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Conserved domains on  [gi|505383091|ref|WP_015570193|]
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LysR family transcriptional regulator [Enterobacter hormaechei]

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 ...
 93-287 6.84e-87

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: 258.26  E-value: 6.84e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVG-MMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPR 171
Cdd:cd08438    2 LRLGLPPLGGsLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEE-EFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDKN 251
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505383091 252 TLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08438  161 GVKVIPLtDPDLRWQLALIWRKGRYLSHAARAWLALL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 5.86e-23

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 89.37  E-value: 5.86e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091    3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGR 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 ...
 93-287 6.84e-87

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: 258.26  E-value: 6.84e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVG-MMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPR 171
Cdd:cd08438    2 LRLGLPPLGGsLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEE-EFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDKN 251
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505383091 252 TLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08438  161 GVKVIPLtDPDLRWQLALIWRKGRYLSHAARAWLALL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 4.81e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 199.71  E-value: 4.81e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLP 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPlLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGP-PPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 160 LFNHPLCVLVPRsgdwlkiesvkpellgEHPLliynedfalsrqlmalfnqhnvkPRIAVRSGQWDFLAAMVQAGVGIAI 239
Cdd:COG0583  160 LGEERLVLVASP----------------DHPL-----------------------ARRAPLVNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 505383091 240 LPQPICER-LDKNTLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:COG0583  201 LPRFLAADeLAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-286 2.21e-40

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 142.40  E-value: 2.21e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILaefRQLEA 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL---QDLEA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ---ELGDINHLTKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVeEESGLA 156
Cdd:PRK11242  78 grrAIHDVADLSRGSLRLAMTPTFTAYLIGPlIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPV-HSPEIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 157 TLPLFNHPLCVLV----PRSGdwlKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQ 232
Cdd:PRK11242 157 AQPLFTETLALVVgrhhPLAA---RRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVR 233

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505383091 233 AGVGIAILPQPICERLDKntLRWIPLESDL-HWQLGMIWREGVYLSHSAQAWLQC 286
Cdd:PRK11242 234 RGRLATLLPAAIAREHDG--LCAIPLDPPLpQRTAALLRRKGAYRSAAARAFIEL 286
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-287 4.82e-39

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: 136.26  E-value: 4.82e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   91 GLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLV 169
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPlLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP-PDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  170 PRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICER-L 248
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAReL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 505383091  249 DKNTLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:pfam03466 161 ADGRLVALPLpEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-288 2.95e-38

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: 136.98  E-value: 2.95e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLG---IPPMvgMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVeEESGLAT 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGastIPGQ--YLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKL-EKKRLVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 158 LPLFNHPLCVLVPRSGDW---LKIESVKPELLGEHplLIYNEDFALSRQLMAlfnqhNVKPRIAVRSGQWDFLA------ 228
Cdd:NF040786 158 TPFYKDRLVLITPNGTEKyrmLKEEISISELQKEP--FIMREEGSGTRKEAE-----KALKSLGISLEDLNVVAslgste 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505383091 229 ---AMVQAGVGIAILPQPICERLDKN-TLRWIPLES-DLHWQLGMIWREGVYLSHSAQAWLQCCE 288
Cdd:NF040786 231 aikQSVEAGLGISVISELAAEKEVERgRVLIFPIPGlPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 5.86e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 89.37  E-value: 5.86e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091    3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-97 1.78e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 66.34  E-value: 1.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRdGRKLLLTDTGRVVfergLAILAEFRQLEA 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRL----LRHARQVRLLEA 76

                         90
                 ....*....|....*...
gi 505383091  81 EL-GDINHLTKGLLRLGI 97
Cdd:PRK03635  77 ELlGELPALDGTPLTLSI 94
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 18-85 6.80e-04

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


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 38.35  E-value: 6.80e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 505383091    18 FTRAAEKLFVTQPTISKMLKNLEDElncTLLIRDGRK-LLLTDTGRvvfERGLAILAEFRQLEAELGDI 85
Cdd:smart00529   1 TSEIAERLNVSPPTVTEMLKKLEKM---GLVEYEPYRgITLTEKGR---RLARRLLRKHRLLERFLVDV 63
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
22-95 7.20e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 39.18  E-value: 7.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  22 AEKLFVTQPTISKMLKNLEDElncTLLIR-----DGRKLL--LTDTGRVVFERGLAILAEF-RQLEAELG--DINHLTKG 91
Cdd:COG1846   59 AERLGLTKSTVSRLLDRLEEK---GLVERepdpeDRRAVLvrLTEKGRALLEEARPALEALlAELLAGLSeeELEALLRL 135


                 ....
gi 505383091  92 LLRL 95
Cdd:COG1846  136 LRRL 139
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 93-287 6.84e-87

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: 258.26  E-value: 6.84e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVG-MMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPR 171
Cdd:cd08438    2 LRLGLPPLGGsLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEE-EFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDKN 251
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505383091 252 TLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08438  161 GVKVIPLtDPDLRWQLALIWRKGRYLSHAARAWLALL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 4.81e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 199.71  E-value: 4.81e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLP 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPlLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGP-PPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 160 LFNHPLCVLVPRsgdwlkiesvkpellgEHPLliynedfalsrqlmalfnqhnvkPRIAVRSGQWDFLAAMVQAGVGIAI 239
Cdd:COG0583  160 LGEERLVLVASP----------------DHPL-----------------------ARRAPLVNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 505383091 240 LPQPICER-LDKNTLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:COG0583  201 LPRFLAADeLAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-287 2.34e-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: 175.48  E-value: 2.34e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVGM-MMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPR 171
Cdd:cd05466    2 LRIGASPSIAAyLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDP-GLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDKN 251
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505383091 252 TLRWIPLES-DLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd05466  161 GLVVLPLEDpPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-286 2.21e-40

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 142.40  E-value: 2.21e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILaefRQLEA 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL---QDLEA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ---ELGDINHLTKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVeEESGLA 156
Cdd:PRK11242  78 grrAIHDVADLSRGSLRLAMTPTFTAYLIGPlIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPV-HSPEIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 157 TLPLFNHPLCVLV----PRSGdwlKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQ 232
Cdd:PRK11242 157 AQPLFTETLALVVgrhhPLAA---RRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVR 233

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505383091 233 AGVGIAILPQPICERLDKntLRWIPLESDL-HWQLGMIWREGVYLSHSAQAWLQC 286
Cdd:PRK11242 234 RGRLATLLPAAIAREHDG--LCAIPLDPPLpQRTAALLRRKGAYRSAAARAFIEL 286
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-287 4.82e-39

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: 136.26  E-value: 4.82e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   91 GLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLV 169
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPlLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP-PDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  170 PRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICER-L 248
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAReL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 505383091  249 DKNTLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:pfam03466 161 ADGRLVALPLpEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-288 2.95e-38

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: 136.98  E-value: 2.95e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLG---IPPMvgMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVeEESGLAT 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGastIPGQ--YLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKL-EKKRLVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 158 LPLFNHPLCVLVPRSGDW---LKIESVKPELLGEHplLIYNEDFALSRQLMAlfnqhNVKPRIAVRSGQWDFLA------ 228
Cdd:NF040786 158 TPFYKDRLVLITPNGTEKyrmLKEEISISELQKEP--FIMREEGSGTRKEAE-----KALKSLGISLEDLNVVAslgste 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505383091 229 ---AMVQAGVGIAILPQPICERLDKN-TLRWIPLES-DLHWQLGMIWREGVYLSHSAQAWLQCCE 288
Cdd:NF040786 231 aikQSVEAGLGISVISELAAEKEVERgRVLIFPIPGlPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-259 7.90e-33

