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Conserved domains on  [gi|446277099|ref|WP_000354954|]
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MULTISPECIES: LysR family transcriptional regulator [Escherichia]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444076)

LysR family transcriptional regulator, similar to Staphylococcus aureus CidR which positively up-regulates the expression of the cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|11741199

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-286 1.08e-89

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: 265.19  E-value: 1.08e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPH 170
Cdd:cd08438    1 HLRLGLPPLGGsLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 171 SGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKN 250
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446277099 251 TLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08438  161 GVKVIPLtDPDLRWQLALIWRKGRYLSHAARAWLALL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.41e-22

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.21  E-value: 1.41e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099    3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-286 1.08e-89

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: 265.19  E-value: 1.08e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPH 170
Cdd:cd08438    1 HLRLGLPPLGGsLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 171 SGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKN 250
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446277099 251 TLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08438  161 GVKVIPLtDPDLRWQLALIWRKGRYLSHAARAWLALL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-283 4.18e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 199.32  E-value: 4.18e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSL 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPlLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 160 FSHPLCVLTPhsgkwlecdavspetlAEHPLliynedfalskqlmklfdehgvkPRIAVRSGQWDFLAAMVQAGVGIAIL 239
Cdd:COG0583  161 GEERLVLVAS----------------PDHPL-----------------------ARRAPLVNSLEALLAAVAAGLGIALL 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 446277099 240 PEPICQR-LDKNTLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWL 283
Cdd:COG0583  202 PRFLAADeLAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFL 247
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 2.29e-41

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: 142.04  E-value: 2.29e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   90 TGVLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLT 168
Cdd:pfam03466   1 SGRLRIGAPPTLAsYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  169 PHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQR-L 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAReL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 446277099  248 DKNTLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:pfam03466 161 ADGRLVALPLpEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-281 3.75e-39

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 138.94  E-value: 3.75e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLaefRQLEA 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL---QDLEA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ---ELSDINQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTT 156
Cdd:PRK11242  78 grrAIHDVADLSRGSLRLAMTPTFTAYLIGPlIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 157 LSLFSHPLCVLT----PHSGKWlecDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQA 232
Cdd:PRK11242 158 QPLFTETLALVVgrhhPLAARR---KALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRR 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 446277099 233 GVGIAILPEPICQRLDKntLKWLPLESELSWK-LGMIWREGVYLSHSAHA 281
Cdd:PRK11242 235 GRLATLLPAAIAREHDG--LCAIPLDPPLPQRtAALLRRKGAYRSAAARA 282
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-241 7.76e-39

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 138.13  E-value: 7.76e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTGVLRLG---IPPMvgMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTL 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGastIPGQ--YLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 158 SLFSHPLCVLTPHSGKWLE--CDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPR---IAVRSGQWDFLAAMVQA 232
Cdd:NF040786 159 PFYKDRLVLITPNGTEKYRmlKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnVVASLGSTEAIKQSVEA 238


                 ....*....
gi 446277099 233 GVGIAILPE 241
Cdd:NF040786 239 GLGISVISE 247
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.41e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.21  E-value: 1.41e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099    3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-91 3.54e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 62.68  E-value: 3.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   2 DIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRdGRRLLLTDTGRVVfergLALLAEFRQLEAE 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRL----LRHLRQVALLEAD 77

                         90
                 ....*....|
gi 446277099  82 LsdINQLKTG 91
Cdd:PRK13348  78 L--LSTLPAE 85
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 18-85 3.86e-04

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 38.74  E-value: 3.86e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446277099    18 FTRAAEKLFVTQPTISKMLKNLEDELnciLLIRDGRR-LLLTDTGRvvfERGLALLAEFRQLEAELSDI 85
Cdd:smart00529   1 TSEIAERLNVSPPTVTEMLKKLEKMG---LVEYEPYRgITLTEKGR---RLARRLLRKHRLLERFLVDV 63
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
22-84 1.31e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.41  E-value: 1.31e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446277099  22 AEKLFVTQPTISKMLKNLEdELNCILLIR---DGRRLL--LTDTGRVVFERGLALLAEF-RQLEAELSD 84
Cdd:COG1846   59 AERLGLTKSTVSRLLDRLE-EKGLVEREPdpeDRRAVLvrLTEKGRALLEEARPALEALlAELLAGLSE 126
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-286 1.08e-89

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: 265.19  E-value: 1.08e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPH 170
Cdd:cd08438    1 HLRLGLPPLGGsLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 171 SGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKN 250
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446277099 251 TLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08438  161 GVKVIPLtDPDLRWQLALIWRKGRYLSHAARAWLALL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-283 4.18e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 199.32  E-value: 4.18e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSL 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPlLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 160 FSHPLCVLTPhsgkwlecdavspetlAEHPLliynedfalskqlmklfdehgvkPRIAVRSGQWDFLAAMVQAGVGIAIL 239
Cdd:COG0583  161 GEERLVLVAS----------------PDHPL-----------------------ARRAPLVNSLEALLAAVAAGLGIALL 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 446277099 240 PEPICQR-LDKNTLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWL 283
Cdd:COG0583  202 PRFLAADeLAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFL 247
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-286 9.41e-54

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 173.56  E-value: 9.41e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLGIPPMVGM-LMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHS 171
Cdd:cd05466    2 LRIGASPSIAAyLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 172 GKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKNT 251
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 446277099 252 LKWLPLES-ELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd05466  162 LVVLPLEDpPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 2.29e-41

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: 142.04  E-value: 2.29e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   90 TGVLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLT 168
Cdd:pfam03466   1 SGRLRIGAPPTLAsYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  169 PHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQR-L 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAReL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 446277099  248 DKNTLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:pfam03466 161 ADGRLVALPLpEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-281 3.75e-39

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 138.94  E-value: 3.75e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLaefRQLEA 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL---QDLEA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ---ELSDINQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTT 156
Cdd:PRK11242  78 grrAIHDVADLSRGSLRLAMTPTFTAYLIGPlIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 157 LSLFSHPLCVLT----PHSGKWlecDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQA 232
Cdd:PRK11242 158 QPLFTETLALVVgrhhPLAARR---KALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRR 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 446277099 233 GVGIAILPEPICQRLDKntLKWLPLESELSWK-LGMIWREGVYLSHSAHA 281
Cdd:PRK11242 235 GRLATLLPAAIAREHDG--LCAIPLDPPLPQRtAALLRRKGAYRSAAARA 282
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-241 7.76e-39

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 138.13  E-value: 7.76e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTGVLRLG---IPPMvgMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTL 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGastIPGQ--YLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 158 SLFSHPLCVLTPHSGKWLE--CDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPR---IAVRSGQWDFLAAMVQA 232
Cdd:NF040786 159 PFYKDRLVLITPNGTEKYRmlKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnVVASLGSTEAIKQSVEA 238


                 ....*....
gi 446277099 233 GVGIAILPE 241
Cdd:NF040786 239 GLGISVISE 247
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-272 1.24e-32

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 121.80  E-value: 1.24e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTgVLRLGIPPMVGM-LMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSL 159
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVnLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 160 FSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFA--LSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIA 237
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSgsLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 446277099 238 ILPEPICQRLDKNTLkWLPLESEL-SWKLGMIWREG 272
Cdd:PRK09906 240 IIPGYMNNFNTGQVV-FRPLAGNVpSIALLMAWKKG 274
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-286 3.86e-31

