15421  82 ACNEPQQTRLRIAIECHSCIQWLTPA-LENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 161 EQLVLITSPEHP----AVLTAKDVAGKAVFTFRqgcSYRMRLEAWyAHAHTPMGRVMEIESYQS---MLACVIAGAGVAM 233
Cdd:PRK15421 161 YEVRLVLAPDHPlaakTRITPEDLASETLLIYP---VQRSRLDVW-RHFLQPAGVSPSLKSVDNtllLIQMVAARMGIAA 236


                 ....*....
gi 499257667 234 MAQSMLDSL 242
Cdd:PRK15421 237 LPHWVVESF 245
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-180 1.11e-18

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 83.97  E-value: 1.11e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   5 QLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRL-------QLSPAGKVLLDYANRMSALRDE 77
Cdd:PRK10837   7 QLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLvvnehgrLLYPRALALLEQAVEIEQLFRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  78 ALGAVRGGQPagdfvlgtmySTAATH-LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGV 156
Cdd:PRK10837  87 DNGALRIYAS----------STIGNYiLPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISE 156

                        170       180
                 ....*....|....*....|....
gi 499257667 157 PLCDEQLVLITSPEHPavLTAKDV 180
Cdd:PRK10837 157 PWLEDELVVFAAPDSP--LARGPV 178
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-250 4.46e-18

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 80.33  E-value: 4.46e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  92 VLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEH 171
Cdd:cd08433    3 SVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 172 PAV----LTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGRDR 247
Cdd:cd08433   83 PLPrgapVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGR 162


                 ...
gi 499257667 248 VRV 250
Cdd:cd08433  163 LVA 165
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-256 5.51e-18

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: 80.26  E-value: 5.51e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  92 VLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEH 171
Cdd:cd08440    3 RVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 172 P----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDsLPGRDR 247
Cdd:cd08440   83 PlarrRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALP-LADHPG 161


                 ....*....
gi 499257667 248 VRVHSLQAP 256
Cdd:cd08440  162 LVARPLTEP 170
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 93-234 2.56e-17

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: 78.35  E-value: 2.56e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP 172
Cdd:cd08434    4 LGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHP 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499257667 173 AV----LTAKDVAGKAVFTFRQGCSYRMRLEAWYAHA-HTPmgRV-MEIESYQSMLACVIAGAGVAMM 234
Cdd:cd08434   84 LAgrdsVDLAELADEPFVLLSPGFGLRPIVDELCAAAgFTP--KIaFEGEEDSTIAGLVAAGLGVAIL 149
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-232 4.84e-17

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 79.65  E-value: 4.84e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   5 QLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANR--------MSALrd 76
Cdd:PRK11013   8 HIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRsyygldriVSAA-- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  77 EALGAVRGGQPAgdfvLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGV 156
Cdd:PRK11013  86 ESLREFRQGQLS----IACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTERT 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 157 PLCDEQLVLITSPEHP----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVA 232
Cdd:PRK11013 162 ELLTLDEVCVLPAGHPlaakKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVGVS 241
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-263 1.94e-16

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: 75.68  E-value: 1.94e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP 172
Cdd:cd08415    4 IAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 ----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGrDRV 248
Cdd:cd08415   84 larkDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAG-AGL 162

                        170
                 ....*....|....*
gi 499257667 249 RVHslqaPFDQAVTW 263
Cdd:cd08415  163 VVR----PFRPAIPF 173
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-244 2.79e-16

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 77.42  E-value: 2.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLldYANRMSALR--DEA 78
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKIL--YTHARAILRqcEQA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  79 LGAV-RGGQP-AGDFVLGTMYSTAATHLP-ALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDG 155
Cdd:PRK11233  79 QLAVhNVGQAlSGQVSIGLAPGTAASSLTmPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSS 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 156 VPLCDEQLVLI-TSPEHPAVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMM 234
Cdd:PRK11233 159 QPLLKEDLFLVgTQDCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVTVL 238

                        250
                 ....*....|
gi 499257667 235 AQSMLDSLPG 244
Cdd:PRK11233 239 PESAARSLCG 248
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 89-256 2.14e-15

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: 72.94  E-value: 2.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  89 GDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITS 168
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 169 PEHP----AVLTAKDVAGKAVFTFRQGcsYRMR---LEAwYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDS 241
Cdd:cd08411   81 KDHPlakrKSVTPEDLAGERLLLLEEG--HCLRdqaLEL-CRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPS 157

                        170
                 ....*....|....*.
gi 499257667 242 LPGR-DRVRVHSLQAP 256
Cdd:cd08411  158 EELRgDRLVVRPFAEP 173
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-276 2.43e-15