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 122.82  E-value: 7.90e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEAEL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  83 GDINHLTKGLLRLGIPPMVGM-MMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMT--ALPVEEESGLATLP 159
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTyLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTELKKILEITP 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 160 LFNHPLCVLVPRSGDWLKIESVKPELLgehplliYNEDF-ALSRQLMA------LFNQHNV-----KPRIAVRSGQwdFL 227
Cdd:CHL00180 167 YVEDELALIIPKSHPFAKLKKIQKEDL-------YRLNFiTLDSNSTIrkvidnILIQNGIdskrfKIEMELNSIE--AI 237

                        250       260       270
                 ....*....|....*....|....*....|...
gi 505383091 228 AAMVQAGVGIAIL-PQPICERLDKNTLRWIPLE 259
Cdd:CHL00180 238 KNAVQSGLGAAFVsVSAIEKELELGLLHWIKIE 270
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-273 2.13e-31

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 118.72  E-value: 2.13e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHlTKGLLRLGIPPMVGM-MMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLP 159
Cdd:PRK09906  81 RARKIVQ-EDRQLTIGFVPSAEVnLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSD-EIDYLE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 160 LFNHPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFA--LSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGI 237
Cdd:PRK09906 159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSgsLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGC 238

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 505383091 238 AILPQPICERLDKNTLrWIPLESDL-HWQLGMIWREG 273
Cdd:PRK09906 239 TIIPGYMNNFNTGQVV-FRPLAGNVpSIALLMAWKKG 274
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-240 6.97e-31

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 117.84  E-value: 6.97e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLL-LTDTGRVVF---ERGLAILAEF 75
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLqivERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  76 RQLEAEL--GDINHL----TKGLLRLGIPPMVgmmmagpiSLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPV 149
Cdd:PRK12683  81 RRLAEQFadRDSGHLtvatTHTQARYALPKVV--------RQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 150 EEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAA 229
Cdd:PRK12683 153 DREPDLVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKT 232

                        250
                 ....*....|.
gi 505383091 230 MVQAGVGIAIL 240
Cdd:PRK12683 233 YVELGMGVGIV 243
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-287 1.77e-30

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: 113.77  E-value: 1.77e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  98 PPMVGMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLVPRSGDWLK 177
Cdd:cd08440    8 PSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEP-EADPDLEFEPLLRDPFVLVCPKDHPLAR 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 178 IESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDKNTLRWIP 257
Cdd:cd08440   87 RRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPGLVARP 166

                        170       180       190
                 ....*....|....*....|....*....|.
gi 505383091 258 L-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08440  167 LtEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-242 4.94e-29

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 112.82  E-value: 4.94e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLGIPPMVG-MMMAGPISLFRQRYPGVELKISEfggLTVQQAVM---NGELDVAMTALpVEEESGLA 156
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGpYLLPHIIPMLHQTFPKLEMYLHE---AQTHQLLAqldSGKLDCAILAL-VKESEAFI 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 157 TLPLFNHPLCVLVPRSGDWLKIESVK-PELLGEHpLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGV 235
Cdd:PRK11151 157 EVPLFDEPMLLAVYEDHPWANRDRVPmSDLAGEK-LLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGS 235


                 ....*..
gi 505383091 236 GIAILPQ 242
Cdd:PRK11151 236 GITLLPA 242
PRK12680 PRK12680
LysR family transcriptional regulator;
1-255 8.68e-29

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 112.41  E-value: 8.68e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKL-LLTDTGRVVFERGLAILAEFRQL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  79 EAELGDINHLTKGLL---------RLGIPPMVgmmmagpiSLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPV 149
Cdd:PRK12680  81 RTYAANQRRESQGQLtlttthtqaRFVLPPAV--------AQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 150 EEESGLATLPLFNHPLCVLVPRsGDWLKIESVKPEL--LGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFL 227
Cdd:PRK12680 153 GEPSAGIAVPLYRWRRLVVVPR-GHALDTPRRAPDMaaLAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLI 231

                        250       260
                 ....*....|....*....|....*...
gi 505383091 228 AAMVQAGVGIAILPQPICERLDKNTLRW 255
Cdd:PRK12680 232 KTYVRAGLGVGLLAEMAVNANDEDLRAW 259
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-273 5.96e-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: 106.82  E-value: 5.96e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIppmVGMMMAGP----ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVL 168
Cdd:cd08414    2 LRIGF---VGSALYGLlprlLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPP-GLASRPLLREPLVVA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 169 VPRSGDWLKIESVKPELLGEHPLLIYNEDFA--LSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICE 246
Cdd:cd08414   78 LPADHPLAARESVSLADLADEPFVLFPREPGpgLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVAR 157

                        170       180
                 ....*....|....*....|....*...
gi 505383091 247 RLDKNtLRWIPLE-SDLHWQLGMIWREG 273
Cdd:cd08414  158 LQRPG-VVYRPLAdPPPRSELALAWRRD 184
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-240 7.13e-28

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 109.68  E-value: 7.13e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLL-LTDTGRVVFERGLAILAEFRQL 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  79 EAELGDINHLTKGLL---------RLGIPPMvgmmmagpISLFRQRYPGVELKISEfgGLTVQQA--VMNGELDVAMTAL 147
Cdd:PRK12684  81 KRVGKEFAAQDQGNLtiatthtqaRYALPAA--------IKEFKKRYPKVRLSILQ--GSPTQIAemVLHGQADLAIATE 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 148 PVEEESGLATLPLF--NHplCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWD 225
Cdd:PRK12684 151 AIADYKELVSLPCYqwNH--CVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDAD 228

                        250
                 ....*....|....*
gi 505383091 226 FLAAMVQAGVGIAIL 240
Cdd:PRK12684 229 VIKTYVELGLGVGIV 243
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 109-282 1.36e-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: 103.38  E-value: 1.36e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTAlPVEEESGLATLPLFNHPLCVLVPRS-----GDWLKIEsvkp 183
Cdd:cd08434   19 IRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCS-PVPDEPDIEWIPLFTEELVLVVPKDhplagRDSVDLA---- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 184 ELLGEhPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPicERLDKNTLRWIPLESDL- 262
Cdd:cd08434   94 ELADE-PFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEM--TLLNPPGVKKIPIKDPDa 170

                        170       180
                 ....*....|....*....|
gi 505383091 263 HWQLGMIWREGVYLSHSAQA 282
Cdd:cd08434  171 ERTIGLAWLKDRYLSPAARR 190
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-282 5.85e-25

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 101.68  E-value: 5.85e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILaefRQLEA 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAIL---RQCEQ 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHltkgllrlgippmVGMMMAGPISL------------------FRQRYPGVELKISEFGGLTVQQAVMNGELDV 142
Cdd:PRK11233  78 AQLAVHN-------------VGQALSGQVSIglapgtaassltmpllqaVRAEFPGIVLYLHENSGATLNEKLMNGQLDM 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 143 AMT--ALPVeeeSGLATLPLFNHPLCVLVPRSGdwlKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVR 220
Cdd:PRK11233 145 AVIyeHSPV---AGLSSQPLLKEDLFLVGTQDC---PGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGE 218