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 118.22  E-value: 3.86e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLL-LTDTGRVVF---ERGLALLAEF 75
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLqivERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  76 RQLEAELSDINqlkTGVL---------RLGIPPMVGMlmagpiglFRQRYPGVELKISEFGGLTVQQAVMNGELDM--AL 144
Cdd:PRK12683  81 RRLAEQFADRD---SGHLtvatthtqaRYALPKVVRQ--------FKEVFPKVHLALRQGSPQEIAEMLLNGEADIgiAT 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 145 TALPvEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWD 224
Cdd:PRK12683 150 EALD-REPDLVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDAD 228

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 225 FLAAMVQAGVGIAILP--------EPICQRLDKNTLkwlpLESELSWkLGMiwREGVYLSHSAHAWLSCC 286
Cdd:PRK12683 229 VIKTYVELGMGVGIVAamaydpqrDTGLVALDTDHL----FEANTTR-VGL--RRGAYLRGYAYRFIELF 291
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-239 1.09e-29

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 114.30  E-value: 1.09e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLL-LTDTGRVVF---ERGLALLAEF 75
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILasvERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  76 RQLEAELSDINQlktGVL---------RLGIPPMvgmlmagpIGLFRQRYPGVELKISEfgGLTVQQA--VMNGELDMAL 144
Cdd:PRK12684  81 KRVGKEFAAQDQ---GNLtiatthtqaRYALPAA--------IKEFKKRYPKVRLSILQ--GSPTQIAemVLHGQADLAI 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 145 TALPVEE-SGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQW 223
Cdd:PRK12684 148 ATEAIADyKELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDA 227

                        250
                 ....*....|....*.
gi 446277099 224 DFLAAMVQAGVGIAIL 239
Cdd:PRK12684 228 DVIKTYVELGLGVGIV 243
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-272 9.09e-29

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 111.66  E-value: 9.09e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTGVLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEfggLTVQQAVM---NGELDMALTALPVEESGLTT 156
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGpYLLPHIIPMLHQTFPKLEMYLHE---AQTHQLLAqldSGKLDCAILALVKESEAFIE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 157 LSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGI 236
Cdd:PRK11151 158 VPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGI 237

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 446277099 237 AILPE-PICQRLDKNTLKWLPLES-ELSWKLGMIWREG 272
Cdd:PRK11151 238 TLLPAlAVPNERKRDGVCYLPCIKpEPRRTIGLVYRPG 275
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-255 4.13e-28

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 109.77  E-value: 4.13e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLaefRQLEA 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAIL---RQCEQ 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDIN---QLKTGVLRLGIPP-MVGMLMAGPI-GLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLT 155
Cdd:PRK11233  78 AQLAVHnvgQALSGQVSIGLAPgTAASSLTMPLlQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLS 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 156 TLSLFSHPLCVLTPHSgkwleC--DAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAG 233
Cdd:PRK11233 158 SQPLLKEDLFLVGTQD-----CpgQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASG 232

                        250       260
                 ....*....|....*....|..
gi 446277099 234 VGIAILPEPICQRLDKNTLKWL 255
Cdd:PRK11233 233 MGVTVLPESAARSLCGAVNGWM 254
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-258 5.20e-28

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 109.72  E-value: 5.20e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVF---ERGLALLAE-FRQL 78
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLrygNRILALCEEtCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  79 EaelsDINQLKTGVLRLGIPPMVGM-LMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALT--ALPVE-ESGL 154
Cdd:CHL00180  87 E----DLKNLQRGTLIIGASQTTGTyLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTElKKIL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 155 TTLSLFSHPLCVLTPHSGKWLECDAVSPETLaehplliYNEDF-ALSKQLM--KLFDEhgVKPRIAVRSGQWDFLAAM-- 229
Cdd:CHL00180 163 EITPYVEDELALIIPKSHPFAKLKKIQKEDL-------YRLNFiTLDSNSTirKVIDN--ILIQNGIDSKRFKIEMELns 233

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 446277099 230 -------VQAGVGIAIL-PEPICQRLDKNTLKWLPLE 258
Cdd:CHL00180 234 ieaiknaVQSGLGAAFVsVSAIEKELELGLLHWIKIE 270
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-272 8.64e-28

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: 106.44  E-value: 8.64e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIppmVGMLMAGP----IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVL 167
Cdd:cd08414    1 RLRIGF---VGSALYGLlprlLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 168 TPHSGKWLECDAVSPETLAEHPLLIYNEDFA--LSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPIcQ 245
Cdd:cd08414   78 LPADHPLAARESVSLADLADEPFVLFPREPGpgLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASV-A 156

                        170       180
                 ....*....|....*....|....*...
gi 446277099 246 RLDKNTLKWLPLE-SELSWKLGMIWREG 272
Cdd:cd08414  157 RLQRPGVVYRPLAdPPPRSELALAWRRD 184
PRK12680 PRK12680
LysR family transcriptional regulator;
1-263 1.28e-27

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 108.94  E-value: 1.28e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRL-LLTDTGRVVFERGLALLAEFRQL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  79 EAELSDINQLKTGVL---------RLGIPPMVGMLmagpiglfRQRYPGVELKISEFGGLTVQQAVMNGELDMAL--TAL 147
Cdd:PRK12680  81 RTYAANQRRESQGQLtlttthtqaRFVLPPAVAQI--------KQAYPQVSVHLQQAAESAALDLLGQGDADIAIvsTAG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 148 PVEESGLtTLSLFSHPLCVLTPhSGKWLECDAVSPE--TLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDF 225
Cdd:PRK12680 153 GEPSAGI-AVPLYRWRRLVVVP-RGHALDTPRRAPDmaALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADL 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 446277099 226 LAAMVQAGVGIAILPEPICQRLDKNTLKW---LPLESELSW 263
Cdd:PRK12680 231 IKTYVRAGLGVGLLAEMAVNANDEDLRAWpapAPIAECIAW 271
PRK09986 PRK09986
LysR family transcriptional regulator;
1-269 6.40e-27

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 106.35  E-value: 6.40e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTGVLRLGIppmVGMLMAGPIGL----FRQRYPGVELKISEFGGLTVQQAVMNGELDMAL--TALPVEESGL 154
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGI---VGTALWGRLRPamrhFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 155 TTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFA-LSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAG 233
Cdd:PRK09986 164 TSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSdWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG 243

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 446277099 234 VGIAILPEPiCQRLDKNTLKWLPLESELSWKLGMIW 269
Cdd:PRK09986 244 IGITLLPDS-YAQIPWPGVVFRPLKERIPADLYAVY 278
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-281 1.34e-26

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: 103.00  E-value: 1.34e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVGM-LMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPH 170
Cdd:cd08434    1 TVRLGFLHSLGTsLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 171 SGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPIcqRLDKN 250
Cdd:cd08434   81 DHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMT--LLNPP 158

                        170       180       190
                 ....*....|....*....|....*....|..
gi 446277099 251 TLKWLPLESELS-WKLGMIWREGVYLSHSAHA 281
Cdd:cd08434  159 GVKKIPIKDPDAeRTIGLAWLKDRYLSPAARR 190
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-286 1.58e-25

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: 100.29  E-value: 1.58e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  98 PPMVGMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLEC 177
Cdd:cd08440    8 PSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 178 DAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKNTLKWLPL 257
Cdd:cd08440   88 RSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPGLVARPL 167

