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Conserved domains on  [gi|2796568602|ref|WP_373238826|]
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LysR family transcriptional regulator [Dorea longicatena]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 1.10e-55

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.45  E-value: 1.10e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRI 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 161 TdRDHWCVGMRPDDPLAEKEFIkkedligkplilpermnvqselanwfgkdfsklqiafTSNLGTNAGvMAANGLGY--- 237
Cdd:COG0583   161 G-EERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLA-AVAAGLGIall 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2796568602 238 PISIegAAKYWREDILVQRRIS-PEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:COG0583   202 PRFL--AADELAAGRLVALPLPdPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 1.10e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.45  E-value: 1.10e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRI 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 161 TdRDHWCVGMRPDDPLAEKEFIkkedligkplilpermnvqselanwfgkdfsklqiafTSNLGTNAGvMAANGLGY--- 237
Cdd:COG0583   161 G-EERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLA-AVAAGLGIall 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2796568602 238 PISIegAAKYWREDILVQRRIS-PEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:COG0583   202 PRFL--AADELAAGRLVALPLPdPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-246 1.68e-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: 1.68e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRI 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 161 TdRDHWCVGMRPDDPLAE--KEFIKKEDLIGKPLILPE-----RMNVQSELANWfGKDFSKLQIAFTsnLGTNAGVMAA- 232
Cdd:NF040786  161 Y-KDRLVLITPNGTEKYRmlKEEISISELQKEPFIMREegsgtRKEAEKALKSL-GISLEDLNVVAS--LGSTEAIKQSv 236

                         250
                  ....*....|....*
gi 2796568602 233 -NGLGYPISIEGAAK 246
Cdd:NF040786  237 eAGLGISVISELAAE 251
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-288 7.90e-31

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 116.79  E-value: 7.90e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEIL-NFEERTL 79
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILeQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  80 EELKGKEEvvESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIR 159
Cdd:PRK09906   81 RARKIVQE--DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 160 ITDrDHWCVGMRPDDPLAEKEFIKKEDLIGKPLILP--ERMNV-QSELANWF---GKDFSKLQIAFTSNLGTNagvMAAN 233
Cdd:PRK09906  159 LLD-EPLVVVLPVDHPLAHEKEITAAQLDGVNFISTdpAYSGSlAPIIKAWFaqhNSQPNIVQVATNILVTMN---LVGM 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2796568602 234 GLGYPIsIEGAAKYWREDILVQRRISPEI-TTSTVIAWRRNiPYSLAVRKMIEEIN 288
Cdd:PRK09906  235 GLGCTI-IPGYMNNFNTGQVVFRPLAGNVpSIALLMAWKKG-EMKPALRDFIAIVQ 288
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-287 3.75e-28

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: 107.30  E-value: 3.75e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWCVgMR 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV-VP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILPERMNVQSELA-NWFGKDFSKLQIAFTSNLGTNAGVMAANGLGypISI--EGAAKYW 248
Cdd:cd05466    80 PDHPLAKRKSVTLADLADEPLILFERGSGLRRLLdRAFAEAGFTPNIALEVDSLEAIKALVAAGLG--IALlpESAVEEL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2796568602 249 REDILVQRRIS-PEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd05466   158 ADGGLVVLPLEdPPLSRTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 7.31e-26

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 96.69  E-value: 7.31e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2796568602   3 LRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 1.10e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.45  E-value: 1.10e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRI 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 161 TdRDHWCVGMRPDDPLAEKEFIkkedligkplilpermnvqselanwfgkdfsklqiafTSNLGTNAGvMAANGLGY--- 237
Cdd:COG0583   161 G-EERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLA-AVAAGLGIall 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2796568602 238 PISIegAAKYWREDILVQRRIS-PEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:COG0583   202 PRFL--AADELAAGRLVALPLPdPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-246 1.68e-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: 1.68e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRI 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 161 TdRDHWCVGMRPDDPLAE--KEFIKKEDLIGKPLILPE-----RMNVQSELANWfGKDFSKLQIAFTsnLGTNAGVMAA- 232
Cdd:NF040786  161 Y-KDRLVLITPNGTEKYRmlKEEISISELQKEPFIMREegsgtRKEAEKALKSL-GISLEDLNVVAS--LGSTEAIKQSv 236

                         250
                  ....*....|....*
gi 2796568602 233 -NGLGYPISIEGAAK 246
Cdd:NF040786  237 eAGLGISVISELAAE 251
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-288 7.90e-31