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 505383091 221 SGQWDFLAAMVQAGVGIAILPQPICERLDKNTLRWIP--LESDLHWQLGMIWREGVYLSHSAQA 282
Cdd:PRK11233 219 IESIATLTAAIASGMGVTVLPESAARSLCGAVNGWMAriTTPSMSLSLSLNLSARLPLSPQAQA 282
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-240 4.94e-24

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 99.30  E-value: 4.94e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLL-LTDTGRVVFERGLAILAEFRQL 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  79 EAELGDINHLTKGLL---------RLGIPPmvgmmmagPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPV 149
Cdd:PRK12682  81 KRIGDDFSNQDSGTLtiatthtqaRYVLPR--------VVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 150 EEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAA 229
Cdd:PRK12682 153 ADDPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKT 232

                        250
                 ....*....|.
gi 505383091 230 MVQAGVGIAIL 240
Cdd:PRK12682 233 YVRLGLGVGIV 243
PRK09986 PRK09986
LysR family transcriptional regulator;
1-270 5.15e-23

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 95.95  E-value: 5.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLGIppmVGMMMAGPI----SLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAM-TALPVEEESGL 155
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGI---VGTALWGRLrpamRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwRMADLEPNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 156 ATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFA-LSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAG 234
Cdd:PRK09986 164 TSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSdWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG 243

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 505383091 235 VGIAILPQPiCERLDKNTLRWIPLESDLHWQLGMIW 270
Cdd:PRK09986 244 IGITLLPDS-YAQIPWPGVVFRPLKERIPADLYAVY 278
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 5.86e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 89.37  E-value: 5.86e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091    3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-240 6.49e-23

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 96.51  E-value: 6.49e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLL-LTDTGRVVFERGLAILAEFRQL 78
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  79 EAELGDINHLTKGLL---------RLGIPPMvgmmmagpISLFRQRYPGVELKISEfgGLTVQ--QAVMNGELDVAMTAL 147
Cdd:PRK12681  81 KSVAGEHTWPDKGSLyiatthtqaRYALPPV--------IKGFIERYPRVSLHMHQ--GSPTQiaEAAAKGNADFAIATE 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 148 PVEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFL 227
Cdd:PRK12681 151 ALHLYDDLIMLPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVI 230

                        250
                 ....*....|...
gi 505383091 228 AAMVQAGVGIAIL 240
Cdd:PRK12681 231 KTYVRLGLGVGVI 243
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-273 6.98e-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: 93.36  E-value: 6.98e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  91 GLLRLGIPPMVGmmmagP------ISLFRQRYPGVELKISEfgGLTVQ--QAVMNGELDVAMTALPVEEEsGLATLPLFN 162
Cdd:cd08411    1 GPLRLGVIPTIA-----PyllprlLPALRQAYPKLRLYLRE--DQTERllEKLRSGELDAALLALPVDEP-GLEEEPLFD 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 163 HPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQ 242
Cdd:cd08411   73 EPFLLAVPKDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPE 152

                        170       180       190
                 ....*....|....*....|....*....|....
gi 505383091 243 --PICERLDKNTLRWIPLESDL-HWQLGMIWREG 273
Cdd:cd08411  153 laVPSEELRGDRLVVRPFAEPApSRTIGLVWRRS 186
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-273 5.71e-22

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 91.12  E-value: 5.71e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLG-IPPMVGMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEESGLATLPLFNHPLcVLVPR 171
Cdd:cd08436    2 LAIGtITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPL-VAVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWL-KIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDK 250
Cdd:cd08436   81 PDHPLaGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPG 160

                        170       180
                 ....*....|....*....|...
gi 505383091 251 ntLRWIPLESDLHWQLGMIWREG 273
Cdd:cd08436  161 --LAALPLEPAPRRRLYLAWSAP 181
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-287 3.29e-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: 88.77  E-value: 3.29e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  92 LLRLG-IPPMVGMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEeSGLATLPLFNHPLCVLVP 170
Cdd:cd08415    1 TLRIAaLPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDH-PGLESEPLASGRAVCVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 171 RsGDWL-KIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLD 249
Cdd:cd08415   80 P-GHPLaRKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYA 158

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 505383091 250 KNTLRWIPLESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08415  159 GAGLVVRPFRPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-287 1.88e-20

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: 86.83  E-value: 1.88e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGI-PPMVGMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTaLPVEEESGLATLPLFNHPLCVLVPR 171
Cdd:cd08412    2 LRIGCfSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALT-YDLDLPEDIAFEPLARLPPYVWLPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLKIESVKPELLGEHPLLIYneDFALSRQ-LMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPIC--ERL 248
Cdd:cd08412   81 DHPLAGKDEVSLADLAAEPLILL--DLPHSREyFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYrpWSY 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 505383091 249 DKNTLRWIPLESDLHWQ-LGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08412  159 DGKRLVRRPLADPVPPLrLGLAWRRGARLTRAARAFVDFA 198
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-242 1.97e-20

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 88.34  E-value: 1.97e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  26 FVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEAELGDINHLTKGLLRL---------G 96
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcsvtaaysH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  97 IPPMvgmmmagpISLFRQRYPGVELKISEfgG---LTVQQaVMNGELDVAMTALPVEEESGLATLPLFNHPLCVLVPRSG 173
Cdd:PRK11716  82 LPPI--------LDRFRAEHPLVEIKLTT--GdaaDAVEK-VQSGEADLAIAAKPETLPASVAFSPIDEIPLVLIAPALP 150

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505383091 174 DWLKIESVKPEL-LGEHPLLIYNEdfALSRQLMAL-FNQHNVKPRI-AVRSGQwDFLAAMVQAGVGIAILPQ 242
Cdd:PRK11716 151 CPVRQQLSQEKPdWSRIPFILPEH--GPARRRIDLwFRRHKIKPNIyATVSGH-EAIVSMVALGCGVGLLPE 219
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 93-242 8.86e-20

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: 84.95  E-value: 8.86e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISE-FGGlTVQQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLVP 170
Cdd:cd08433    2 VSVGLPPSAASVLAVPlLRAVRRRYPGIRLRIVEgLSG-HLLEWLLNGRLDLALLYGP-PPIPGLSTEPLLEEDLFLVGP 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505383091 171 RSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQ 242
Cdd:cd08433   80 ADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPA 151
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 3.05e-19

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: 83.78  E-value: 3.05e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  92 LLRLG-IPPMVGMMMAGPISLFRQRYPGVELKISEfgGLTVQ--QAVMNGELDVAMTALPVEE-ESGLATLPLFNHPLCV 167
Cdd:cd08427    1 RLRLGaIATVLTGLLPRALARLRRRHPDLEVHIVP--GLSAEllARVDAGELDAAIVVEPPFPlPKDLVWTPLVREPLVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 168 LVPR---SGDWLkiesvkpELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPI 244
Cdd:cd08427   79 IAPAelaGDDPR-------ELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIA 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 505383091 245 CERLDKNTLRWIPL-ESDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08427  152 VPLPAGPRVRVLPLgDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-253 9.79e-19