                        170       180       190
                 ....*....|....*....|....*....|
gi 446277099 258 -ESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08440  168 tEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-241 6.25e-24

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 98.52  E-value: 6.25e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLL-LTDTGRVVFERGLALLAEFRQL 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  79 EAELSDINQLKTGVL---------RLGIPPmvgmlmagPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPV 149
Cdd:PRK12682  81 KRIGDDFSNQDSGTLtiatthtqaRYVLPR--------VVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 150 EE-SGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAA 228
Cdd:PRK12682 153 ADdPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKT 232

                        250
                 ....*....|...
gi 446277099 229 MVQAGVGIAILPE 241
Cdd:PRK12682 233 YVRLGLGVGIVAE 245
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-241 1.26e-23

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: 95.28  E-value: 1.26e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  91 GVLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEfgGLTVQ--QAVMNGELDMALTALPVEESGLTTLSLFSHPLCVL 167
Cdd:cd08411    1 GPLRLGVIPTIApYLLPRLLPALRQAYPKLRLYLRE--DQTERllEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLA 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446277099 168 TPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08411   79 VPKDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPE 152
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-272 2.78e-23

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: 94.20  E-value: 2.78e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLG-IPPMVGMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEE-SGLTTLSLFSHPLCVLTPH 170
Cdd:cd08436    2 LAIGtITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRpPGLASRELAREPLVAVVAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 171 SGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKn 250
Cdd:cd08436   82 DHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPG- 160

                        170       180
                 ....*....|....*....|..
gi 446277099 251 tLKWLPLESELSWKLGMIWREG 272
Cdd:cd08436  161 -LAALPLEPAPRRRLYLAWSAP 181
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.41e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.21  E-value: 1.41e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099    3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-286 5.50e-22

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: 91.07  E-value: 5.50e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLGI-PPMVGMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHS 171
Cdd:cd08412    2 LRIGCfSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 172 GKWLECDAVSPETLAEHPLLIYneDFALSKQ-LMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPIC--QRLD 248
Cdd:cd08412   82 HPLAGKDEVSLADLAAEPLILL--DLPHSREyFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYrpWSYD 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446277099 249 KNTLKWLPLESEL-SWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08412  160 GKRLVRRPLADPVpPLRLGLAWRRGARLTRAARAFVDFA 198
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-286 4.93e-21

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: 88.39  E-value: 4.93e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLG-IPPMVGMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTP-- 169
Cdd:cd08415    2 LRIAaLPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPpg 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 170 H--SGKwlecDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRL 247
Cdd:cd08415   82 HplARK----DVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGY 157

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446277099 248 DKNTLKWLPLESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08415  158 AGAGLVVRPFRPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-238 7.82e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 89.90  E-value: 7.82e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFER---GLALLAE-FRQLEAE 81
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDireIFDQLAEaTRKLRAR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  82 LSDinqlktGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISefgglTVQQAV--MNGELDMALTALPVEESGLTTLS 158
Cdd:PRK11139  91 SAK------GALTVSLLPSFAIQWLVPrLSSFNEAHPDIDVRLK-----AVDRLEdfLRDDVDVAIRYGRGNWPGLRVEK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 159 LFSH---PLCvlTPH---SGKWLEcdavSPETLAEHPLLiynedFALSKQLMKL-FDEHGVKPrIAVRSGQWDFLAAMV- 230
Cdd:PRK11139 160 LLDEyllPVC--SPAllnGGKPLK----TPEDLARHTLL-----HDDSREDWRAwFRAAGLDD-LNVQQGPIFSHSSMAl 227

                        250
                 ....*....|.
gi 446277099 231 QA---GVGIAI 238
Cdd:PRK11139 228 QAaihGQGVAL 238
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-239 2.46e-20

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 89.19  E-value: 2.46e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLL-LTDTGRVVFERGLALLAE---F 75
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKvesI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  76 RQLEAELSDINQlktGVL---------RLGIPPMvgmlmagpIGLFRQRYPGVELKISEfgGLTVQ--QAVMNGELDMAL 144
Cdd:PRK12681  81 KSVAGEHTWPDK---GSLyiatthtqaRYALPPV--------IKGFIERYPRVSLHMHQ--GSPTQiaEAAAKGNADFAI 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 145 TAlpveESglttLSLFSHPL---------CVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPR 215
Cdd:PRK12681 148 AT----EA----LHLYDDLImlpcyhwnrSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPR 219

                        250       260
                 ....*....|....*....|....
gi 446277099 216 IAVRSGQWDFLAAMVQAGVGIAIL 239
Cdd:PRK12681 220 IVFTATDADVIKTYVRLGLGVGVI 243
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 93-241 1.36e-19

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: 84.57  E-value: 1.36e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLGIPPMVGMLMAGPIGL-FRQRYPGVELKISE-FGGlTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPH 170
Cdd:cd08433    2 VSVGLPPSAASVLAVPLLRaVRRRYPGIRLRIVEgLSG-HLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446277099 171 SGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08433   81 DAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPA 151
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-252 3.99e-18

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 82.94  E-value: 3.99e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLL-LTDTGRvvferglALLAEFRQL 78
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGK-------ALLVIAERI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  79 EAELSDINQL-------KTGVL---------RLGIPPMvgmlmagpIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDM 142
Cdd:PRK12679  74 LNEASNVRRLadlftndTSGVLtiatthtqaRYSLPEV--------IKAFRELFPEVRLELIQGTPQEIATLLQNGEADI 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 143 ALTA-LPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSG 221
Cdd:PRK12679 146 GIASeRLSNDPQLVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQ 225

                        250       260       270
                 ....*....|....*....|....*....|.
gi 446277099 222 QWDFLAAMVQAGVGIAILPEPICQRLDKNTL 252
Cdd:PRK12679 226 DSDVIKTYVALGLGIGLVAEQSSGEQEESNL 256
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-252 1.29e-16

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 78.31  E-value: 1.29e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQlktGVLR---------LGIPPMVGMLMAgpigLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALtalpvee 151
Cdd:PRK10094  82 ELQQVND---GVERqvnivinnlLYNPQAVAQLLA----WLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAI------- 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 152 sGLTTLSLFSHPLCVLTPHSGKWLEcdAVSPetlaEHPLLiyNEDFALSKQLMKLFDEHGVK-------PRIAVR-SGQW 223
Cdd:PRK10094 148 -GVTGTEALANTFSLDPLGSVQWRF--VMAA----DHPLA--NVEEPLTEAQLRRFPAVNIEdsartltKRVAWRlPGQK 218

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 446277099 224 DF--------LAAMVqAGVGIAILPEPICQRL-DKNTL 252
Cdd:PRK10094 219 EIivpdmetkIAAHL-AGVGIGFLPKSLCQSMiDNQQL 255
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-283 2.56e-16

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 75.42  E-value: 2.56e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 101 VGMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAV 180
Cdd:cd08426   11 AAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 181 SPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE-PICQRLDKNTLKWLPL-E 258
Cdd:cd08426   91 TLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTElAVRREIRRGQLVAVPLaD 170

                        170       180
                 ....*....|....*....|....*.
gi 446277099 259 SELSWK-LGMIWREGVYLSHSAHAWL 283
Cdd:cd08426  171 PHMNHRqLELQTRAGRQLPAAASAFL 196
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-283 1.02e-15