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 116.79  E-value: 7.90e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEIL-NFEERTL 79
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILeQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  80 EELKGKEEvvESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIR 159
Cdd:PRK09906   81 RARKIVQE--DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 160 ITDrDHWCVGMRPDDPLAEKEFIKKEDLIGKPLILP--ERMNV-QSELANWF---GKDFSKLQIAFTSNLGTNagvMAAN 233
Cdd:PRK09906  159 LLD-EPLVVVLPVDHPLAHEKEITAAQLDGVNFISTdpAYSGSlAPIIKAWFaqhNSQPNIVQVATNILVTMN---LVGM 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2796568602 234 GLGYPIsIEGAAKYWREDILVQRRISPEI-TTSTVIAWRRNiPYSLAVRKMIEEIN 288
Cdd:PRK09906  235 GLGCTI-IPGYMNNFNTGQVVFRPLAGNVpSIALLMAWKKG-EMKPALRDFIAIVQ 288
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-287 3.75e-28

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: 107.30  E-value: 3.75e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWCVgMR 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV-VP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILPERMNVQSELA-NWFGKDFSKLQIAFTSNLGTNAGVMAANGLGypISI--EGAAKYW 248
Cdd:cd05466    80 PDHPLAKRKSVTLADLADEPLILFERGSGLRRLLdRAFAEAGFTPNIALEVDSLEAIKALVAAGLG--IALlpESAVEEL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2796568602 249 REDILVQRRIS-PEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd05466   158 ADGGLVVLPLEdPPLSRTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 7.31e-26

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 96.69  E-value: 7.31e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2796568602   3 LRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-193 1.34e-24

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 100.45  E-value: 1.34e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFL-TVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKI-SLTDEGILLKRRALEILNfEERT 78
Cdd:PRK12682    1 MNLQQLRFVReAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILR-EVGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  79 LEELKGKEEVVES-TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPV-DTEGLD 156
Cdd:PRK12682   80 IKRIGDDFSNQDSgTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLaDDPDLA 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2796568602 157 YIRITDRDHWCVgMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:PRK12682  160 TLPCYDWQHAVI-VPPDHPLAQEERITLEDLAEYPLI 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-287 1.12e-23

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: 95.43  E-value: 1.12e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITdRDHWCVGMR 171
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLG-EEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILPER-MNVQSELANWFGKDFSKLQIAFTSNLGTNAGVMAANGLGypISI--EGAAKYW 248
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPgSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLG--IALlpRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2796568602 249 -REDILVQRRIS-PEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:pfam03466 160 lADGRLVALPLPePPLPRELYLVWRKGRPLSPAVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-187 3.62e-23

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 96.63  E-value: 3.62e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   3 LRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNF-EE--RTL 79
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALcEEtcRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  80 EELKGKEevvESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIR 159
Cdd:CHL00180   87 EDLKNLQ---RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILE 163

                         170       180       190
                  ....*....|....*....|....*....|
gi 2796568602 160 ITD--RDHWCVGMRPDDPLAEKEFIKKEDL 187
Cdd:CHL00180  164 ITPyvEDELALIIPKSHPFAKLKKIQKEDL 193
PRK09986 PRK09986
LysR family transcriptional regulator;
3-193 7.06e-23

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 95.56  E-value: 7.06e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   3 LRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLEEL 82
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  83 K--GKEEvvESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFME--PVDTEGLDYI 158
Cdd:PRK09986   89 EqiGRGE--AGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMadLEPNPGFTSR 166

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2796568602 159 RITdRDHWCVGMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:PRK09986  167 RLH-ESAFAVAVPEEHPLASRSSVPLKALRNEYFI 200
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-193 5.83e-22

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 93.12  E-value: 5.83e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKeQSF--TKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKI-SLTDEGillkrraLEILNFEER 77
Cdd:PRK12684    1 MNLHQLRFVREAVR-QNFnlTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPG-------RIILASVER 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  78 TLEElkgkeevVESTITIGcGEFAAVET---------------LAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVD 142
Cdd:PRK12684   73 ILQE-------VENLKRVG-KEFAAQDQgnltiatthtqaryaLPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQAD 144

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2796568602 143 IAlfmepVDTEGldyirITDRD--------HW--CVGMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:PRK12684  145 LA-----IATEA-----IADYKelvslpcyQWnhCVVVPPDHPLLERKPLTLEDLAQYPLI 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-79 2.64e-20

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 88.47  E-value: 2.64e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEG---ILLKRRALEILNFEER 77
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGevyLRYARRALQDLEAGRR 80