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 84.48  E-value: 9.79e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQ-SFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLL-LTDTGR---VVFERGLAILAEF 75
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKallVIAERILNEASNV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  76 RQLeAELgdINHLTKGLL---------RLGIPPMvgmmmagpISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTA 146
Cdd:PRK12679  81 RRL-ADL--FTNDTSGVLtiatthtqaRYSLPEV--------IKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAS 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 147 LPVEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDF 226
Cdd:PRK12679 150 ERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDV 229

                        250       260
                 ....*....|....*....|....*..
gi 505383091 227 LAAMVQAGVGIAILPQPICERLDKNTL 253
Cdd:PRK12679 230 IKTYVALGLGIGLVAEQSSGEQEESNL 256
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-143 1.86e-18

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 83.35  E-value: 1.86e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFER---GLAILAE-FRQLEAe 81
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDireIFDQLAEaTRKLRA- 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505383091  82 LGDINHLTkgllrLGIPPMVGMMMAGP-ISLFRQRYPGVELKISefgglTVQQAV--MNGELDVA 143
Cdd:PRK11139  90 RSAKGALT-----VSLLPSFAIQWLVPrLSSFNEAHPDIDVRLK-----AVDRLEdfLRDDVDVA 144
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-253 1.73e-16

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 78.31  E-value: 1.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLGI------PPMVGMMMAgpisLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEES- 153
Cdd:PRK10094  82 ELQQVNDGVERQVNIVInnllynPQAVAQLLA----WLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALAn 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 154 GLATLPL----------FNHPLC-VLVPRSGDWLKIESVkpellgehpllIYNEDFA--LSRQLMALF-NQHNVK-PRIA 218
Cdd:PRK10094 158 TFSLDPLgsvqwrfvmaADHPLAnVEEPLTEAQLRRFPA-----------VNIEDSArtLTKRVAWRLpGQKEIIvPDME 226

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 505383091 219 VRsgqwdfLAAMVqAGVGIAILPQPICERL-DKNTL 253
Cdd:PRK10094 227 TK------IAAHL-AGVGIGFLPKSLCQSMiDNQQL 255
PRK09791 PRK09791
LysR family transcriptional regulator;
6-262 1.25e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 75.57  E-value: 1.25e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEAELGDI 85
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  86 NHLTKGLLRLGIPPMVG-MMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAM-TALPVEEESGLATLPLFNH 163
Cdd:PRK09791  90 QGQLAGQINIGMGASIArSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTInTYYQGPYDHEFTFEKLLEK 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 164 PLCVLVPRSGDWLKIESVKpELLgEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQP 243
Cdd:PRK09791 170 QFAVFCRPGHPAIGARSLK-QLL-DYSWTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSACISLVAKSDFLSILPEE 247

                        250       260
                 ....*....|....*....|
gi 505383091 244 -ICERLDKNTLRWIPLESDL 262
Cdd:PRK09791 248 mGCDPLHGQGLVMLPVSEIL 267
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 109-242 1.67e-15

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: 73.38  E-value: 1.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISefgglTVQQA-----VMNGELDVAMTALPVEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKP 183
Cdd:cd08430   19 LERFRAQHPQVEIKLH-----TGDPAdaidkVLNGEADIAIAARPDKLPARLAFLPLATSPLVFIAPNIACAVTQQLSQG 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505383091 184 EL-LGEHPLLIynEDFALSRQLMAL-FNQHNVKPRI-AVRSGQwDFLAAMVQAGVGIAILPQ 242
Cdd:cd08430   94 EIdWSRLPFIL--PERGLARERLDQwFRRRGIKPNIyAQVAGH-EAIVSMVALGCGVGIVPE 152
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-284 2.25e-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: 73.13  E-value: 2.25e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  91 GLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEeSGLATLPLFNHPLCVLV 169
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPlIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRS-PDIDAQPLFDERLALVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 170 PRSGDWLKIE-SVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICErl 248
Cdd:cd08425   80 GATHPLAQRRtALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAR-- 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505383091 249 DKNTLRWIPLESDL-HWQLGMIWREGVYLSHSAQAWL 284
Cdd:cd08425  158 EQPGLCAVALEPPLpGRTAALLRRKGAYRSAAARAFA 194
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-285 6.26e-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: 71.78  E-value: 6.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGE 188
Cdd:cd08421   19 LASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAA-GLETRPYRTDRLVVVVPRDHPLAGRASVAFADTLD 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 189 HPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDKNT-LRWIPLESDlhW--- 264
Cdd:cd08421   98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALgLRVVPLDDA--Warr 175

                        170       180
                 ....*....|....*....|.
gi 505383091 265 QLGMIWREGVYLSHSAQAWLQ 285
Cdd:cd08421  176 RLLLCVRSFDALPPAARALVD 196
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 107-240 9.99e-15

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: 71.11  E-value: 9.99e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 107 GPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEESGLATLPLF--NHplCVLVPRSGDWLKIESVKPE 184
Cdd:cd08413   17 PVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVTLPCYrwNH--CVIVPPGHPLADLGPLTLE 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 505383091 185 LLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAIL 240
Cdd:cd08413   95 DLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGII 150
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 109-273 1.56e-14

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: 70.67  E-value: 1.56e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGE 188
Cdd:cd08451   20 IRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLLEEPMLVALPAGHPLARERSIPLAALAD 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 189 HPLLIYNEDFA--LSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPIcERLDKNTLRWIPLESD-LHWQ 265
Cdd:cd08451  100 EPFILFPRPVGpgLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASM-RQLQAPGVVYRPLAGApLTAP 178


                 ....*...
gi 505383091 266 LGMIWREG 273
Cdd:cd08451  179 LALAYRRG 186
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-253 4.29e-14

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 71.59  E-value: 4.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAefrQLEA 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTA--LPveeESGLAT 157
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPaLENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSdiLP---RSGLHY 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 158 LPLFNHPL-CVLVPRSGDWLKIEsVKPELLGEHPLLIYnedfALSRQLMALFnQHNVKPR-IAVRSGQWD---FLAAMVQ 232
Cdd:PRK15421 156 SPMFDYEVrLVLAPDHPLAAKTR-ITPEDLASETLLIY----PVQRSRLDVW-RHFLQPAgVSPSLKSVDntlLLIQMVA 229

                        250       260
                 ....*....|....*....|.
gi 505383091 233 AGVGIAILPQPICERLDKNTL 253
Cdd:PRK15421 230 ARMGIAALPHWVVESFERQGL 250
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 112-273 6.85e-14

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: 68.93  E-value: 6.85e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 112 FRQRYPGVELKISEFGGlTVQ-QAVMNGELDVAMT--ALPVEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGE 188
Cdd:cd08453   22 FREAYPDVELQLREATS-DVQlEALLAGEIDAGIVipPPGASAPPALAYRPLLSEPLVLAVPAAWAAEGGAPLALAAVAA 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 189 HPLLIYNEDFA--LSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICeRLDKNTLRWIPLESD-LHWQ 265
Cdd:cd08453  101 EPLVIFPRRIApaFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLR-NLARPGVVYRELADPaPVLE 179