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: 73.90  E-value: 1.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  91 GVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLT- 168
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPlIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVg 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 169 -PHSGKWLEcDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQrl 247
Cdd:cd08425   81 aTHPLAQRR-TALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAR-- 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446277099 248 DKNTLKWLPLESELSWK-LGMIWREGVYLSHSAHAWL 283
Cdd:cd08425  158 EQPGLCAVALEPPLPGRtAALLRRKGAYRSAAARAFA 194
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 109-272 1.35e-15

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 73.37  E-value: 1.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 109 IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEES-GLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAE 187
Cdd:cd08451   20 IRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSdGLVLELLLEEPMLVALPAGHPLARERSIPLAALAD 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 188 HPLLIYNEDFA--LSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPIcQRLDKNTLKWLPLESE-LSWK 264
Cdd:cd08451  100 EPFILFPRPVGpgLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASM-RQLQAPGVVYRPLAGApLTAP 178


                 ....*...
gi 446277099 265 LGMIWREG 272
Cdd:cd08451  179 LALAYRRG 186
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-290 1.64e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 75.11  E-value: 1.64e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEfrqlEAEL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ----AVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  83 SDINQLKTGVLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTT----- 156
Cdd:PRK10837  81 EQLFREDNGALRIYASSTIGnYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISepwle 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 157 --LSLFSHPLCVLTPHSgkwlecdaVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGV 234
Cdd:PRK10837 161 deLVVFAAPDSPLARGP--------VTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGL 232

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446277099 235 GIAILPEP-ICQRLDKNTLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWLSCCEGYW 290
Cdd:PRK10837 233 GISCLSRRvIADQLQAGTLVEVAVpLPRLMRTLYRIHHRQKHLSNALQRFLSYCQEAN 290
PRK09791 PRK09791
LysR family transcriptional regulator;
6-261 2.09e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 74.80  E-value: 2.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEAELSDI 85
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  86 NQLKTGVLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMAL-TALPVE-ESGLTTLSLFSH 162
Cdd:PRK09791  90 QGQLAGQINIGMGASIArSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTInTYYQGPyDHEFTFEKLLEK 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 163 PLCVLT----PHSGkwlecdAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAI 238
Cdd:PRK09791 170 QFAVFCrpghPAIG------ARSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSACISLVAKSDFLSI 243

                        250       260
                 ....*....|....*....|....
gi 446277099 239 LP-EPICQRLDKNTLKWLPLESEL 261
Cdd:PRK09791 244 LPeEMGCDPLHGQGLVMLPVSEIL 267
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-241 6.15e-15

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 72.93  E-value: 6.15e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  26 FVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEAELSDINQLKTGVLRL---------G 96
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcsvtaaysH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  97 IPPMvgmlmagpIGLFRQRYPGVELKISEfgG---LTVQQaVMNGELDMALTALPveE---SGLTTLSLFSHPLCVLTP- 169
Cdd:PRK11716  82 LPPI--------LDRFRAEHPLVEIKLTT--GdaaDAVEK-VQSGEADLAIAAKP--EtlpASVAFSPIDEIPLVLIAPa 148

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446277099 170 HSGKWLECDAVSPETLAEHPLLIYNEDFAlSKQLMKLFDEHGVKPRI-AVRSGQwDFLAAMVQAGVGIAILPE 241
Cdd:PRK11716 149 LPCPVRQQLSQEKPDWSRIPFILPEHGPA-RRRIDLWFRRHKIKPNIyATVSGH-EAIVSMVALGCGVGLLPE 219
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-283 9.50e-15

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 71.01  E-value: 9.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 109 IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEH 188
Cdd:cd08421   19 LASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAFADTLDH 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 189 PLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKNT-LKWLPLESelSW---K 264
Cdd:cd08421   99 DFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALgLRVVPLDD--AWarrR 176

                        170
                 ....*....|....*....
gi 446277099 265 LGMIWREGVYLSHSAHAWL 283
Cdd:cd08421  177 LLLCVRSFDALPPAARALV 195
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-286 7.70e-14

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 68.75  E-value: 7.70e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLG-IPPMVGMLMAGPIGLFRQRYPGVELKISEfgGLTVQ--QAVMNGELDMALTALPVE--ESGLTTLSLFSHPLCVL 167
Cdd:cd08427    2 LRLGaIATVLTGLLPRALARLRRRHPDLEVHIVP--GLSAEllARVDAGELDAAIVVEPPFplPKDLVWTPLVREPLVLI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 168 TPHsgkwlECDAVSPET-LAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQR 246
Cdd:cd08427   80 APA-----ELAGDDPRElLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPL 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446277099 247 LDKNTLKWLPL-ESELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08427  155 PAGPRVRVLPLgDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-240 9.20e-14

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 70.17  E-value: 9.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEAEL 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  83 SDINQLKTGVLRLGIPP-MVGMLMAGPIGLFRQRYPGveLKISEFGGLTVQQAVMNGeLDMALTALPVEESGLTTLSLFS 161
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSStMAQNVLAGLTAKMLKEYPG--LSVNLVTGIPAPDLIADG-LDVVIRVGALQDSSLFSRRLGA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 162 HPLCVLTPHSGKWLECDAVSPETLAEHPLLIYN----EDFalskqlmKLFDEHGVKPRIavrSGQWDF-------LAAMV 230
Cdd:PRK10632 161 MPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSvrpdNEF-------ELIAPEGISTRL---IPQGRFvtndpqtLVRWL 230

                        250
                 ....*....|
gi 446277099 231 QAGVGIAILP 240
Cdd:PRK10632 231 TAGAGIAYVP 240
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-252 9.28e-14

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 70.43  E-value: 9.28e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAefrQLEA 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 ELSDINQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSL 159
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPaLENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 160 F----------SHPLCVLTphsgkwlecdAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWdFLAAM 229
Cdd:PRK15421 159 FdyevrlvlapDHPLAAKT----------RITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTL-LLIQM 227

                        250       260
                 ....*....|....*....|...
gi 446277099 230 VQAGVGIAILPEPICQRLDKNTL 252
Cdd:PRK15421 228 VAARMGIAALPHWVVESFERQGL 250
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-247 9.59e-14

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 69.80  E-value: 9.59e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRdGRRLLLTDTGRVVfergLALLAEFRQLEA 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRL----LRHARQVRLLEA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  81 EL-SDINQLKTGVLRLGI-----------PPMVGMLMAGpiglfrqryPGVELKIsefggLTVQQAVM-----NGELDMA 143
Cdd:PRK03635  77 ELlGELPALDGTPLTLSIavnadslatwfLPALAPVLAR---------SGVLLDL-----VVEDQDHTaellrRGEVVGA 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 144 LTALPVEESGLTtlslfSHPL------CVLTPH-SGKWLEcDAVSPETLAEHPLLIYNEDFALSKQLM-KLFDEH-GVKP 214
Cdd:PRK03635 143 VTTEPQPVQGCR-----VDPLgamrylAVASPAfAARYFP-DGVTAEALAKAPAVVFNRKDDLQDRFLrQAFGLPpGSVP 216

                        250       260       270
                 ....*....|....*....|....*....|...
gi 446277099 215 RIAVRSGQwDFLAAmVQAGVGIAILPEPICQRL 247
Cdd:PRK03635 217 CHYVPSSE-AFVRA-ALAGLGWGMIPELQIEPE 247
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 107-241 1.54e-13