                  ..
gi 2796568602  78 TL 79
Cdd:PRK11242   81 AI 82
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 115-286 3.02e-18

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: 80.68  E-value: 3.02e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 115 EKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWCVgMRPDDPLAEKEFIKKEDLIGKPLI- 193
Cdd:cd08415    24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCV-LPPGHPLARKDVVTPADLAGEPLIs 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 194 LPERMNVQSELANWFGKDFSKLQIAFTSNLGTNAGVMAANGLGypISI--EGAAKYWREDILVQRRISPEITTSTVIAWR 271
Cdd:cd08415   103 LGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLG--VAIvdPLTAAGYAGAGLVVRPFRPAIPFEFALVRP 180

                         170
                  ....*....|....*
gi 2796568602 272 RNIPYSLAVRKMIEE 286
Cdd:cd08415   181 AGRPLSRLAQAFIDL 195
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-208 5.69e-18

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 81.40  E-value: 5.69e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  26 HITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLEELKGKEEVVESTITIGCGEFAAVET 105
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 106 LAKICKTYKEKYPLVQIVLHT-ATADAVYEMMNkGLVDIALFMEPvDT--EGLDYIRITDrdhwcVGMR---PDDPLAEK 179
Cdd:PRK11716   82 LPPILDRFRAEHPLVEIKLTTgDAADAVEKVQS-GEADLAIAAKP-ETlpASVAFSPIDE-----IPLVliaPALPCPVR 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2796568602 180 EFIKKE--DLIGKPLILPERMNVQSELANWF 208
Cdd:PRK11716  155 QQLSQEkpDWSRIPFILPEHGPARRRIDLWF 185
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-193 3.88e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 79.70  E-value: 3.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQ-SFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKIS-LTDEGILLKRRALEILNFEE-- 76
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAEnl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  77 -RTLEELKGKEevvESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTE-G 154
Cdd:PRK12683   81 rRLAEQFADRD---SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREpD 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2796568602 155 LDYIRITDRDHwCVGMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:PRK12683  158 LVSFPYYSWHH-VVVVPKGHPLTGRENLTLEAIAEYPII 195
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-193 4.18e-16

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 76.86  E-value: 4.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQ-SFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKIS-LTDEGILLKRRALEILN----- 73
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSkvesi 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  74 ---FEERTLEElKGkeevvesTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIAlfmepV 150
Cdd:PRK12681   81 ksvAGEHTWPD-KG-------SLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFA-----I 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2796568602 151 DTEGLD----------YiritdrdHW--CVGMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:PRK12681  148 ATEALHlyddlimlpcY-------HWnrSVVVPPDHPLAKKKKLTIEELAQYPLV 195
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-172 4.66e-16

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 76.64  E-value: 4.66e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLA-KICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIR 159
Cdd:PRK11233   81 AVHNVGQALSGQVSIGLAPGTAASSLTmPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160

                         170
                  ....*....|...
gi 2796568602 160 ITDRDHWCVGMRP 172
Cdd:PRK11233  161 LLKEDLFLVGTQD 173
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-71 6.70e-16

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 76.04  E-value: 6.70e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2796568602   6 LRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGillKRRALEI 71
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG---QRYFLDI 73
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-287 1.12e-15

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: 73.75  E-value: 1.12e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWCVgMR 171
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAV-LP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILpermnvqselanwFGKDFS--------------KLQIAFTSNLGTNAGVMAANGLG- 236
Cdd:cd08438    80 RGHPLAGRKTVSLADLADEPFIL-------------FNEDFAlhdriidacqqagfTPNIAARSSQWDFIAELVAAGLGv 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2796568602 237 --YPISIegAAKYWREDILVQRRISPEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd08438   147 alLPRSI--AQRLDNAGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-287 1.41e-15

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: 73.31  E-value: 1.41e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRItDRDHWCVGMR 171
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPL-LREPLVVALP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILPERMNVQS---ELANWFGKDFSKLQIAFTSNLGTNAGVMAANGLGypISI--EGAAK 246
Cdd:cd08414    80 ADHPLAARESVSLADLADEPFVLFPREPGPGlydQILALCRRAGFTPRIVQEASDLQTLLALVAAGLG--VALvpASVAR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2796568602 247 YWREDIlVQRRIS-PEITTSTVIAWRRNIPySLAVRKMIEEI 287
Cdd:cd08414   158 LQRPGV-VYRPLAdPPPRSELALAWRRDNA-SPALRAFLELA 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-194 1.54e-15