                 ....*...
gi 505383091 266 LGMIWREG 273
Cdd:cd08453  180 TGLVWRRD 187
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-285 1.63e-13

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 68.10  E-value: 1.63e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 101 VGMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMT-ALPveEESGLATLPLFNHPLCVLVPRSGDWLKIE 179
Cdd:cd08426   11 AAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAfSPP--PEPGIRVHSRQPAPIGAVVPPGHPLARQP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 180 SVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQ-PICERLDKNTLRWIPL 258
Cdd:cd08426   89 SVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTElAVRREIRRGQLVAVPL 168

                        170       180
                 ....*....|....*....|....*....
gi 505383091 259 -ESDLHW-QLGMIWREGVYLSHSAQAWLQ 285
Cdd:cd08426  169 aDPHMNHrQLELQTRAGRQLPAAASAFLQ 197
PRK10341 PRK10341
transcriptional regulator TdcA;
4-262 2.43e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 69.12  E-value: 2.43e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   4 RTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEAELG 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  84 DINHLTKGLLRLGIPPMVGM-MMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEE-SGLATLPLF 161
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFtFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKlQDLHVEPLF 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 162 NHPLCVLVPRSGDWLKIESVkpELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILP 241
Cdd:PRK10341 170 ESEFVLVASKSRTCTGTTTL--ESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIP 247

                        250       260
                 ....*....|....*....|.
gi 505383091 242 QPICERLDKNTLRWIPLESDL 262
Cdd:PRK10341 248 CDMTSPFGSNQFITIPIEETL 268
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-97 1.78e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 66.34  E-value: 1.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRdGRKLLLTDTGRVVfergLAILAEFRQLEA 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRL----LRHARQVRLLEA 76

                         90
                 ....*....|....*...
gi 505383091  81 EL-GDINHLTKGLLRLGI 97
Cdd:PRK03635  77 ELlGELPALDGTPLTLSI 94
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-272 2.02e-12

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: 64.98  E-value: 2.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGippMVGMMMAGPI----SLFRQRYPGVELKISEFGGLTVQQAVMNGELD---VAMTALPveeeSGLATLPLFNHPL 165
Cdd:cd08448    2 LRIG---FVGSMLYRGLprilRAFRAEYPGIEVALHEMSSAEQIEALLRGELDlgfVHSRRLP----AGLSARLLHREPF 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 166 CVLVPRsGDWLKIESVKP--ELLGEhPLLIYNEDFA--LSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILP 241
Cdd:cd08448   75 VCCLPA-GHPLAARRRIDlrELAGE-PFVLFSREVSpdYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVP 152

                        170       180       190
                 ....*....|....*....|....*....|..
gi 505383091 242 QPICeRLDKNTLRWIPLE-SDLHWQLGMIWRE 272
Cdd:cd08448  153 RSLA-RAGLAGVRFLPLKgATQRSELYAAWKA 183
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 109-287 3.23e-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: 64.44  E-value: 3.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKI----SEfgglTVQQAVMNGELDVAMtalpVE---EESGLATLPLFNHPLCVLVPRSGDWLKIESV 181
Cdd:cd08420   19 LARFRKRYPEVRVSLtignTE----EIAERVLDGEIDLGL----VEgpvDHPDLIVEPFAEDELVLVVPPDHPLAGRKEV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 182 KPELLGEHPLLIYNEDfalS------RQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQ-PICERLDKNTLR 254
Cdd:cd08420   91 TAEELAAEPWILREPG---SgtrevfERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRlAVRKELELGRLV 167

                        170       180       190
                 ....*....|....*....|....*....|....
gi 505383091 255 WIPLES-DLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08420  168 ALPVEGlRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 109-276 7.40e-12

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: 63.35  E-value: 7.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGE 188
Cdd:cd08443   19 IKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLITLPCYHWNRCVVVKRDHPLADKQSISIEELAT 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 189 HPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDKNTLRWIPLESDLHWQLGM 268
Cdd:cd08443   99 YPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVIRDARDLFPWSVTK 178


                 ....*....
gi 505383091 269 I-WREGVYL 276
Cdd:cd08443  179 IaFRRGTFL 187
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-242 1.33e-11

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: 62.62  E-value: 1.33e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLG-IPPMVGMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMT----ALPVEEESGLATLPLFNHPLCV 167
Cdd:cd08423    2 LRVGaFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypVTPPPDDPGLTRVPLLDDPLDL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505383091 168 LVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQ 242
Cdd:cd08423   82 VLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-123 1.71e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 63.87  E-value: 1.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFergLAILAEFRQLEAELGDI 85
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF---WALKSSLDTLNQEILDI 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 505383091  86 NHL-TKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKI 123
Cdd:PRK10086  96 KNQeLSGTLTVYSRPSIAQCWLVPrLADFTRRYPSISLTI 135
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-144 3.23e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 62.78  E-value: 3.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILaefrqleAEL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL-------EQA 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 505383091  83 GDINHLTK---GLLRLGIPPMVG-MMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAM 144
Cdd:PRK10837  78 VEIEQLFRednGALRIYASSTIGnYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGL 143
PRK09801 PRK09801
LysR family transcriptional regulator;
4-126 4.68e-11

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 62.36  E-value: 4.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   4 RTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEAELG 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 505383091  84 DINHLTKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEF 126
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPaITELMRNYPELQVHFELF 132
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-82 1.32e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 60.76  E-value: 1.32e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   2 DIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRdGRKLLLTDTGRVVfergLAILAEFRQLEAE 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRL----LRHLRQVALLEAD 77


                 .
gi 505383091  82 L 82
Cdd:PRK13348  78 L 78
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-241 2.00e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.54  E-value: 2.00e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   3 IRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEAEL 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  83 GDINHLTKGLLRLGIPP-MVGMMMAGPISLFRQRYPGveLKISEFGGLTVQQAVMNGeLDVAMTALPVeEESGLATLPLF 161
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSStMAQNVLAGLTAKMLKEYPG--LSVNLVTGIPAPDLIADG-LDVVIRVGAL-QDSSLFSRRLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 162 NHPLCVLVPRSgdWLKIESV--KPELLGEHPLLIYN----EDFAL------SRQLMALFNQHNVKPRIAVRsgqWdflaa 229
Cdd:PRK10632 160 AMPMVVCAAKS--YLAQYGTpeKPADLSSHSWLEYSvrpdNEFELiapegiSTRLIPQGRFVTNDPQTLVR---W----- 229

                        250
                 ....*....|..
gi 505383091 230 mVQAGVGIAILP 241
Cdd:PRK10632 230 -LTAGAGIAYVP 240
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 94-286 8.91e-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: 57.36  E-value: 8.91e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  94 RLGIPPMVG-MMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEESG-LATLPLFNHPLCVLVPR 171
Cdd:cd08418    3 SIGVSSLIAhTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKeLISEPLFESDFVVVARK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLKIESVKPELLGEHPLLiyNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQP-ICERLDK 250
Cdd:cd08418   83 DHPLQGARSLEELLDASWVLP--GTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDmGRGPLDS 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505383091 251 NTLRWIPLESDL-HWQLGMIWREGVYLSHSAQAWLQC 286
Cdd:cd08418  161 FRLITIPVEEPLpSADYYLIYRKKSRLTPLAEQLVEL 197
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 112-285 1.29e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176133  Cd Length: 193  Bit Score: 56.85  E-value: 1.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 112 FRQRYPGVELKISEfgGLTVQ--QAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPRSGdwlkIESVKPELLGEH 189
Cdd:cd08442   22 YHARYPKVDLSLST--GTTGAliQAVLEGRLDGAFVAGPVEHP-RLEQEPVFQEELVLVSPKGH----PPVSRAEDLAGS 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 190 PLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERL-DKNTLRWIPLESDLHW-QLG 267
Cdd:cd08442   95 TLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLqGRGSVSIHPLPEPFADvTTW 174