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: 67.65  E-value: 1.54e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 107 GPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMAL--TALPvEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPET 184
Cdd:cd08413   17 PVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIatEALD-DHPDLVTLPCYRWNHCVIVPPGHPLADLGPLTLED 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446277099 185 LAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08413   96 LAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAE 152
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 112-272 3.98e-13

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: 66.62  E-value: 3.98e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISEFGGlTVQ-QAVMNGELDMALTALPVEES---GLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAE 187
Cdd:cd08453   22 FREAYPDVELQLREATS-DVQlEALLAGEIDAGIVIPPPGASappALAYRPLLSEPLVLAVPAAWAAEGGAPLALAAVAA 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 188 HPLLIYNEDFA--LSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQrLDKNTLKWLPL-ESELSWK 264
Cdd:cd08453  101 EPLVIFPRRIApaFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLRN-LARPGVVYRELaDPAPVLE 179


                 ....*...
gi 446277099 265 LGMIWREG 272
Cdd:cd08453  180 TGLVWRRD 187
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-123 7.35e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 67.72  E-value: 7.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFergLALLAEFRQLEAELSDI 85
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF---WALKSSLDTLNQEILDI 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446277099  86 -NQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKI 123
Cdd:PRK10086  96 kNQELSGTLTVYSRPSIAQCWLVPrLADFTRRYPSISLTI 135
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-241 2.10e-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: 64.54  E-value: 2.10e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLG-IPPMVGMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMAL-----TALPVEESGLTTLSLFSHPLCV 166
Cdd:cd08423    2 LRVGaFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVvfdypVTPPPDDPGLTRVPLLDDPLDL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446277099 167 LTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08423   82 VLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 109-286 4.17e-12

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: 63.66  E-value: 4.17e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 109 IGLFRQRYPGVELKI----SEfgglTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPET 184
Cdd:cd08420   19 LARFRKRYPEVRVSLtignTE----EIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 185 LAEHPLLIYNEDfalS------KQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE-PICQRLDKNTLKWLPL 257
Cdd:cd08420   95 LAAEPWILREPG---SgtrevfERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRlAVRKELELGRLVALPV 171

                        170       180       190
                 ....*....|....*....|....*....|
gi 446277099 258 ES-ELSWKLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08420  172 EGlRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-239 4.25e-12

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: 63.59  E-value: 4.25e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLGIPPMVGM-LMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHS 171
Cdd:cd08456    2 LRIAVLPALSQsFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPG 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446277099 172 GKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAIL 239
Cdd:cd08456   82 HRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVV 149
PRK10341 PRK10341
transcriptional regulator TdcA;
4-279 5.72e-12

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 64.88  E-value: 5.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   4 RTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLaefRQLEAELS 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESIT---REMKNMVN 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  84 DINQL--KTGV-LRLGIPPMVGM-LMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEE--SGLTTL 157
Cdd:PRK10341  87 EINGMssEAVVdVSFGFPSLIGFtFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMklQDLHVE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 158 SLFSHPLCVLT----PHSGkwlecdAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAG 233
Cdd:PRK10341 167 PLFESEFVLVAsksrTCTG------TTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 446277099 234 VGIAILPEPICQRLDKNTLKWLPLESEL-SWKLGMIWREGVYLSHSA 279
Cdd:PRK10341 241 DFLTVIPCDMTSPFGSNQFITIPIEETLpVAQYAAVWSKNYRIKKAA 287
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 92-283 1.74e-11

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 62.23  E-value: 1.74e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVGMLMAGPI-GLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPH 170
Cdd:cd08417    1 TFRIAASDYLEALLLPPLlARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 171 SGKWLEcDAVSPETLAEHP--LLIYNEDFALSkqLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRL- 247
Cdd:cd08417   81 DHPLAG-GPLTLEDYLAAPhvLVSPRGRGHGL--VDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALa 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446277099 248 DKNTLKWLPLESEL-SWKLGMIWREgVYLSHSAHAWL 283
Cdd:cd08417  158 ERLGLRVLPLPFELpPFTVSLYWHP-RRDRDPAHRWL 193
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 93-276 2.27e-11

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176128  Cd Length: 198  Bit Score: 61.58  E-value: 2.27e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMAL--TALPVEESGLTTLSLFSHPLCVLTP 169
Cdd:cd08437    2 LRFGLPPIIGNYYFPKlAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALlgSLTPLENSALHSKIIKTQHFMIIVS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 170 HSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDk 249
Cdd:cd08437   82 KDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKPDD- 160

                        170       180
                 ....*....|....*....|....*....
gi 446277099 250 nTLKWLPL--ESELSWKLGMIWREGVYLS 276
Cdd:cd08437  161 -HLVAIPLldNEQPTFYISLAHRKDQLLT 188
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-91 3.54e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 62.68  E-value: 3.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   2 DIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRdGRRLLLTDTGRVVfergLALLAEFRQLEAE 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRL----LRHLRQVALLEAD 77

                         90
                 ....*....|
gi 446277099  82 LsdINQLKTG 91
Cdd:PRK13348  78 L--LSTLPAE 85
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 112-241 6.05e-11

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: 60.67  E-value: 6.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISefgglTVQQA-----VMNGELDMALTALPVE-ESGLTTLSLFSHPLCVLTPHSGKWLEcDAVSPETL 185
Cdd:cd08430   22 FRAQHPQVEIKLH-----TGDPAdaidkVLNGEADIAIAARPDKlPARLAFLPLATSPLVFIAPNIACAVT-QQLSQGEI 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 186 --AEHPLLIynEDFALSKQLM-KLFDEHGVKPRI-AVRSGQwDFLAAMVQAGVGIAILPE 241
Cdd:cd08430   96 dwSRLPFIL--PERGLARERLdQWFRRRGIKPNIyAQVAGH-EAIVSMVALGCGVGIVPE 152
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-271 6.72e-11

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 60.36  E-value: 6.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLL 191
Cdd:cd08448   22 FRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDLRELAGEPFV 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 192 IYNEDFA--LSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPIcQRLDKNTLKWLPLE-----SELSwk 264
Cdd:cd08448  102 LFSREVSpdYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRSL-ARAGLAGVRFLPLKgatqrSELY-- 178


                 ....*..
gi 446277099 265 lgMIWRE 271
Cdd:cd08448  179 --AAWKA 183
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-238 8.95e-11

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 61.55  E-value: 8.95e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   5 TLRY---FVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFER------GL------ 69
Cdd:PRK11013   5 SLRHieiFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEvqrsyyGLdrivsa 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  70 -ALLAEFRQleAELSDInqlktgvlrlGIPPMVGMLMAGPIGLFRQRYPGVELKIS--------EFggLTVQQAvmngel 140
Cdd:PRK11013  85 aESLREFRQ--GQLSIA----------CLPVFSQSLLPGLCQPFLARYPDVSLNIVpqesplleEW--LSAQRH------ 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 141 DMALTALPVEESGLTTLSLFS-HPLCVLTPHsgkwlecdavspetlaeHPLL----IYNEDFA------LS------KQL 203
Cdd:PRK11013 145 DLGLTETLHTPAGTERTELLTlDEVCVLPAG-----------------HPLAakkvLTPDDFAgenfisLSrtdsyrQLL 207