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 74.85  E-value: 2.43e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIF-QAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQR-LQLSPAGKVLLDYANRmsaLRDEA 78
Cdd:PRK12679   1 MNFQQLKIIrEAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAER---ILNEA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  79 -----LGAVRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAAL----VDGPPS 149
Cdd:PRK12679  78 snvrrLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIaserLSNDPQ 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 150 LAGLdgvPLCDEQLVLITSPEHPAV----LTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACV 225
Cdd:PRK12679 158 LVAF---PWFRWHHSLLVPHDHPLTqitpLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYV 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 499257667 226 IAGAGVAMMAQSMLDSLPGRDRVRVHSLQApFDQAVTWLmwrqGMRGANLQ 276
Cdd:PRK12679 235 ALGLGIGLVAEQSSGEQEESNLIRLDTRHL-FDANTVWL----GLKRGQLQ 280
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-172 2.55e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 74.42  E-value: 2.55e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDEA-L 79
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAkL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  80 GAVRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLC 159
Cdd:PRK09906  81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELL 160

                        170
                 ....*....|...
gi 499257667 160 DEQLVLITSPEHP 172
Cdd:PRK09906 161 DEPLVVVLPVDHP 173
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-171 3.04e-15

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 74.68  E-value: 3.04e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   6 LRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRE-RQRLqLSPAGKVLLDYANRMSALRDEALGAVRG 84
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHgRNKL-LTEHGIQLLGYARKILRFNDEACSSLMY 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  85 GQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALvdgppSLAGLDGVPlcdeQLV 164
Cdd:PRK15092  95 SNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV-----TTHRPSSFP----ALN 165


                 ....*..
gi 499257667 165 LITSPEH 171
Cdd:PRK15092 166 LRTSPTL 172
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-123 4.27e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 73.82  E-value: 4.27e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   6 LRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYA----NRMSALRDEALGA 81
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEArsviKKMQETRRQCQQV 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 499257667  82 VRGGQPAGDFVLGTMYSTAATHlpALLARYHQSYPQVNLQVR 123
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTR--QLIVDFYRHFDDVELIIR 126
PRK12680 PRK12680
LysR family transcriptional regulator;
1-172 1.18e-14

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 73.12  E-value: 1.18e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAE-EGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQ-LSPAGKVLLDYANRMSA----L 74
Cdd:PRK12680   1 MTLTQLRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSeannI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  75 RDEALGAVRGGQpaGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVD---GPPSlA 151
Cdd:PRK12680  81 RTYAANQRRESQ--GQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVStagGEPS-A 157

                        170       180
                 ....*....|....*....|.
gi 499257667 152 GLdGVPLCDEQLVLITSPEHP 172
Cdd:PRK12680 158 GI-AVPLYRWRRLVVVPRGHA 177
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-171 1.61e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 72.34  E-value: 1.61e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   3 FSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGK-VLLDYANRMSALRDEALgA 81
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKrVFWALKSSLDTLNQEIL-D 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  82 VRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRaapSGELLEGLLNHTLDAALV--DGPPslAGLDGVPLC 159
Cdd:PRK10086  95 IKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTIL---TGNENVNFQRAGIDLAIYfdDAPS--AQLTHHFLM 169

                        170
                 ....*....|..
gi 499257667 160 DEQLVLITSPEH 171
Cdd:PRK10086 170 DEEILPVCSPEY 181
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-261 1.99e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.18  E-value: 1.99e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   6 LRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKvllDYANRMSALRD---EALGAV 82
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQ---RYFLDIREIFDqlaEATRKL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  83 RGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSgelLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQ 162
Cdd:PRK11139  88 RARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDR---LEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 163 LVLITSPE-----HPaVLTAKDVAGKavfTFRQGCSYRMrLEAWYAHA--HTPMGRVMEIESYQSM-LACVIAGAGVAM- 233
Cdd:PRK11139 165 LLPVCSPAllnggKP-LKTPEDLARH---TLLHDDSRED-WRAWFRAAglDDLNVQQGPIFSHSSMaLQAAIHGQGVALg 239

                        250       260       270
                 ....*....|....*....|....*....|.
gi 499257667 234 ---MAQSMLDSlpGRdrvrvhsLQAPFDQAV 261
Cdd:PRK11139 240 nrvLAQPEIEA--GR-------LVCPFDTVL 261
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-88 4.26e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 68.07  E-value: 4.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   4 SQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQrLQLSPAGKVLLDYANRMSALRDEALGAVR 83
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQVALLEADLLSTLP 83


                 ....*
gi 499257667  84 GGQPA 88
Cdd:PRK13348  84 AERGS 88
PRK09791 PRK09791
LysR family transcriptional regulator;
1-140 5.37e-13