                        170
                 ....*....|....*...
gi 505383091 268 MIWREGvYLSHSAQAWLQ 285
Cdd:cd08442  175 LVWRKD-SFTAALQAFLD 191
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-286 1.50e-09

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 56.66  E-value: 1.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVGM-MMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTAlPVEEESGLATLPLFNHPLCVLVPr 171
Cdd:cd08456    2 LRIAVLPALSQsFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVS-TLHEPPGIERERLLRIDGVCVLP- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLkieSVKPELlgeHPLLIYNEDFA------LSRQLM-ALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPI 244
Cdd:cd08456   80 PGHRL---AVKKVL---TPSDLEGEPFIslartdGTRQRVdALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLT 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 505383091 245 CERLDKNTLRWIPLESDLHWQLGMIWREGVYLSHSAQAWLQC 286
Cdd:cd08456  154 ALDYAAAGLVVRRFSPAVPFEVSLIRPKHRPSSALVAAFSAC 195
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 93-285 1.57e-09

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: 56.57  E-value: 1.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMT-ALPVEEESGLATLPLFNHPLCVLVP 170
Cdd:cd08437    2 LRFGLPPIIGNYYFPKlAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLgSLTPLENSALHSKIIKTQHFMIIVS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 171 RSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICERLDk 250
Cdd:cd08437   82 KDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKPDD- 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505383091 251 nTLRWIPLESD--LHWQLGMIWREGVYLSHSAQAWLQ 285
Cdd:cd08437  161 -HLVAIPLLDNeqPTFYISLAHRKDQLLTPAQKKLLD 196
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 109-258 2.12e-09

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: 56.04  E-value: 2.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKIS---EFGGLtvqQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPEL 185
Cdd:cd08441   19 LDQFRERWPDVELDLSsgfHFDPL---PALLRGELDLVITSDP-LPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPED 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 505383091 186 LGEHPLLIYNEDfalsRQLMALFNQ----HNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQ-PICERLDKNTLRWIPL 258
Cdd:cd08441   95 LADETLITYPVE----RERLDVFRHflqpAGIEPKRRRTVELTLMILQLVASGRGVAALPNwAVREYLDQGLVVARPL 168
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-261 3.44e-09

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


Pssm-ID: 176136  Cd Length: 203  Bit Score: 55.70  E-value: 3.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISEFGglTVQQ--AVMNGELDVAMTALPVEEESgLATLPLFNHPLCVLVPrSGDWLKIESVKPEL- 185
Cdd:cd08445   20 IRRFRQAAPDVEIELIEMT--TVQQieALKEGRIDVGFGRLRIEDPA-IRRIVLREEPLVVALP-AGHPLAQEKAPLTLa 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 186 -LGEHPLLIY----NEDFAlsRQLMALFNQHNVKPRIA--VRSGQwdfLA-AMVQAGVGIAILPQPIcERLDKNTLRWIP 257
Cdd:cd08445   96 qLADEPLILYpaspRPSFA--DQVLSLFRDHGLRPRVIqeVRELQ---TAlGLVAAGEGVTLVPASV-QRLRRDDVVYRP 169


                 ....
gi 505383091 258 LESD 261
Cdd:cd08445  170 LLDP 173
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-148 4.02e-09

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 56.54  E-value: 4.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEA 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGDINHLTKGLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISEfgglTVQQAVMNGE-LDVAMTALP 148
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPmLAKFMARYPDVSLQLEA----TNRRVDVVGEgVDVAIRVRP 147
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-287 4.95e-09

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: 55.36  E-value: 4.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGIPPMVG---MMMAgpISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTAL-PVEEESGLATLPLFNHPLCVL 168
Cdd:cd08435    2 VRVGAVPAAApvlLPPA--IARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLaDDEQPPDLASEELADEPLVVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 169 VPRSGDWLKIESVKPELLGEHPLLIYNEDfALSRQLM-ALFNQHNVK-PRIAVRSGQWDFLAAMVQAGVGIAILPQPICE 246
Cdd:cd08435   80 ARPGHPLARRARLTLADLADYPWVLPPPG-TPLRQRLeQLFAAAGLPlPRNVVETASISALLALLARSDMLAVLPRSVAE 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 505383091 247 R-LDKNTLRWIPLE-SDLHWQLGMIWREGVYLSHSAQAWLQCC 287
Cdd:cd08435  159 DeLRAGVLRELPLPlPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 133-261 9.56e-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: 54.27  E-value: 9.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 133 QAVMNGELDVAMTALPVE-EESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQH 211
Cdd:cd08416   43 KKLKDGELDAILVATPEGlNDPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIA 122

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 505383091 212 NVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPIcERLDKNTLRWIPLESD 261
Cdd:cd08416  123 GFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRI-ADVYEDKVQLIPLAEP 171
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 112-285 1.33e-08

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: 53.66  E-value: 1.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 112 FRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPL 191
Cdd:cd08419   21 FCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP-PEDLDLVAEPFLDNPLVVIAPPDHPLAGQKRIPLERLAREPF 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 192 LIyNEDFALSRQLM-ALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICER-LDKNTLRWIPLES---DLHWQL 266
Cdd:cd08419  100 LL-REPGSGTRLAMeRFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALeLATGRLAVLDVEGfpiRRQWYV 178

                        170
                 ....*....|....*....
gi 505383091 267 gmIWREGVYLSHSAQAWLQ 285
Cdd:cd08419  179 --VHRKGKRLSPAAQAFLD 195
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-239 1.43e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 55.00  E-value: 1.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   5 TLRY---FVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFER------GL------ 69
Cdd:PRK11013   5 SLRHieiFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEvqrsyyGLdrivsa 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  70 -AILAEFRQLEAELGDINHLTKGLLRLGIPPmvgmmmagpislFRQRYPGVELKIS--------EFggLTVQQAvmngel 140
Cdd:PRK11013  85 aESLREFRQGQLSIACLPVFSQSLLPGLCQP------------FLARYPDVSLNIVpqesplleEW--LSAQRH------ 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 141 DVAMT---ALPveeeSGLATLPLFN-HPLCVLVPRsgdwlkiesvkpellgeHPLL----IYNEDFA------LS----- 201
Cdd:PRK11013 145 DLGLTetlHTP----AGTERTELLTlDEVCVLPAG-----------------HPLAakkvLTPDDFAgenfisLSrtdsy 203

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 505383091 202 RQLM-ALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAI 239
Cdd:PRK11013 204 RQLLdQLFAEHGVKRRMVVETHSAASVCAMVRAGVGVSI 242
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 113-272 1.69e-08