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 75.07  E-value: 1.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNfEERTLE 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLR-EVKVLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 EL-KGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIR 159
Cdd:PRK11151   80 EMaSQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVP 159

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2796568602 160 ITDrDHWCVGMRPDDPLAEKEFIKKEDLIGKPLIL 194
Cdd:PRK11151  160 LFD-EPMLLAVYEDHPWANRDRVPMSDLAGEKLLM 193
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 2.04e-15

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: 72.94  E-value: 2.04e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITdRDHWCVGMR 171
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLL-RDPFVLVCP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILperMNVQSELANWFGKDFS----KLQIAFTSNLGTNAGVMAANGLGypISI--EGAA 245
Cdd:cd08440    80 KDHPLARRRSVTWAELAGYPLIA---LGRGSGVRALIDRALAaaglTLRPAYEVSHMSTALGMVAAGLG--VAVlpALAL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2796568602 246 KYWREDILVQRRIS-PEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd08440   155 PLADHPGLVARPLTePVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 113-287 2.05e-14

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 70.21  E-value: 2.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 113 YKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDrDHWCVGMRPDDPLAEKEFIKKEDLIGKPL 192
Cdd:cd08420    22 FRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAE-DELVLVVPPDHPLAGRKEVTAEELAAEPW 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 193 ILPE-----RMNVQSELANwFGKDFSKLQIAFTsnLGTNAGVMAA--NGLGYPI-SIEGAAKYWREDILVQRRIS-PEIT 263
Cdd:cd08420   101 ILREpgsgtREVFERALAE-AGLDGLDLNIVME--LGSTEAIKEAveAGLGISIlSRLAVRKELELGRLVALPVEgLRLT 177

                         170       180
                  ....*....|....*....|....
gi 2796568602 264 TSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd08420   178 RPFSLIYHKDKYLSPAAEAFLEFL 201
PRK12680 PRK12680
LysR family transcriptional regulator;
1-154 1.10e-13

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 70.04  E-value: 1.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAK-EQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKI-SLTDEGILLKRRALEIL----NF 74
Cdd:PRK12680    1 MTLTQLRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLseanNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  75 EERTLEELKGKEEVVESTITIGCGEFAAVETLAKIcktyKEKYPLVQIVLHTATADAVYEMMNKGLVDIALfmepVDTEG 154
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQI----KQAYPQVSVHLQQAAESAALDLLGQGDADIAI----VSTAG 152
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-194 1.19e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 70.05  E-value: 1.19e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEvVESTITIGCgeFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRI 160
Cdd:PRK15421   82 ACNEPQQ-TRLRIAIEC--HSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2796568602 161 TDRDHWCVgMRPDDPLAEKEFIKKEDLIGKPLIL 194
Cdd:PRK15421  159 FDYEVRLV-LAPDHPLAAKTRITPEDLASETLLI 191
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-121 1.87e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 69.45  E-value: 1.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   6 LRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLEELKGK 85
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2796568602  86 EEVVESTITIGCGEFA-AVETLAKICKTYKEKYPLVQ 121
Cdd:PRK10094   87 NDGVERQVNIVINNLLyNPQAVAQLLAWLNERYPFTQ 123
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-86 1.51e-12

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 66.56  E-value: 1.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   6 LRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLK---RRALEILNFEertLEEL 82
Cdd:PRK10086   19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFwalKSSLDTLNQE---ILDI 95


                  ....
gi 2796568602  83 KGKE 86
Cdd:PRK10086   96 KNQE 99
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-145 1.74e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 66.59  E-value: 1.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2796568602  81 ELKGKEevVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIAL 145
Cdd:PRK15092   91 SLMYSN--LQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-285 5.00e-12

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: 63.72  E-value: 5.00e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRdHWCVGMR 171
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARL-PPYVWLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILPErmnvQSELANWFGKDFSKL----QIAF-TSNLGTNAGvMAANGLGYPISIEGAAK 246
Cdd:cd08412    80 ADHPLAGKDEVSLADLAAEPLILLD----LPHSREYFLSLFAAAgltpRIAYrTSSFEAVRS-LVANGLGYSLLNDRPYR 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2796568602 247 YWRED--ILVQRRISPEI-TTSTVIAWRRNIPYSLAVRKMIE 285
Cdd:cd08412   155 PWSYDgkRLVRRPLADPVpPLRLGLAWRRGARLTRAARAFVD 196
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-197 4.41e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 62.01  E-value: 4.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   3 LRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILnfeERTLE-- 80
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL---EQAVEie 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ----ELKGKEEVVESTiTIgcGEFAAVETLAKicktYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLd 156
Cdd:PRK10837   82 qlfrEDNGALRIYASS-TI--GNYILPAMIAR----YRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPEL- 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2796568602 157 yirITD---RDHWCVGMRPDDPLAEKEfIKKEDLIGKPLILPER 197
Cdd:PRK10837  154 ---ISEpwlEDELVVFAAPDSPLARGP-VTLEQLAAAPWILRER 193
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-160 1.84e-10