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 67.86  E-value: 5.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYAN----RMSALRD 76
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASlileELRAAQE 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499257667  77 EALGavRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVR----AAPSGELLEGLLNHTLD 140
Cdd:PRK09791  85 DIRQ--RQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMegqlVSMINELRQGELDFTIN 150
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-253 1.10e-12

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 65.70  E-value: 1.10e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVD-----GPPSLAGLDGVPLCDEQLVLIT 167
Cdd:cd08423    4 VGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFdypvtPPPDDPGLTRVPLLDDPLDLVL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 168 SPEHP----AVLTAKDVAGKAVFTFRQGCSY-RMRLEAWYAHAHTPmgRV-MEIESYQSMLACVIAGAGVAMMAQSMLDS 241
Cdd:cd08423   84 PADHPlagrEEVALADLADEPWIAGCPGSPChRWLVRACRAAGFTP--RIaHEADDYATVLALVAAGLGVALVPRLALGA 161

                        170
                 ....*....|..
gi 499257667 242 LPgrDRVRVHSL 253
Cdd:cd08423  162 RP--PGVVVRPL 171
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-87 5.14e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.79  E-value: 5.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRErQRLQLSPAGKVLLDYANRMSALRDEALG 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVRLLEAELLG 80


                 ....*..
gi 499257667  81 AVRGGQP 87
Cdd:PRK03635  81 ELPALDG 87
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-250 5.39e-12

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 63.69  E-value: 5.39e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  98 STAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP----A 173
Cdd:cd08421    9 SAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPlagrA 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499257667 174 VLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGRDRVRV 250
Cdd:cd08421   89 SVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRV 165
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-258 7.02e-12

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 64.45  E-value: 7.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  26 HRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRM----SALRDEAlgavrggQPAGDFVLGT--MYS- 98
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTllqwQQLRHTL-------DQQGPSLSGElsLFCs 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  99 -TAA-THLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSL-AGLDGVPLCDEQLVLItSPEHPAVL 175
Cdd:PRK11716  75 vTAAySHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLpASVAFSPIDEIPLVLI-APALPCPV 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 176 TAKDVAGK---AVFTF---RQGCSyRMRLEAWYAHAH-TP--MGRVMEIESYQSMLACviaGAGVAMMAQSMLDSLPGRD 246
Cdd:PRK11716 154 RQQLSQEKpdwSRIPFilpEHGPA-RRRIDLWFRRHKiKPniYATVSGHEAIVSMVAL---GCGVGLLPEVVLENSPVRN 229

                        250
                 ....*....|....*
gi 499257667 247 RVRVHSLQ---APFD 258
Cdd:PRK11716 230 RVQILERVppiTPFE 244
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 104-281 1.36e-11

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: 62.19  E-value: 1.36e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 104 LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP----AVLTAKD 179
Cdd:cd08438   15 FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPlagrKTVSLAD 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 180 VAGKAVFTFRQGCS-YRMRLEAWYAHAHTPMgrvmeiESYQS-----MLACVIAGAGVAMMAQSMLDSLpGRDRVRVHSL 253
Cdd:cd08438   95 LADEPFILFNEDFAlHDRIIDACQQAGFTPN------IAARSsqwdfIAELVAAGLGVALLPRSIAQRL-DNAGVKVIPL 167

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 499257667 254 QAPfdqAVTW---LMWRqgmRGANL----QAWIDL 281
Cdd:cd08438  168 TDP---DLRWqlaLIWR---KGRYLshaaRAWLAL 196
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 99-240 3.45e-11

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: 61.13  E-value: 3.45e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  99 TAATH-LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAAL--VDGPPSLAGLDGVPLCDEQLVLITSPEHP--- 172
Cdd:cd08435    9 AAAPVlLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVARPGHPlar 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 -AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGR-VMEIESYQSMLACVIAGAGVAMMAQSMLD 240
Cdd:cd08435   89 rARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRnVVETASISALLALLARSDMLAVLPRSVAE 158
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
20-68 6.76e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 61.57  E-value: 6.76e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 499257667  20 RAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYA 68
Cdd:PRK03601  20 RAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 92-264 4.17e-10

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 58.27  E-value: 4.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  92 VLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPpslagldgvpLCDEQLVLITSPEH 171
Cdd:cd08457    3 RIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGP----------LEERQGFLIETRSL 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 172 PAV--------------LTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQS 237
Cdd:cd08457   73 PAVvavpmghplaqldvVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPA 152

                        170       180
                 ....*....|....*....|....*..
gi 499257667 238 MLDSLPGRDRVrvhslQAPFDQAVTWL 264
Cdd:cd08457  153 TAIGLPLDGIV-----IRPFDTFIDAG 174
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 91-268 2.85e-09