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 53.42  E-value: 1.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 113 RQRYPGVELKISEFggLTVQQ--AVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHP 190
Cdd:cd08447   23 RAALPDVDLVLREM--VTTDQieALESGRIDLGLLRPPFARP-GLETRPLVREPLVAAVPAGHPLAGAERLTLEDLDGQP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 191 LLIY--NEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPICE-RLDKNTLRWIPLESDLHWQLG 267
Cdd:cd08447  100 FIMYspTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRlRFEGVVFRPLDLPRDVPVELH 179


                 ....*
gi 505383091 268 MIWRE 272
Cdd:cd08447  180 LAWRR 184
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-65 2.94e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 53.86  E-value: 2.94e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   6 LRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVF 65
Cdd:PRK11062   9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVF 68
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-247 1.16e-07

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: 50.90  E-value: 1.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  91 GLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISefggLTVQQA-VMNGELDVA--MTALPveeESGLATLPLFNHPLC 166
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPlLAEFLARYPDVRLELV----LSDRLVdLVEEGFDLAirIGELP---DSSLVARRLGPVRRV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 167 VL----------VPRSgdwlkiesvkPELLGEHPLLIYNEDFALSR-QLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGV 235
Cdd:cd08422   74 LVaspaylarhgTPQT----------PEDLARHRCLGYRLPGRPLRwRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGL 143

                        170
                 ....*....|..
gi 505383091 236 GIAILPQPICER 247
Cdd:cd08422  144 GIALLPDFLVAE 155
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 93-263 1.22e-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: 51.12  E-value: 1.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLGippMVGMMMAGP----ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEE-SGLATLPLFNHPLCV 167
Cdd:cd08449    2 LNIG---MVGSVLWGGlgpaLRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNdPPLASELLWREPMVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 168 LVPRSGDWLKIESVKPELLGEHPLLIYN-EDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQPIcE 246
Cdd:cd08449   79 ALPEEHPLAGRKSLTLADLRDEPFVFLRlANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESY-A 157

                        170
                 ....*....|....*..
gi 505383091 247 RLDKNTLRWIPLESDLH 263
Cdd:cd08449  158 RLPWPGVRFIPLKQAIS 174
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-284 5.55e-07

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: 49.13  E-value: 5.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  94 RLGIPPMVGMMMAGPI-SLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLVPRS 172
Cdd:cd08417    3 RIAASDYLEALLLPPLlARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFP-ELPPGLRSQPLFEDRFVCVARKD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 173 gdwlkiesvkpellgeHPLLIYN---EDFALSRQLM------------ALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGI 237
Cdd:cd08417   82 ----------------HPLAGGPltlEDYLAAPHVLvsprgrghglvdDALAELGLSRRVALTVPHFLAAPALVAGTDLI 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 505383091 238 AILPQPICERL-DKNTLRWIPLESDL-HWQLGMIWREgVYLSHSAQAWL 284
Cdd:cd08417  146 ATVPRRLAEALaERLGLRVLPLPFELpPFTVSLYWHP-RRDRDPAHRWL 193
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 93-284 1.02e-06

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: 48.25  E-value: 1.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  93 LRLG-IPPMVGMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLPLFNHPLCVLVPR 171
Cdd:cd08457    2 LRIAaMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGP-LEERQGFLIETRSLPAVVAVPM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 172 SGDWLKIESVKPELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAIL-PQPICE-RLD 249
Cdd:cd08457   81 GHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIdPATAIGlPLD 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 505383091 250 KNTLRwiPLESDLHWQLGMIWREGVYLSHSAQAWL 284
Cdd:cd08457  161 GIVIR--PFDTFIDAGFLVVRAANGPPSTMVDRFI 193
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 105-271 1.24e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176135  Cd Length: 198  Bit Score: 48.27  E-value: 1.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 105 MAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEESGLATLPLFNHPLCVLVPRSGdwlKIESVKP- 183
Cdd:cd08444   15 LPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPELVSFPYYDWHHHIIVPVGH---PLESITPl 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 184 --ELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILPQ--------------PICER 247
Cdd:cd08444   92 tiETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAEmafegqrdtnliklDTSHL 171

                        170       180
                 ....*....|....*....|....
gi 505383091 248 LDKNTLrWIPLESDlHWQLGMIWR 271
Cdd:cd08444  172 FGKNTT-WIALRRG-GDLRNFAYR 193
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-168 1.40e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 48.78  E-value: 1.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  12 VVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVvferglaILAEFRQLEAELGDINHLTK- 90
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEW-------FVKEARSVIKKMQETRRQCQq 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  91 ------GLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKISE--FGGltVQQAVMNGELDVAM---TALPVEEE---SGL 155
Cdd:PRK11074  86 vangwrGQLSIAVDNIVRPDRTRQlIVDFYRHFDDVELIIRQevFNG--VWDALADGRVDIAIgatRAIPVGGRfafRDM 163

                        170
                 ....*....|....*...
gi 505383091 156 ATLP-LF----NHPLCVL 168
Cdd:PRK11074 164 GMLSwACvvssDHPLASM 181
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 112-241 2.28e-05

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: 44.41  E-value: 2.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 112 FRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEESgLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGEHPL 191
Cdd:cd08452   22 YRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTA-LHIETVQSSPCVLALPKQHPLASKEEITIEDLRDEPI 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 505383091 192 LIYNEDF--ALSRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILP 241
Cdd:cd08452  101 ITVAREAwpTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVP 152
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 109-241 2.39e-05

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: 44.29  E-value: 2.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPVEEEsGLATLPLFNHPLCVLVPRSGDWLKIESVKPE-LLG 187
Cdd:cd08450   19 LPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSD-GIDYQLLLKEPLIVVLPADHRLAGREKIPPQdLAG 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 505383091 188 EHPLLIYNEDFALSRQLMALFNQHNVKPRIaVRSGQwDFLAAM--VQAGVGIAILP 241
Cdd:cd08450   98 ENFISPAPTAPVLQQVIENYAAQHNIQPNI-IQEAD-NLLSAMslVASTLGCALLP 151
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-61 5.00e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 43.85  E-value: 5.00e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTG 61
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PBP2_NhaR cd08429
The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA ...
 183-244 1.22e-04

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: 42.30  E-value: 1.22e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505383091 183 PELLGEHPLLIYNEDFALSRQLMALFNQHNVKPRIAvrsGQWD---FLAAMVQAGVGIAILPQPI 244
Cdd:cd08429   94 PASLDEAPLLLPGEDSALRRKLLQWFERQGLRPQIV---GEFDdsaLMKAFGQAGAGIFAAPTVI 155
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-61 2.28e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 42.32  E-value: 2.28e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTG 61
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 71
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
1-161 4.79e-04

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 41.34  E-value: 4.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   1 MDIRTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTgRVVFERGlaiLAEFRQLEA 80
Cdd:PRK10216   8 LDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPL-MVSMEQN---LAEWMQMGN 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  81 ELGD-INHLTKGLLRLGI---PPMVGMMMAGPISLFRQRYPGVELKIS--EFGGLtvqQAVMNGELDVAMT---ALPVEE 151
Cdd:PRK10216  84 QLLDkPHHQTPRGLKFELaaeSPLMMIMLNALSKRIYQRYPQATIKLRnwDYDSL---DAITRGEVDIGFTgreSHPRSR 160