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 60.45  E-value: 1.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:PRK10082   11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICktyKEKYPLVQIVLHTATADAVYEMMNKGLVD--IALFMEPVDTEGLDYI 158
Cdd:PRK10082   91 ELRGGSDYAQRKIKIAAAHSLSLGLLPSII---SQMPPLFTWAIEAIDVDEAVDKLREGQSDciFSFHDEDLLEAPFDHI 167


                  ..
gi 2796568602 159 RI 160
Cdd:PRK10082  168 RL 169
PRK10341 PRK10341
transcriptional regulator TdcA;
6-145 6.31e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 59.11  E-value: 6.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   6 LRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLEELKGK 85
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  86 EEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIAL 145
Cdd:PRK10341   92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAI 151
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-287 7.21e-10

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: 57.28  E-value: 7.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIAL--FMEPVDTEGLDYIRITDrDHWCVG 169
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELAD-EPLVVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 170 MRPDDPLAEKEFIKKEDLIGKPLILPE-----RMNVQSELANWfGKDFSKLQIAFTSNLGTNAGVmAANGLGYPISIEGA 244
Cdd:cd08435    80 ARPGHPLARRARLTLADLADYPWVLPPpgtplRQRLEQLFAAA-GLPLPRNVVETASISALLALL-ARSDMLAVLPRSVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2796568602 245 AKYWREDILvqRRISPEITTST---VIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd08435   158 EDELRAGVL--RELPLPLPTSRrpiGITTRRGGPLSPAARALLDAL 201
PRK09791 PRK09791
LysR family transcriptional regulator;
1-177 7.24e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 58.62  E-value: 7.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIAL---FMEPVDTEgLDY 157
Cdd:PRK09791   85 DIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyYQGPYDHE-FTF 163

                         170       180
                  ....*....|....*....|
gi 2796568602 158 IRITDRDhWCVGMRPDDPLA 177
Cdd:PRK09791  164 EKLLEKQ-FAVFCRPGHPAI 182
cbl PRK12679
HTH-type transcriptional regulator Cbl;
19-148 1.11e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 58.28  E-value: 1.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  19 TKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKK-ISLTDEGILLKRRALEILNFEE--RTLEELKGKEEvvESTITI 95
Cdd:PRK12679   20 TEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASnvRRLADLFTNDT--SGVLTI 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2796568602  96 GCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFME 148
Cdd:PRK12679   98 ATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE 150
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 5.74e-09

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 55.01  E-value: 5.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGldyIRITDRDHW--CVG 169
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPG---IRVHSRQPApiGAV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 170 MRPDDPLAEKEFIKKEDLIGKPLILPERMN-VQSELANWFGKDFSKLQIAFTSNLGTNAGVMAANGLGYPISIE-GAAKY 247
Cdd:cd08426    78 VPPGHPLARQPSVTLAQLAGYPLALPPPSFsLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTElAVRRE 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2796568602 248 WREDILVQRRIS-PEITTSTV-IAWRRNIPYSLAVRKMIEEI 287
Cdd:cd08426   158 IRRGQLVAVPLAdPHMNHRQLeLQTRAGRQLPAAASAFLQLL 199
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-193 6.85e-09

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 55.77  E-value: 6.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   3 LRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILL---KRRA---LE-ILNFE 75
Cdd:PRK11013    6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLfeeVQRSyygLDrIVSAA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  76 ERtLEELKGKEevvestITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALfmepvdTEGL 155
Cdd:PRK11013   86 ES-LREFRQGQ------LSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGL------TETL 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2796568602 156 DYIRITDR------DHWCVgMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:PRK11013  153 HTPAGTERtelltlDEVCV-LPAGHPLAAKKVLTPDDFAGENFI 195
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-78 8.40e-09

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 55.40  E-value: 8.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   6 LRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRA----------LEILNFE 75
Cdd:PRK11062    9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYAdkmftlsqemLDIVNYR 88