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: 55.68  E-value: 2.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  91 FVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPE 170
Cdd:cd08417    2 FRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 171 HPAV---LTAKDV--AGKAVFTFRQgcSYRMRLEAWYAHahtpMGR----VMEIESYQSMLACVIAGAGVAMMAQSMLDS 241
Cdd:cd08417   82 HPLAggpLTLEDYlaAPHVLVSPRG--RGHGLVDDALAE----LGLsrrvALTVPHFLAAPALVAGTDLIATVPRRLAEA 155

                        170       180
                 ....*....|....*....|....*..
gi 499257667 242 LPGRDRVRVHSLQAPFDQAVTWLMWRQ 268
Cdd:cd08417  156 LAERLGLRVLPLPFELPPFTVSLYWHP 182
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 108-271 3.99e-09

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: 55.28  E-value: 3.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 108 LARYHQSYPQVNLQVRAAPSgelLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHPAVLTAKDVAGKAVFT 187
Cdd:cd08432   19 LARFQARHPDIDLRLSTSDR---LVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLPLLSPADLARHT 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 188 FRQGCSYRMRLEAWYAHA---HTPMGRVMEIESYQSMLACVIAGAGVAM----MAQSMLDSlpGRdrvrvhsLQAPFDQA 260
Cdd:cd08432   96 LLHDATRPEAWQWWLWAAgvaDVDARRGPRFDDSSLALQAAVAGLGVALapraLVADDLAA--GR-------LVRPFDLP 166

                        170
                 ....*....|....*.
gi 499257667 261 VT-----WLMWRQGMR 271
Cdd:cd08432  167 LPsggayYLVYPPGRA 182
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 11-172 4.36e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 56.58  E-value: 4.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  11 AVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRM----SALRDEALGavRGGQ 86
Cdd:PRK11151  11 ALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVlrevKVLKEMASQ--QGET 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  87 PAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLI 166
Cdd:PRK11151  89 MSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPLFDEPMLLA 168


                 ....*.
gi 499257667 167 TSPEHP 172
Cdd:PRK11151 169 VYEDHP 174
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 98-281 5.39e-09

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: 54.88  E-value: 5.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  98 STAATH--LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSL-AGLDGVPLCDEQLVLITSPEHP-- 172
Cdd:cd08451    8 SSAAFHplVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARsDGLVLELLLEEPMLVALPAGHPla 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 --AVLTAKDVAGKAVFTFRQGCS---YRMRLEAWYAHAHTPMgRVMEIESYQSMLACVIAGAGVAMMAQSMldSLPGRDR 247
Cdd:cd08451   88 reRSIPLAALADEPFILFPRPVGpglYDAIIAACRRAGFTPR-IGQEAPQMASAINLVAAGLGVSIVPASM--RQLQAPG 164

                        170       180       190
                 ....*....|....*....|....*....|....
gi 499257667 248 VRVHSLQAPFDQAVTWLMWRQGMRGANLQAWIDL 281
Cdd:cd08451  165 VVYRPLAGAPLTAPLALAYRRGERSPAVRNFIAL 198
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 98-232 6.12e-09

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


Pssm-ID: 176111  Cd Length: 197  Bit Score: 54.82  E-value: 6.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  98 STAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHPAV--- 174
Cdd:cd08419    8 STAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDHPLAgqk 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 175 -LTAKDVAGKAvFTFR-QGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVA 232
Cdd:cd08419   88 rIPLERLAREP-FLLRePGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLS 146
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-280 6.38e-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: 54.50  E-value: 6.38e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  91 FVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSL--AGLDGVPLCDEQLVLITS 168
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPlpKDLVWTPLVREPLVLIAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 169 PEHPAVLTAKDVAG-------KAVFTFRQgcsyrmrLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSmLDS 241
Cdd:cd08427   82 AELAGDDPRELLATqpfirydRSAWGGRL-------VDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDI-AVP 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 499257667 242 LPGRDRVRVHSLQAPFDQAVTWLMWRQG-MRGANLQAWID 280
Cdd:cd08427  154 LPAGPRVRVLPLGDPAFSRRVGLLWRRSsPRSRLIQALLE 193
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 106-281 9.88e-09

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 54.26  E-value: 9.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 106 ALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP-----AVLTAKDV 180
Cdd:cd08425   18 PLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPlaqrrTALTLDDL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 181 AGKAVFTFRQGCSYRMRLEAWY-AHAHTPmgRV-MEIESYQSMLACVIAGAGVAMMAQSMLDSLPGrdrVRVHSLQAPFD 258
Cdd:cd08425   98 AAEPLALLSPDFATRQHIDRYFqKQGIKP--RIaIEANSISAVLEVVRRGRLATILPDAIAREQPG---LCAVALEPPLP 172