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 446277099 204 MKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAI 238
Cdd:PRK11013 208 DQLFAEHGVKRRMVVETHSAASVCAMVRAGVGVSI 242
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-258 1.35e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176136  Cd Length: 203  Bit Score: 59.55  E-value: 1.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 109 IGLFRQRYPGVELKISEFGglTVQQ--AVMNGELDMALTALPVEESGLTTLSLFSHPLCV-LTPHSGKWLECDAVSPETL 185
Cdd:cd08445   20 IRRFRQAAPDVEIELIEMT--TVQQieALKEGRIDVGFGRLRIEDPAIRRIVLREEPLVVaLPAGHPLAQEKAPLTLAQL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 186 AEHPLLIY----NEDFAlsKQLMKLFDEHGVKPRIA--VRSGQwdfLA-AMVQAGVGIAILPEPIcQRLDKNTLKWLPLE 258
Cdd:cd08445   98 ADEPLILYpaspRPSFA--DQVLSLFRDHGLRPRVIqeVRELQ---TAlGLVAAGEGVTLVPASV-QRLRRDDVVYRPLL 171
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 112-276 2.75e-10

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: 58.39  E-value: 2.75e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISEfgGLTVQ--QAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKwlecDAVSPETLAEHP 189
Cdd:cd08442   22 YHARYPKVDLSLST--GTTGAliQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHP----PVSRAEDLAGST 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 190 LLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRL-DKNTLKWLPLESELSWKLGM- 267
Cdd:cd08442   96 LLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLqGRGSVSIHPLPEPFADVTTWl 175


                 ....*....
gi 446277099 268 IWREGVYLS 276
Cdd:cd08442  176 VWRKDSFTA 184
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-270 2.93e-10

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: 58.52  E-value: 2.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVE--ESGLTTLSLFSHPLCVLT 168
Cdd:cd08418    1 KVSIGVSSLIAhTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEmyLKELISEPLFESDFVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 169 PHSGKWLECDAVSPETLAEHPLLiyNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEP-ICQRL 247
Cdd:cd08418   81 RKDHPLQGARSLEELLDASWVLP--GTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDmGRGPL 158

                        170       180
                 ....*....|....*....|....
gi 446277099 248 DKNTLKWLPLESEL-SWKLGMIWR 270
Cdd:cd08418  159 DSFRLITIPVEEPLpSADYYLIYR 182
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 112-275 7.53e-10

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 57.57  E-value: 7.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPV-EESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPL 190
Cdd:cd08443   22 FIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALhDYDDLITLPCYHWNRCVVVKRDHPLADKQSISIEELATYPI 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 191 LIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKNTLKWLPLESELSWKLGMI-W 269
Cdd:cd08443  102 VTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVIRDARDLFPWSVTKIaF 181


                 ....*.
gi 446277099 270 REGVYL 275
Cdd:cd08443  182 RRGTFL 187
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-232 1.59e-09

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 57.71  E-value: 1.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVF---ERGLALLAE------FR 76
Cdd:PRK11062   9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFryaDKMFTLSQEmldivnYR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  77 QLEAELSDI-------NQLKTGVLRLGIPPmvgmlmAGPIGL--FRQRYPGVELKISEFggltvqqavmngELDMALTAL 147
Cdd:PRK11062  89 KESNLLFDVgvadalsKRLVSRVLLTAVPE------DESIHLrcFESTHEMLLEQLSQH------------KLDMILSDC 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 148 PVEESglTTLSLFSHPL--CVLTPHSGKWLEcDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAvrsGQWDF 225
Cdd:PRK11062 151 PVDST--QQEGLFSKKLgeCGVSFFCTNPLP-EKPFPACLEERRLLIPGRRTMLGRKLLNWFNSQGLNVEIL---GEFDD 224


                 ....*..
gi 446277099 226 lAAMVQA 232
Cdd:PRK11062 225 -AALMKA 230
PRK09801 PRK09801
LysR family transcriptional regulator;
4-126 1.66e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 57.74  E-value: 1.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   4 RTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEAELS 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446277099  84 DINQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEF 126
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPaITELMRNYPELQVHFELF 132
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 133-259 1.83e-09

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: 56.20  E-value: 1.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 133 QAVMNGELDMALTALPVE--ESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEH 210
Cdd:cd08416   43 KKLKDGELDAILVATPEGlnDPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIA 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446277099 211 GVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPIcQRLDKNTLKWLPLES 259
Cdd:cd08416  123 GFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRI-ADVYEDKVQLIPLAE 170
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-246 2.59e-09

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: 55.91  E-value: 2.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  91 GVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISefggLTVQQA-VMNGELDMALTALPVEESGLTTLSLFSHPLCVL- 167
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPlLAEFLARYPDVRLELV----LSDRLVdLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVa 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 168 ---------TPHSgkwlecdavsPETLAEHPLLIYNEDFALSK-QLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIA 237
Cdd:cd08422   77 spaylarhgTPQT----------PEDLARHRCLGYRLPGRPLRwRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIA 146


                 ....*....
gi 446277099 238 ILPEPICQR 246
Cdd:cd08422  147 LLPDFLVAE 155
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-241 3.01e-09

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 55.73  E-value: 3.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEFggLTVQQ--AVMNGELDMALTALPVEESGLTTLSLFSHPLCVLT 168
Cdd:cd08447    1 SLRIGFTAASAYSFLPRlLAAARAALPDVDLVLREM--VTTDQieALESGRIDLGLLRPPFARPGLETRPLVREPLVAAV 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446277099 169 PHSGKWLECDAVSPETLAEHPLLIY--NEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08447   79 PAGHPLAGAERLTLEDLDGQPFIMYspTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPA 153
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 109-283 3.60e-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: 55.21  E-value: 3.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 109 IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPhSGKWL-ECDAVSPETLAE 187
Cdd:cd08419   18 LGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAP-PDHPLaGQKRIPLERLAR 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 188 HPLLIyNEDFALSKQLM-KLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILP------EPICQRLDKNTLKWLPLESe 260
Cdd:cd08419   97 EPFLL-REPGSGTRLAMeRFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSlhtlalELATGRLAVLDVEGFPIRR- 174

                        170       180
                 ....*....|....*....|...
gi 446277099 261 lSWKLgmIWREGVYLSHSAHAWL 283
Cdd:cd08419  175 -QWYV--VHRKGKRLSPAAQAFL 194
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-154 1.18e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 55.00  E-value: 1.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEA 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446277099  81 ELSDINQLKTGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKISEfgglTVQQAVMNGE-LDMALTA--LPVEESGL 154
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPmLAKFMARYPDVSLQLEA----TNRRVDVVGEgVDVAIRVrpRPFEDSDL 155
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 93-242 1.67e-08

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: 53.65  E-value: 1.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLG-IPPMVGMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHS 171
Cdd:cd08457    2 LRIAaMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMG 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446277099 172 GKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILpEP 242
Cdd:cd08457   82 HPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAII-DP 151
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 111-272 4.51e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 52.38  E-value: 4.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 111 LFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAehpl 190
Cdd:cd08450   21 ILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPPQDLA---- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 191 liyNEDF--------ALSKQLMKLFDEHGVKPRIaVRSGQwDFLAAM--VQAGVGIAILPEPIcqrldKNTLKW----LP 256
Cdd:cd08450   97 ---GENFispaptapVLQQVIENYAAQHNIQPNI-IQEAD-NLLSAMslVASTLGCALLPLYA-----NNLLPPsvvaRP 166