                  ...
gi 2796568602  76 ERT 78
Cdd:PRK11062   89 KES 91
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-287 1.48e-08

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: 53.58  E-value: 1.48e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWCVgMR 171
Cdd:cd08456     1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCV-LP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLI-LPERMNVQSELANWFGKDFSKLQIAFTSNLGTNAGVMAANGLGYPISIEGAAKYWRE 250
Cdd:cd08456    80 PGHRLAVKKVLTPSDLEGEPFIsLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAA 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2796568602 251 DILVQRRISPEITTSTVIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd08456   160 AGLVVRRFSPAVPFEVSLIRPKHRPSSALVAAFSACL 196
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 114-281 1.74e-08

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: 53.37  E-value: 1.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 114 KEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWCVGmRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:cd08433    23 RRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVG-PADAPLPRGAPVPLAELARLPLI 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 194 LPE-----RMNVQSELANwFGkdfSKLQIAFTSNLGTNAGVMAANGLGYPISIEGAAkywREDI----LVQRRI-SPEIT 263
Cdd:cd08433   102 LPSrghglRRLVDEAAAR-AG---LTLNVVVEIDSVATLKALVAAGLGYTILPASAV---AAEVaagrLVAAPIvDPALT 174

                         170
                  ....*....|....*...
gi 2796568602 264 TSTVIAWRRNIPYSLAVR 281
Cdd:cd08433   175 RTLSLATPRDRPLSPAAL 192
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-193 9.79e-08

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: 51.08  E-value: 9.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVD-TEGLDYIRITDRDHwCVGM 170
Cdd:cd08413     1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDdHPDLVTLPCYRWNH-CVIV 79

                          90       100
                  ....*....|....*....|...
gi 2796568602 171 RPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:cd08413    80 PPGHPLADLGPLTLEDLAQYPLI 102
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-84 2.58e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 50.93  E-value: 2.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRnGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLG 80


                  ....
gi 2796568602  81 ELKG 84
Cdd:PRK03635   81 ELPA 84
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 93-232 4.15e-07

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: 49.48  E-value: 4.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  93 ITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEglDYIRITDRDHW--CVGM 170
Cdd:cd08443     2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDY--DDLITLPCYHWnrCVVV 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2796568602 171 RPDDPLAEKEFIKKEDLIGKPLILPER-MNVQSELANWFGKDFSKLQIAFTSN----------LGTNAGVMAA 232
Cdd:cd08443    80 KRDHPLADKQSISIEELATYPIVTYTFgFTGRSELDTAFNRAGLTPNIVLTATdadviktyvrLGLGVGVIAS 152
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-83 5.14e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.97  E-value: 5.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   4 RLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRnGKKISLTDEG--ILLKRRALEILnfEERTLEE 81
Cdd:PRK13348    5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGqrLLRHLRQVALL--EADLLST 81


                  ..
gi 2796568602  82 LK 83
Cdd:PRK13348   82 LP 83
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 114-287 7.28e-07

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: 48.68  E-value: 7.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 114 KEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWcVGMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:cd08411    24 RQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFL-LAVPKDHPLAKRKSVTPEDLAGERLL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 194 LPER---MNVQS-ELANWFGKDfSKLQIAFTSnLGTNAGvMAANGLGYPISIEGAAKYW--REDILVQRRIS-PEITTST 266
Cdd:cd08411   103 LLEEghcLRDQAlELCRLAGAR-EQTDFEATS-LETLRQ-MVAAGLGITLLPELAVPSEelRGDRLVVRPFAePAPSRTI 179

                         170       180
                  ....*....|....*....|.
gi 2796568602 267 VIAWRRNIPYSLAVRKMIEEI 287
Cdd:cd08411   180 GLVWRRSSPRAAAFEALAELI 200
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 94-272 8.00e-07

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: 48.53  E-value: 8.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  94 TIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDrDHWCVGMRPD 173
Cdd:cd08450     3 TIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLK-EPLIVVLPAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 174 DPLAEKEFIKKEDLIGKPLILPERMN--VQSELANWFGKDFSKLQIAFTSNLGTNAGVMAANGLGYPIsIEGAAKYWRED 251
Cdd:cd08450    82 HRLAGREKIPPQDLAGENFISPAPTApvLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCAL-LPLYANNLLPP 160

                         170       180
                  ....*....|....*....|..
gi 2796568602 252 ILVQRRISPEI-TTSTVIAWRR 272
Cdd:cd08450   161 SVVARPLSGETpTIDLVMGYNK 182
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 105-285 1.05e-06