                        170
                 ....*....|
gi 505383091 152 ESgLATLPLF 161
Cdd:PRK10216 161 EL-LSLLPLA 169
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-83 5.00e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 41.19  E-value: 5.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091   4 RTLRYFVEVVRQQSFTRAAEKLFVTQPTISKMLKNLEDELNCTLLIRDGRKLLLTDTGRVVFERGLAILAEFRQLEAELG 83
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEIG 86
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 18-85 6.80e-04

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


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 38.35  E-value: 6.80e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 505383091    18 FTRAAEKLFVTQPTISKMLKNLEDElncTLLIRDGRK-LLLTDTGRvvfERGLAILAEFRQLEAELGDI 85
Cdd:smart00529   1 TSEIAERLNVSPPTVTEMLKKLEKM---GLVEYEPYRgITLTEKGR---RLARRLLRKHRLLERFLVDV 63
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 89-265 6.97e-04

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 40.01  E-value: 6.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  89 TKGLLRL-GIPPMVGMMMAGPISLFRQRYPGVELKisefggLTVQQAVMN---GELDVAMTALPVeEESGLATLPLFNHP 164
Cdd:cd08478    1 PSGLLRVdAATPFVLHLLAPLIAKFRERYPDIELE------LVSNEGIIDlieRKTDVAIRIGEL-TDSTLHARPLGKSR 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 165 LCVLVprSGDWLKIESV--KPELLGEHPLLIYNEDFALSRQLMALF--NQHNVKPRIAVRSGQwdFLAAMVQAGVGIAIL 240
Cdd:cd08478   74 LRILA--SPDYLARHGTpqSIEDLAQHQLLGFTEPASLNTWPIKDAdgNLLKIQPTITASSGE--TLRQLALSGCGIACL 149

                        170       180
                 ....*....|....*....|....*..
gi 505383091 241 PQPICERlDKNTLRWIPL--ESDLHWQ 265
Cdd:cd08478  150 SDFMTDK-DIAEGRLIPLfaEQTSDVR 175
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
22-95 7.20e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 39.18  E-value: 7.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  22 AEKLFVTQPTISKMLKNLEDElncTLLIR-----DGRKLL--LTDTGRVVFERGLAILAEF-RQLEAELG--DINHLTKG 91
Cdd:COG1846   59 AERLGLTKSTVSRLLDRLEEK---GLVERepdpeDRRAVLvrLTEKGRALLEEARPALEALlAELLAGLSeeELEALLRL 135


                 ....
gi 505383091  92 LLRL 95
Cdd:COG1846  136 LRRL 139
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 102-284 7.21e-04

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: 40.08  E-value: 7.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 102 GMMMAGPISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTA---LPveeeSGLATLPLFNHPLcVLVPRSGDWLKI 178
Cdd:cd08469   12 AVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIfeqIP----PRFRRRTLFDEDE-VWVMRKDHPAAR 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 179 ESVKPELLGEHPLLI-------------YNEDFALSRQ--------LMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGI 237
Cdd:cd08469   87 GALTIETLARYPHIVvslggeeegavsgFISERGLARQtemfdrraLEEAFRESGLVPRVAVTVPHALAVPPLLADSDML 166

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 505383091 238 AILPQPICERLdKNTL---RWIPLESDLHWQLGMIWREGvYLSHSAQAWL 284
Cdd:cd08469  167 ALLPRSLARAF-AERGglvMKEPPYPPPPVQIRAVWHER-HDNDPAVAWL 214
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-241 1.50e-03

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: 38.80  E-value: 1.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 109 ISLFRQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALpVEEESGLATLPLFNHPLCVLVPRSGDWLKIESVKPELLGE 188
Cdd:cd08446   20 LRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRF-YPVEPDIAVENVAQERLYLAVPKSHPLAARPAVSLADLRN 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 505383091 189 HPLLIY----NEDFAlsRQLMALFNQHNVKPRIAVRSGQWDFLAAMVQAGVGIAILP 241
Cdd:cd08446   99 EPLILFprggRPSFA--DEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVP 153
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-247 1.52e-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: 39.08  E-value: 1.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  91 GLLRLGIPPMVGMMMAGP-ISLFRQRYPGVELKisefggLTVQQAVMN--GE-LDVAMTA-LPVEEESGLATLPLFNHPL 165
Cdd:cd08473    3 GTVRVSCPPALAQELLAPlLPRFMAAYPQVRLQ------LEATNRRVDliEEgIDVALRVrFPPLEDSSLVMRVLGQSRQ 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 166 CV-----LVPRSGdwlkiESVKPELLGEHPLLIYNEdfALSRQLMALFNQ------HNVKPRIAvrSGQWDFLAAMVQAG 234
Cdd:cd08473   77 RLvaspaLLARLG-----RPRSPEDLAGLPTLSLGD--VDGRHSWRLEGPdgesitVRHRPRLV--TDDLLTLRQAALAG 147

                        170
                 ....*....|...
gi 505383091 235 VGIAILPQPICER 247
Cdd:cd08473  148 VGIALLPDHLCRE 160
PBP2_ToxR cd08465
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ...
 113-176 3.62e-03

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: 37.67  E-value: 3.62e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 505383091 113 RQRYPGVELKISEFGGLTVQQAVMNGELDVAMTALPvEEESGLATLPLF-NHPLCVL----VPRSG-----DWL 176
Cdd:cd08465   23 RAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFP-ELPEELHAETLFeERFVCLAdratLPASGglsldAWL 95
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
22-82 3.82e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.03  E-value: 3.82e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 505383091    22 AEKLFVTQPTISKMLKNLEDElncTLLIR-----DGRKLL--LTDTGRVVFERglaILAEFRQLEAEL 82
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLEKK---GLVRRepspeDRRSVLvsLTEEGRELIEQ---LLEARSETLAEL 92
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-254 5.57e-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 7. 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: 176165  Cd Length: 197  Bit Score: 37.22  E-value: 5.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091  91 GLLRLGIPpMVGMMMAGPISLFRQRYPGVELKIsEF---------GGLTVqqAVMNGELDvamtalpveeESGLATLPL- 160
Cdd:cd08476    1 GRLRVSLP-LVGGLLLPVLAAFMQRYPEIELDL-DFsdrlvdvidEGFDA--VIRTGELP----------DSRLMSRRLg 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383091 161 -FNHPLC--------VLVPRSgdwlkiesvkPELLGEHPLLIY---NEDFALSRQLMALFNQHNVKPRIAVRSGQWDFLA 228
Cdd:cd08476   67 sFRMVLVaspdylarHGTPET----------PADLAEHACLRYrfpTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALI 136

                        170       180
                 ....*....|....*....|....*..
gi 505383091 229 AMVQAGVGIAILPQ-PICERLDKNTLR 254
Cdd:cd08476  137 EFALQGLGIACLPDfSVREALADGRLV 163
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
22-72 5.87e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 36.33  E-value: 5.87e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 505383091  22 AEKLFVTQPTISKMLKNLEDElncTLLIRD-GRKLLLTDTGRvvfERGLAIL 72
Cdd:COG1321   31 AERLGVSPPSVTEMLKKLEEK---GLVEYEpYGGITLTEEGR---ELALRIV 76
 
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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