                        170       180
                 ....*....|....*....|....
gi 499257667 259 QAVTWLMWRQG-MRGANLQAWIDL 281
Cdd:cd08425  173 GRTAALLRRKGaYRSAAARAFAAL 196
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-124 1.08e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 55.38  E-value: 1.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   9 FQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRM---SALRDEALGAVRgG 85
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMlveAQAAQDAIAALQ-V 88

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 499257667  86 QPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRA 124
Cdd:PRK14997  89 EPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEA 127
PRK10341 PRK10341
transcriptional regulator TdcA;
5-168 1.38e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.87  E-value: 1.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   5 QLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYA--------NRMSALRD 76
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSesitremkNMVNEING 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  77 EALGAVRggqpagDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAAL--VDGPPSLAGLD 154
Cdd:PRK10341  91 MSSEAVV------DVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLH 164

                        170
                 ....*....|....
gi 499257667 155 GVPLCDEQLVLITS 168
Cdd:PRK10341 165 VEPLFESEFVLVAS 178
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-280 1.71e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 53.43  E-value: 1.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  91 FVLGTMYSTaathLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPE 170
Cdd:cd08448    6 FVGSMLYRG----LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 171 HP-AVLTAKDVAGKAVFTF--------------------RQGCSYRMRLEAwyAHAHTpmgrvmeiesyqsMLACVIAGA 229
Cdd:cd08448   82 HPlAARRRIDLRELAGEPFvlfsrevspdyydqiialcmDAGFHPKIRHEV--RHWLT-------------VVALVAAGM 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 499257667 230 GVAMMAQSMLDSlpGRDRVRVHSLQAPFDQAVTWLMWRQGMRGANLQAWID 280
Cdd:cd08448  147 GVALVPRSLARA--GLAGVRFLPLKGATQRSELYAAWKASAPNPALQAFLA 195
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 104-281 2.71e-08

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: 53.13  E-value: 2.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 104 LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSL---AGLDGVPLCDEQLVLITSPEHPAV----LT 176
Cdd:cd08453   15 LPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGAsapPALAYRPLLSEPLVLAVPAAWAAEggapLA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 177 AKDVAGKAVFTFRQGCS---YRMRLEAWYAHAHTPMGRVMEIEsYQSMLACVIAGAGVAMMAQSmLDSLpGRDRVRVHSL 253
Cdd:cd08453   95 LAAVAAEPLVIFPRRIApafHDAVTGYYRAAGQTPRIAQEAIQ-MQTIISLVSAGMGVALVPAS-LRNL-ARPGVVYREL 171

                        170       180
                 ....*....|....*....|....*...
gi 499257667 254 QAPFDQAVTWLMWRQGMRGANLQAWIDL 281
Cdd:cd08453  172 ADPAPVLETGLVWRRDDASPVLARFLDL 199
nhaR PRK11062
transcriptional activator NhaR; Provisional
 3-82 3.47e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 53.47  E-value: 3.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   3 FSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDEALGAV 82
Cdd:PRK11062   6 YNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEMLDIV 85
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 99-239 4.39e-08

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: 51.95  E-value: 4.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  99 TAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPS--------------LAGLDGVPLCDEQLV 164
Cdd:cd08439   10 YADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPgasatilrrsptvwYCAAGYILAPGEPLP 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499257667 165 LI----TSPEHPAVLTAKDVAGKAvftfrqgcsYRMrleawyAHAHTpmgrvmeieSYQSMLACVIAGAGVAMMAQSML 239
Cdd:cd08439   90 LAlldePTLDRRAALAALDAAGIP---------WRI------AYAAS---------SLSGLRAAVRAGLGITARTQEMV 144
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-268 9.14e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 51.49  E-value: 9.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 104 LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP----AVLTAKD 179
Cdd:cd08447   15 LPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPlagaERLTLED 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 180 VAGKAVFTF--RQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMldSLPGRDRVRVHSLQAPF 257
Cdd:cd08447   95 LDGQPFIMYspTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASA--SRLRFEGVVFRPLDLPR 172

                        170
                 ....*....|..
gi 499257667 258 DQAVT-WLMWRQ 268
Cdd:cd08447  173 DVPVElHLAWRR 184
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-122 1.14e-07

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 52.21  E-value: 1.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 MEFSQLR-IFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRL-QLSPAGKVLLDYANRMSAlRDEA 78
Cdd:PRK12681   1 MKLQQLRyIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILS-KVES 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499257667  79 LGAVrggqpAGDFVL---GTMySTAATH------LPALLARYHQSYPQVNLQV 122
Cdd:PRK12681  80 IKSV-----AGEHTWpdkGSL-YIATTHtqaryaLPPVIKGFIERYPRVSLHM 126
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 104-188 1.84e-07