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: 48.30  E-value: 1.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 105 TLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHWCVgMRPDDPLAEKEFIKK 184
Cdd:cd08434    14 LVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLV-VPKDHPLAGRDSVDL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 185 EDLIGKPLI-LPE----RMNVQSELANWfgkDFSkLQIAF-TSNLGTNAGVMAAnGLGypISI--EGAAKYWREdiLVQR 256
Cdd:cd08434    93 AELADEPFVlLSPgfglRPIVDELCAAA---GFT-PKIAFeGEEDSTIAGLVAA-GLG--VAIlpEMTLLNPPG--VKKI 163

                         170       180       190
                  ....*....|....*....|....*....|
gi 2796568602 257 RISPEITTSTV-IAWRRNIPYSLAVRKMIE 285
Cdd:cd08434   164 PIKDPDAERTIgLAWLKDRYLSPAARRFKD 193
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-61 2.51e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 47.70  E-value: 2.51e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEG 61
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-73 8.13e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 46.47  E-value: 8.13e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2796568602  11 TVAKEQSFTKAAEQLHITQPTLS---RQMaafEEDLGITLFIRNGKKISLTDEGILLKRRALEILN 73
Cdd:PRK11074   12 AVARTGSFSAAAQELHRVPSAVSytvRQL---EEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK 74
PRK09801 PRK09801
LysR family transcriptional regulator;
6-122 8.13e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 46.57  E-value: 8.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   6 LRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLEELKGK 85
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2796568602  86 EEVVESTITIGCGEFAAVETLAKICKTYKEKYPLVQI 122
Cdd:PRK09801   91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV 127
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 104-197 4.13e-05

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: 43.42  E-value: 4.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 104 ETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIAlF--MEPVDTeGLDYIRITDRDHWcVGMRPDDPLAEKEF 181
Cdd:cd08446    14 DTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIG-FgrFYPVEP-DIAVENVAQERLY-LAVPKSHPLAARPA 90

                          90
                  ....*....|....*.
gi 2796568602 182 IKKEDLIGKPLILPER 197
Cdd:cd08446    91 VSLADLRNEPLILFPR 106
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-118 4.25e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 44.37  E-value: 4.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 ME-LRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTL 79
Cdd:PRK10632    1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2796568602  80 EELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYP 118
Cdd:PRK10632   81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYP 119
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 93-273 7.48e-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: 42.87  E-value: 7.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  93 ITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHT-ATADAVYEMMnKGLVDIALFMEPVDTEGLdYIRITDRDHWCVGMR 171
Cdd:cd08452     2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRElSSPDQVEELL-KGRIDIGFLHPPIQHTAL-HIETVQSSPCVLALP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLILPERmnvqsELANWFGKDFSKL--QIAFTSNLGTNA-------GVMAAnGLGYPISIE 242
Cdd:cd08452    80 KQHPLASKEEITIEDLRDEPIITVAR-----EAWPTLYDEIIQLceQAGFRPKIVQEAteyqtviGLVSA-GIGVTFVPS 153

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2796568602 243 GAAKYWREDILVQRRISPEITTSTVIAWRRN 273
Cdd:cd08452   154 SAKKLFNLEVAYRKIDQINLNAEWSIAYRKD 184
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-193 1.15e-04

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: 42.25  E-value: 1.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITdRDHWCVGMR 171
Cdd:cd08447     1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLV-REPLVAAVP 79

                          90       100
                  ....*....|....*....|..
gi 2796568602 172 PDDPLAEKEFIKKEDLIGKPLI 193
Cdd:cd08447    80 AGHPLAGAERLTLEDLDGQPFI 101
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 108-246 1.51e-04

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: 41.93  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 108 KICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALF--MEPVDTEGLdYIRITDRDHWCVGMRPDDPLAEKEFIKKE 185
Cdd:cd08437    17 KLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLgsLTPLENSAL-HSKIIKTQHFMIIVSKDHPLAKAKKVNFA 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2796568602 186 DLIGKPLILPERMNVQSELANWFGK--DFSKlQIAFTSNLGTNAGVMAANGLGYPISIEGAAK 246
Cdd:cd08437    96 DLKKENFILLNEHFVHPKAFDSLCQqaNFQP-NIVYRTNDIHILKSMVRENVGIGFLTDIAVK 157
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 95-193 4.89e-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: 40.47  E-value: 4.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  95 IGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIAL--FME-PvdtEGLDYIRITDRDHWCVgMR 171
Cdd:cd08469     4 IAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIgiFEQiP---PRFRRRTLFDEDEVWV-MR 79