                        170
                 ....*....|....*..
gi 446277099 257 LESEL-SWKLGMIWREG 272
Cdd:cd08450  167 LSGETpTIDLVMGYNKA 183
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 112-240 4.77e-08

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: 52.18  E-value: 4.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKIS---EFGGLtvqQAVMNGELDMALTALPVEESGLTTLSLF----------SHPLCvltphSGKWLEcd 178
Cdd:cd08441   22 FRERWPDVELDLSsgfHFDPL---PALLRGELDLVITSDPLPLPGIAYEPLFdyevvlvvapDHPLA-----AKEFIT-- 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446277099 179 avsPETLAEHPLLIYN-EDFALSkqLMKLF-DEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILP 240
Cdd:cd08441   92 ---PEDLADETLITYPvERERLD--VFRHFlQPAGIEPKRRRTVELTLMILQLVASGRGVAALP 150
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 102-283 4.90e-08

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


Pssm-ID: 176158  Cd Length: 221  Bit Score: 52.41  E-value: 4.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 102 GMLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLT----PHSGKwlec 177
Cdd:cd08469   12 AVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIFEQIPPRFRRRTLFDEDEVWVMrkdhPAARG---- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 178 dAVSPETLAEHPLLI-------------YNEDFALSKQ--------LMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGI 236
Cdd:cd08469   88 -ALTIETLARYPHIVvslggeeegavsgFISERGLARQtemfdrraLEEAFRESGLVPRVAVTVPHALAVPPLLADSDML 166

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 446277099 237 AILPEPIC---QRLDKNTLKWLPLESELSwKLGMIWREGvYLSHSAHAWL 283
Cdd:cd08469  167 ALLPRSLArafAERGGLVMKEPPYPPPPV-QIRAVWHER-HDNDPAVAWL 214
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 112-283 7.74e-08

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 51.67  E-value: 7.74e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLEcDAVSPETLAEHPLL 191
Cdd:cd08467   22 LRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRHGHPALA-QEWTLDDFATLRHV 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 192 IYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDKNT-LKWLPLESEL-SWKLGMIW 269
Cdd:cd08467  101 AIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAMLpLRVVPPPVDLgTFPVMLIW 180

                        170
                 ....*....|....
gi 446277099 270 REGvYLSHSAHAWL 283
Cdd:cd08467  181 HER-YQHDPAHRWL 193
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 93-262 2.11e-07

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: 50.35  E-value: 2.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  93 LRLGippMVGMLMAGPIG----LFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEES--GLTTLSLFSHPLCV 166
Cdd:cd08449    2 LNIG---MVGSVLWGGLGpalrRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNdpPLASELLWREPMVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 167 LTP--H---SGKWLECDAVSPETLAEHPLliynEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08449   79 ALPeeHplaGRKSLTLADLRDEPFVFLRL----ANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPE 154

                        170       180
                 ....*....|....*....|.
gi 446277099 242 PIcQRLDKNTLKWLPLESELS 262
Cdd:cd08449  155 SY-ARLPWPGVRFIPLKQAIS 174
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-286 5.47e-07

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: 49.19  E-value: 5.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVG-MLMAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALP--VEESGLTTLSLFSHPLCVLT 168
Cdd:cd08435    1 TVRVGAVPAAApVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLAddEQPPDLASEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 169 PHSGKWLECDAVSPETLAEHPLLIYNEDFALSKQLMKLFDEHGVK-PRIAVRSGQWDFLAAMVQAGVGIAILPEPICQR- 246
Cdd:cd08435   81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPlPRNVVETASISALLALLARSDMLAVLPRSVAEDe 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446277099 247 LDKNTLKWLPLESELSW-KLGMIWREGVYLSHSAHAWLSCC 286
Cdd:cd08435  161 LRAGVLRELPLPLPTSRrPIGITTRRGGPLSPAARALLDAL 201
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 112-240 6.58e-07

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


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 49.04  E-value: 6.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEHPLL 191
Cdd:cd08452   22 YRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIEDLRDEPII 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446277099 192 IYNEDF--ALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILP 240
Cdd:cd08452  102 TVAREAwpTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVP 152
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-149 3.09e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 47.63  E-value: 3.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  12 VVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLaefRQLEAELSDINQLKTG 91
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI---KKMQETRRQCQQVANG 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446277099  92 ---VLRLGIPPMV-----GMLMAGpiglFRQRYPGVELKISE--FGGltVQQAVMNGELDMAL---TALPV 149
Cdd:PRK11074  90 wrgQLSIAVDNIVrpdrtRQLIVD----FYRHFDDVELIIRQevFNG--VWDALADGRVDIAIgatRAIPV 154
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-240 4.53e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 47.33  E-value: 4.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTdtgrvvfERGLALLAEFRQL-- 78
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLT-------EHGIQLLGYARKIlr 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  79 ---EAELS----DINqlktGVLRLGIP-PMVGMLMAGPIGLFRQRYP----GVELKISEFggltVQQAVMNGELDMAlta 146
Cdd:PRK15092  84 fndEACSSlmysNLQ----GVLTIGASdDTADTILPFLLNRVSSVYPklalDVRVKRNAF----MMEMLESQEVDLA--- 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 147 lpveesgLTTLSLFSHPLCVLTPHSGKWLeCDA----VSPETLaehPLLIYNE-----DFALSKqlmklFDEHGVKPRIA 217
Cdd:PRK15092 153 -------VTTHRPSSFPALNLRTSPTLWY-CAAeyvlQKGEPI---PLVLLDEpspfrDMALAT-----LNAAGIPWRIA 216

                        250       260
                 ....*....|....*....|...
gi 446277099 218 VRSGQWDFLAAMVQAGVGIAILP 240
Cdd:PRK15092 217 YVASTLSAVRAAVKAGLGVTARP 239
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-283 9.29e-06

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 45.30  E-value: 9.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVGMLMAGPI-GLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFS-HPLCVLTP 169
Cdd:cd08464    1 TFRIGLSDDVESWLAPPLlAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTeGYACLFDP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 170 HSgkwleCDAVSPETL-----AEHPLLIYNEDF------ALSKQlmklfdehGVKPRIAVRSGQWDFLAAMVQAGVGIAI 238
Cdd:cd08464   81 QQ-----LSLSAPLTLedyvaRPHVLVSYRGGLrgfvddALAEL--------GRSRRVVASTPHFAALPALLRGTPLIAT 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 446277099 239 LPEPICQRL-DKNTLKWLPLESEL-SWKLGMIWReGVYLSHSAHAWL 283
Cdd:cd08464  148 VPARLARAWaAALGLRASPPPLDLpEFPISLLWH-ARTDNDPALVWL 193
PBP2_NhaR cd08429
The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA ...
 139-240 1.20e-05

The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine (PGA) .Thus, it is suggested that NhaR has an extended role in promoting bacterial survival. 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: 176120 [Multi-domain]  Cd Length: 204  Bit Score: 45.38  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 139 ELDMALTALPVEESglTTLSLFSHPL--CVL----TPHSGKWLECDAvsPETLAEHPLLIYNEDFALSKQLMKLFDEHGV 212
Cdd:cd08429   49 RLDMVLADRPMPSS--LDVKGYSHRLgeCGVsffaAPPLAKRLEKPF--PASLDEAPLLLPGEDSALRRKLLQWFERQGL 124