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: 50.64  E-value: 1.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 104 LPALlARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP----AVLTAKD 179
Cdd:cd08441   16 MPVL-DQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPlaakEFITPED 94


                 ....*....
gi 499257667 180 VAGKAVFTF 188
Cdd:cd08441   95 LADETLITY 103
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-271 2.12e-07

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 50.24  E-value: 2.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  92 VLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEH 171
Cdd:cd08412    3 RIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 172 P----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPmgRV-MEIESYQSMLACVIAGAGVAMMAQS-MLDSLPGR 245
Cdd:cd08412   83 PlagkDEVSLADLAAEPLILLDLPHSREYFLSLFAAAGLTP--RIaYRTSSFEAVRSLVANGLGYSLLNDRpYRPWSYDG 160

                        170       180
                 ....*....|....*....|....*.
gi 499257667 246 DRVRVHSLQAPFDQAVTWLMWRQGMR 271
Cdd:cd08412  161 KRLVRRPLADPVPPLRLGLAWRRGAR 186
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-261 1.18e-06

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: 48.18  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHP 172
Cdd:cd08456    4 IAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGHR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 173 ----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHtpMGRVMEIESYQSMLAC--VIAGAGVammaqSMLDSLPGRD 246
Cdd:cd08456   84 lavkKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAG--VKRRIVVETSYAATICalVAAGVGV-----SVVNPLTALD 156

                        170
                 ....*....|....*
gi 499257667 247 RVRVHSLQAPFDQAV 261
Cdd:cd08456  157 YAAAGLVVRRFSPAV 171
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 99-258 3.35e-06

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


Pssm-ID: 176121  Cd Length: 199  Bit Score: 46.80  E-value: 3.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  99 TAA-THLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLD---AALVDGPPslAGLDGVPLCDEQLVLITSPEHPAV 174
Cdd:cd08430    9 TASySFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADiaiAARPDKLP--ARLAFLPLATSPLVFIAPNIACAV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 175 LTAKDVAGKA-----VFTFRQGCSyRMRLEAWYA-HAHTPM--GRVMEIESYQSMLACviaGAGVAMMAQSMLDSLPGRD 246
Cdd:cd08430   87 TQQLSQGEIDwsrlpFILPERGLA-RERLDQWFRrRGIKPNiyAQVAGHEAIVSMVAL---GCGVGIVPELVLDNSPLKD 162

                        170
                 ....*....|....*
gi 499257667 247 RVRVHSLQ---APFD 258
Cdd:cd08430  163 KVRILEVQpelEPFE 177
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 100-269 3.54e-06

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: 46.85  E-value: 3.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 100 AATH------LPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALV----DGPPSLAGLdgvPLCDEQLVLITSP 169
Cdd:cd08413    5 ATTHtqaryvLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAtealDDHPDLVTL---PCYRWNHCVIVPP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 170 EHP----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVME------IESYqsmlacVIAGAGVAMMAQSML 239
Cdd:cd08413   82 GHPladlGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTaldadvIKTY------VRLGLGVGIIAEMAY 155

                        170       180       190
                 ....*....|....*....|....*....|
gi 499257667 240 DSLPGRDRVRVhSLQAPFDQAVTWLMWRQG 269
Cdd:cd08413  156 DPQRDADLVAL-DAGHLFGPNTTRIALRRG 184
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-252 4.64e-06

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 46.53  E-value: 4.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  98 STAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHPAV--- 174
Cdd:cd08426    9 GLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLArqp 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 175 -LTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMM---------AQSMLDSLPG 244
Cdd:cd08426   89 sVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLtelavrreiRRGQLVAVPL 168


                 ....*...
gi 499257667 245 RDRVRVHS 252
Cdd:cd08426  169 ADPHMNHR 176
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 108-262 4.24e-05

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: 43.44  E-value: 4.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 108 LARYHQSYPQVNLQVRAAPSGELLEGllnHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHPAVLTAKDVAGKAVFT 187
Cdd:cd08481   19 LPDFLARHPDITVNLVTRDEPFDFSQ---GSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRALAAPADLAHLP 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 188 FRQGCSyrmRLEAW--------YAHAHTPMGrvMEIESYQSMLACVIAGAGVA----MMAQSMLDSlpGRdrvrvhsLQA 255
Cdd:cd08481   96 LLQQTT---RPEAWrdwfeevgLEVPTAYRG--MRFEQFSMLAQAAVAGLGVAllprFLIEEELAR--GR-------LVV 161