                          90       100
                  ....*....|....*....|..
gi 2796568602 172 PDDPLAEKEfIKKEDLIGKPLI 193
Cdd:cd08469    80 KDHPAARGA-LTIETLARYPHI 100
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 92-180 5.65e-04

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: 40.28  E-value: 5.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITdRDHWCVGMR 171
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLF-EDRFVCVAR 79


                  ....*....
gi 2796568602 172 PDDPLAEKE 180
Cdd:cd08417    80 KDHPLAGGP 88
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-209 5.99e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 40.74  E-value: 5.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602   1 MELRLLRYFLTVAKEQSFTKAAEQLHITQPTLSRQMAAFEEDLGITLFIRNGKKISLTDEGILLKRRALEILNFEERTLE 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  81 ELKGKEEVVESTITIGCGEFAAVETLAKICKTYKEKYPlvQIVLHTATADAVYEMMNKGlVDIALFMEPVDTEGLDYIR- 159
Cdd:PRK14997   82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYP--DVSLQLEATNRRVDVVGEG-VDVAIRVRPRPFEDSDLVMr 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2796568602 160 -ITDRDHwCVGMRPDdpLAEKefikkedlIGKPlilpermNVQSELANWFG 209
Cdd:PRK14997  159 vLADRGH-RLFASPD--LIAR--------MGIP-------SAPAELSHWPG 191
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 118-286 7.75e-04

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: 39.78  E-value: 7.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 118 PLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRItdRDHWCVGMRP-DDPLAEKEFIKKEDLIGKPLIL-- 194
Cdd:cd08457    27 PNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIET--RSLPAVVAVPmGHPLAQLDVVSPQDLAGERIITle 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 195 -PERMNVQSELAnwFGKDFSKLQIAFTSNLGTNAGVMAANGLGYPISIEGAAKYWREDILVQRRISPEITTSTVIAWRRN 273
Cdd:cd08457   105 nGYLFRMRVEVA--LGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPLDGIVIRPFDTFIDAGFLVVRAAN 182

                         170
                  ....*....|...
gi 2796568602 274 IPYSLAVRKMIEE 286
Cdd:cd08457   183 GPPSTMVDRFIDE 195
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 106-241 1.76e-03

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: 38.64  E-value: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 106 LAKICKtykeKYPLVQIVLHTATADAVYEMMNKGLVDIALFMEPVDTEGLDYIRITDRDHwCVGMRPDDPLAEKEFIKKE 185
Cdd:cd08419    18 LGAFCR----RHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPL-VVIAPPDHPLAGQKRIPLE 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2796568602 186 DLIGKPLILPE-----RMNVQSELANwfgkdfSKLQIAFTSNLGTN----AGVMAanGLGypISI 241
Cdd:cd08419    93 RLAREPFLLREpgsgtRLAMERFFAE------HGVTLRVRMELGSNeaikQAVMA--GLG--LSV 147
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-193 1.94e-03

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: 38.35  E-value: 1.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602  92 TITIGCGEFAAVETLAKICKTYKEKYPLVQIVLHTATADAVYEMMNKGLVDIALF-MEPVDTEGLDYIRITDRDHWCVgM 170
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVgLPERRPPGLASRELAREPLVAV-V 79

                          90       100
                  ....*....|....*....|...
gi 2796568602 171 RPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:cd08436    80 APDHPLAGRRRVALADLADEPFV 102
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 139-193 2.14e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 38.32  E-value: 2.14e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2796568602 139 GLVDIALFMEPVDTEGLDYIRITDRDHWCVgMRPDDPLAEKEFIKKEDLIGKPLI 193
Cdd:cd08441    48 GELDLVITSDPLPLPGIAYEPLFDYEVVLV-VAPDHPLAAKEFITPEDLADETLI 101
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-193 3.55e-03

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: 37.89  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796568602 101 AAVETLAKICKTYKEKYPLVQIVL--HTAT--ADAVYEmmnkGLVDIALFMEPVDTEGLDYIRITDrDHWCVGMRPDDPL 176
Cdd:cd08421    10 AIVEFLPEDLASFLAAHPDVRIDLeeRLSAdiVRAVAE----GRADLGIVAGNVDAAGLETRPYRT-DRLVVVVPRDHPL 84

                          90
                  ....*....|....*..
gi 2796568602 177 AEKEFIKKEDLIGKPLI 193
Cdd:cd08421    85 AGRASVAFADTLDHDFV 101
 
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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