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446277099 213 KPRIAvrsGQWD---FLAAMVQAGVGIAILP 240
Cdd:cd08429  125 RPQIV---GEFDdsaLMKAFGQAGAGIFAAP 152
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 105-241 1.91e-05

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: 44.42  E-value: 1.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 105 MAGPIGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVE-ESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPE 183
Cdd:cd08444   15 LPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALEnHPELVSFPYYDWHHHIIVPVGHPLESITPLTIE 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446277099 184 TLAEHPLLIYNEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08444   95 TIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAE 152
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-56 5.53e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 43.85  E-value: 5.53e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446277099   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDEL---------NCILLIRDGRRLL 56
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLgvnlftrhrNNIRLTAAGERLL 65
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 91-241 8.15e-05

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 42.71  E-value: 8.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  91 GVLRL-GIPPMVGMLMAGPIGLFRQRYPGVELKisefggLTVQQAVMN---GELDMALTALPVEESGLTTLSLFSHPLCV 166
Cdd:cd08478    3 GLLRVdAATPFVLHLLAPLIAKFRERYPDIELE------LVSNEGIIDlieRKTDVAIRIGELTDSTLHARPLGKSRLRI 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446277099 167 LTphSGKWLECDAV--SPETLAEHPLLIYNEDFALSKQLMKLFDE--HGVKPRIAVRSGQwdFLAAMVQAGVGIAILPE 241
Cdd:cd08478   77 LA--SPDYLARHGTpqSIEDLAQHQLLGFTEPASLNTWPIKDADGnlLKIQPTITASSGE--TLRQLALSGCGIACLSD 151
PBP2_ToxR cd08465
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ...
 113-171 1.02e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. 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: 176154  Cd Length: 200  Bit Score: 42.30  E-value: 1.02e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 113 RQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFS-HPLCVLTPHS 171
Cdd:cd08465   23 RAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEELHAETLFEeRFVCLADRAT 82
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 18-85 3.86e-04

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 38.74  E-value: 3.86e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446277099    18 FTRAAEKLFVTQPTISKMLKNLEDELnciLLIRDGRR-LLLTDTGRvvfERGLALLAEFRQLEAELSDI 85
Cdd:smart00529   1 TSEIAERLNVSPPTVTEMLKKLEKMG---LVEYEPYRgITLTEKGR---RLARRLLRKHRLLERFLVDV 63
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-241 9.03e-04

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 39.57  E-value: 9.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 109 IGLFRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFSHPLCVLTPHSGKWLECDAVSPETLAEH 188
Cdd:cd08446   20 LRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVPKSHPLAARPAVSLADLRNE 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446277099 189 PLLIY----NEDFAlsKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPE 241
Cdd:cd08446  100 PLILFprggRPSFA--DEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPE 154
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
22-84 1.31e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.41  E-value: 1.31e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446277099  22 AEKLFVTQPTISKMLKNLEdELNCILLIR---DGRRLL--LTDTGRVVFERGLALLAEF-RQLEAELSD 84
Cdd:COG1846   59 AERLGLTKSTVSRLLDRLE-EKGLVEREPdpeDRRAVLvrLTEKGRALLEEARPALEALlAELLAGLSE 126
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 92-242 2.44e-03

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: 38.33  E-value: 2.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  92 VLRLGIPPMVGM--LMagP-IGLFRQRYPGVELKISefgglTVQQAV--MNGELDMALTALPVEESGLTTLSLFSHPLC- 165
Cdd:cd08432    1 VLTVSVTPSFAArwLI--PrLARFQARHPDIDLRLS-----TSDRLVdfAREGIDLAIRYGDGDWPGLEAERLMDEELVp 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 166 VLTPH--SGKWLEcdavSPETLAEHPLLiynEDFALSKQLMKLFDEHGVKPRIAVRSGQWDFLAAMVQA---GVGIAILP 240
Cdd:cd08432   74 VCSPAllAGLPLL----SPADLARHTLL---HDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAavaGLGVALAP 146


                 ..
gi 446277099 241 EP 242
Cdd:cd08432  147 RA 148
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 112-240 2.55e-03

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: 38.12  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 112 FRQRYPGVELKISefgglTVQQAV-MNGE-LDMALTALPVEESGLTTLSLFSHPLCVL-TPHSGKWLEcdavSPETLAEH 188
Cdd:cd08484   22 FRQLHPFIDLRLS-----TNNNRVdIAAEgLDFAIRFGEGAWPGTDATRLFEAPLSPLcTPELARRLS----EPADLANE 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446277099 189 PLL-IYNEDfalskQLMKLFDEHGVKPRIaVRSGQWDFLAAMVQA---GVGIAILP 240
Cdd:cd08484   93 TLLrSYRAD-----EWPQWFEAAGVPPPP-INGPVFDSSLLMVEAalqGAGVALAP 142
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-89 3.03e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 38.50  E-value: 3.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099   4 RTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCILLIRDGRRLLLTDTGRVVFERGLALLAEFRQLEAELS 83
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEIG 86


                 ....*.
gi 446277099  84 DINQLK 89
Cdd:PRK15243  87 PTGKTK 92
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
22-84 3.17e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.42  E-value: 3.17e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446277099    22 AEKLFVTQPTISKMLKNLEDE--LNCILLIRDGRRLL--LTDTGRVVFERglaLLAEFRQLEAELSD 84
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLEKKglVRREPSPEDRRSVLvsLTEEGRELIEQ---LLEARSETLAELLA 94
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-283 6.08e-03

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 37.26  E-value: 6.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  97 IPPMVGMLmagpiglfRQRYPGVELKISEFGGLTVQQAVMNGELDMALTALPVEESGLTTLSLFS-HPLCVLTPHSgkwl 175
Cdd:cd08461   15 LPPLLAAL--------RQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEeRYVCVTRRGH---- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 176 eCDAVSPETLA-----EHPLLIYNE-DFALSKQlmKLFDEHGVKPRIAVRSGQWDFLAAMVQAGVGIAILPEPICQRLDK 249
Cdd:cd08461   83 -PLLQGPLSLDqfcalDHIVVSPSGgGFAGSTD--EALAALGLTRNVVLSVPSFLVVPEILAATDMVAFVPSRLVPNLEG 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446277099 250 ntLKWLPLESELS-WKLGMIWREGVYLsHSAHAWL 283
Cdd:cd08461  160 --LQEVELPLEPPgFDVVMAWHERTHR-DPAHRWL 191
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-246 8.89e-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 4. 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: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 36.76  E-value: 8.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099  90 TGVLRLGIPPMVGMLMAGP-IGLFRQRYPGVELKisefggLTVQQAVMN--GE-LDMALTAL--PVEESGLTTLSLFSHP 163
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPlLPRFMAAYPQVRLQ------LEATNRRVDliEEgIDVALRVRfpPLEDSSLVMRVLGQSR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446277099 164 LC------VLTPHSgkwlecDAVSPETLAEHPLLIYNEdfALSKQLMKLFDEHGVKPRIAVR----SGQWDFLAAMVQAG 233
Cdd:cd08473   76 QRlvaspaLLARLG------RPRSPEDLAGLPTLSLGD--VDGRHSWRLEGPDGESITVRHRprlvTDDLLTLRQAALAG 147

                        170
                 ....*....|...
gi 446277099 234 VGIAILPEPICQR 246
Cdd:cd08473  148 VGIALLPDHLCRE 160
 
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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