                 ....*..
gi 499257667 256 PFDQAVT 262
Cdd:cd08481  162 PFNLPLT 168
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-134 5.18e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 43.98  E-value: 5.18e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   1 ME-FSQLRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRD--- 76
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQdvh 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499257667  77 EALGAVrGGQPAGDFVLGTMYSTAATHLPALLARYHQSYP--QVNLqVRAAPSGELL-EGL 134
Cdd:PRK10632  81 EQLYAF-NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPglSVNL-VTGIPAPDLIaDGL 139
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 100-238 7.14e-05

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: 42.81  E-value: 7.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 100 AATHLPALLARYHQSYPQVNLQVRAAPSgelLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPE----HPAVL 175
Cdd:cd08422   12 GRLHLAPLLAEFLARYPDVRLELVLSDR---LVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAylarHGTPQ 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499257667 176 TAKDVAGKAVFTFRqgcsYRMRLEAWY------AHAHTPMGRvMEIESYQSMLACVIAGAGVAMMAQSM 238
Cdd:cd08422   89 TPEDLARHRCLGYR----LPGRPLRWRfrrgggEVEVRVRGR-LVVNDGEALRAAALAGLGIALLPDFL 152
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 108-269 1.01e-04

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. 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: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 42.36  E-value: 1.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 108 LARYHQSYPQVNLQV-----RAAPSGEllegllnhTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPE------HPAvlt 176
Cdd:cd08484   19 LAEFRQLHPFIDLRLstnnnRVDIAAE--------GLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPElarrlsEPA--- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 177 akDVAGKAVFTfrqgcSYRM-RLEAWYAHAHTPMGRVMEI--ESYQSMLACVIAGAGVAMMAQSMLDSLPGRDRvrvhsL 253
Cdd:cd08484   88 --DLANETLLR-----SYRAdEWPQWFEAAGVPPPPINGPvfDSSLLMVEAALQGAGVALAPPSMFSRELASGA-----L 155

                        170       180
                 ....*....|....*....|
gi 499257667 254 QAPFDQAVT----WLMWRQG 269
Cdd:cd08484  156 VQPFKITVStgsyWLTRLKS 175
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 94-171 1.46e-04

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 41.94  E-value: 1.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  94 GTMYSTAAT----HLPA-LLARYHQSYPQVNLQVRaapSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITS 168
Cdd:cd08478    3 GLLRVDAATpfvlHLLApLIAKFRERYPDIELELV---SNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILAS 79


                 ...
gi 499257667 169 PEH 171
Cdd:cd08478   80 PDY 82
PBP_like_2 pfam12849
PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
 81-182 1.58e-04

PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.


Pssm-ID: 432831 [Multi-domain]  Cd Length: 267  Bit Score: 42.53  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   81 AVRGGQPAGDFVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPS-----LAGLDG 155
Cdd:pfam12849   1 SAAASAPTVGTILIAGSSTQAPGLLDLAEAFEKKYPGAKVKVTSVGSGEGIKALLNGDVDVALVSRPLTeeefeAFGANG 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 499257667  156 ------VPLCDEQLVLITSPEHPA-VLTAKDVAG 182
Cdd:pfam12849  81 agglveVPVAYDGIAIVVNKDNPAnILTVEALKK 114
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
32-190 1.73e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 42.35  E-value: 1.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  32 LSTRLRQLEEQLGVELFLRERQRLQLSPAGKVLLDYANRMSALRDEALGAVRGGQpagDFVLGTMySTAATH------LP 105
Cdd:PRK10082  42 FSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGS---DYAQRKI-KIAAAHslslglLP 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 106 ALLAryhQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSL--AGLDGVPLCDEQLVLItspehpavlTAKDVAGK 183
Cdd:PRK10082 118 SIIS---QMPPLFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLleAPFDHIRLFESQLFPV---------CASDEHGE 185


                 ....*..
gi 499257667 184 AVFTFRQ 190
Cdd:PRK10082 186 ALFNLAQ 192
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 91-277 2.67e-04

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: 41.18  E-value: 2.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  91 FVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSL--AGLDGVPLCDEQLVL--- 165
Cdd:cd08416    2 LRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLndPDFEVVPLFEDDIFLavp 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 166 ITSP--EHPAVlTAKDVAGKAVFTFRQG-CSYRMRLEAWYAHAHTPmGRVMEIESYQSMLACVIAGAGVAMmaqsmldsL 242
Cdd:cd08416   82 ATSPlaASSEI-DLRDLKDEKFVTLSEGfATYRGFDEAFEIAGFEP-NVVMRVNDIFSLMSMVSGGVGYAL--------L 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 499257667 243 PGR------DRVRVHSLQAPFD--QAVTWLMWRQGMRGANLQA 277
Cdd:cd08416  152 PGRiadvyeDKVQLIPLAEPYQirQTIGLVFLRSRERDPNLLA 194
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 93-238 2.95e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 41.10  E-value: 2.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSL--AGLDGVPLCDEQLVLITSPE 170
Cdd:cd08449    4 IGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLndPPLASELLWREPMVVALPEE 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499257667 171 HP----AVLTAKDVAGK--AVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESyQSMLACVIAGAGVAMMAQSM 238
Cdd:cd08449   84 HPlagrKSLTLADLRDEpfVFLRLANSRFADFLINCCLQAGFTPQITQEVVEP-QTLMALVAAGFGVALVPESY 156
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 108-269 7.64e-04

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. 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: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 39.84  E-value: 7.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 108 LARYHQSYPQVNLQVRaapSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPEHPAVLT-AKDVAGKAVF 186
Cdd:cd08487   19 LAEFRQLHPFIELRLR---TNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEIAKRLShPADLINETLL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 187 TfrqgcSYRM-RLEAWYAHAHTPMGRVME--IESYQSMLACVIAGAGVAMMAQSMLDSlpgrdRVRVHSLQAPFDQAVT- 262
Cdd:cd08487   96 R-----SYRTdEWLQWFEAANMPPIKIRGpvFDSSRLMVEAAMQGAGVALAPAKMFSR-----EIENGQLVQPFKIEVEt 165

                        170
                 ....*....|
gi 499257667 263 ---WLMWRQG 269
Cdd:cd08487  166 gsyWLTWLKS 175
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
6-123 1.61e-03

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 39.42  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667   6 LRIFQAVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELFLRERQRLQLSP-AGKVLLDYANRMSaLRDEALGAVRG 84
Cdd:PRK10216  13 LLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPlMVSMEQNLAEWMQ-MGNQLLDKPHH 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 499257667  85 GQPAG-DFVLGTMYSTAATHLPALLARYHQSYPQVNLQVR 123
Cdd:PRK10216  92 QTPRGlKFELAAESPLMMIMLNALSKRIYQRYPQATIKLR 131
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 93-269 1.97e-03

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: 38.64  E-value: 1.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  93 LGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALV-DGPPSLAGLDGVPLCDEQLVLITSPEH 171
Cdd:cd08444    4 IATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIAtEALENHPELVSFPYYDWHHHIIVPVGH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 172 P----AVLTAKDVAGKAVFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSMLDSLPGRDR 247
Cdd:cd08444   84 PlesiTPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRDTNL 163

                        170       180
                 ....*....|....*....|..
gi 499257667 248 VRVHSLQApFDQAVTWLMWRQG 269
Cdd:cd08444  164 IKLDTSHL-FGKNTTWIALRRG 184
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 98-173 2.47e-03

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: 38.49  E-value: 2.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  98 STAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALvdGPPSLAGLDG----VPLCDEQLVLITSPEHPA 173
Cdd:cd08418    9 LIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAI--GTLPDEMYLKelisEPLFESDFVVVARKDHPL 86
HTH_30 pfam13556
PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the ...
 6-57 3.44e-03

PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators such as Swiss:O32138 and is likely to be DNA-binding.


Pssm-ID: 433305 [Multi-domain]  Cd Length: 56  Bit Score: 35.12  E-value: 3.44e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 499257667    6 LRIFqaVAEEGSVTRAAERLHRVPSNLSTRLRQLEEQLGVELfLRERQRLQL 57
Cdd:pfam13556   2 LRAY--LENGGNISATARALHVHRNTLRYRLRRIEELLGLDL-DDPEDRLAL 50
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 91-239 4.61e-03

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: 37.36  E-value: 4.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667  91 FVLGTMYSTAATHLPALLARYHQSYPQVNLQVRAAPSGELLEGLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSPE 170
Cdd:cd08450    2 LTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPAD 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499257667 171 HPAV----LTAKDVAGKA-VFTFRQGCSYRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMM---AQSML 239
Cdd:cd08450   82 HRLAgrekIPPQDLAGENfISPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLplyANNLL 158
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-239 4.86e-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 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: 37.21  E-value: 4.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499257667 107 LLARYHQSYPQVNlqVRAAPSGELLEgLLNHTLDAALVDGPPSLAGLDGVPLCDEQLVLITSP---------EHPAVLTA 177
Cdd:cd08477   19 ALAEYLARYPDVR--VDLVLSDRLVD-LVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPdylarhgtpTTPEDLAR 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499257667 178 KDVAGKAVFTFRQgcsyRMRLEAWYAHAHTPMGRVMEIESYQSMLACVIAGAGVAMMAQSML 239
Cdd:cd08477   96 HECLGFSYWRARN----RWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALL 153
 
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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