NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|749307175|ref|WP_040131321|]
View 

LysR family transcriptional regulator [Burkholderia pseudomultivorans]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-247 1.31e-46

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.95  E-value: 1.31e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   4 FDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFD 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  84 EVRG--QAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVmnlsSGPFRPASGD 161
Cdd:COG0583   81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR----LGPPPDPGLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 162 ARwVLRREPLSWVASPAmaellpeplplvllpddcmmHQIAVRSLDeqrvpyvlvhsASGVAGLQSMLAAGLGVGCLCAS 241
Cdd:COG0583  157 AR-PLGEERLVLVASPD--------------------HPLARRAPL-----------VNSLEALLAAVAAGLGIALLPRF 204


                 ....*.
gi 749307175 242 AIGDGL 247
Cdd:COG0583  205 LAADEL 210
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-247 1.31e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.95  E-value: 1.31e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   4 FDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFD 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  84 EVRG--QAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVmnlsSGPFRPASGD 161
Cdd:COG0583   81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR----LGPPPDPGLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 162 ARwVLRREPLSWVASPAmaellpeplplvllpddcmmHQIAVRSLDeqrvpyvlvhsASGVAGLQSMLAAGLGVGCLCAS 241
Cdd:COG0583  157 AR-PLGEERLVLVASPD--------------------HPLARRAPL-----------VNSLEALLAAVAAGLGIALLPRF 204


                 ....*.
gi 749307175 242 AIGDGL 247
Cdd:COG0583  205 LAADEL 210
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-266 1.89e-31

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 118.98  E-value: 1.89e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK15092  12 DLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  85 VRGQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMNlssgpfRPASGDaRW 164
Cdd:PRK15092  92 LMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTH------RPSSFP-AL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 165 VLRREPLSWVASPAMAELLPEPLPLVLLPDDCMMHQIAVRSLDEQRVPYVLVHSASGVAGLQSMLAAGLGVGCLCASAIG 244
Cdd:PRK15092 165 NLRTSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMS 244

                        250       260
                 ....*....|....*....|..
gi 749307175 245 DGLVRLGAKYRLPALPDAVFSL 266
Cdd:PRK15092 245 PDLRVLGESEGLPPLPDTEYLL 266
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-147 1.89e-26

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: 105.01  E-value: 1.89e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNE---AA 81
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEkleEE 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 749307175  82 FDEVRGQaIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVV 147
Cdd:NF040786  82 FDRYGKE-SKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT 146
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 8.41e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.28  E-value: 8.41e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 749307175    6 LDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAG 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 93-266 1.27e-16

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 75.83  E-value: 1.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  93 ELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMnlssgpfRPASGDARWVLRREPLS 172
Cdd:cd08439    1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALIT-------HPPPGASATILRRSPTV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 173 WVASPAMAELLPEPLPLVLLPDDCMMHQIAVRSLDEQRVPYVLVHSASGVAGLQSMLAAGLGVGCLCASAIGDGLVRLGA 252
Cdd:cd08439   74 WYCAAGYILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGE 153

                        170
                 ....*....|....
gi 749307175 253 KYRLPALPDAVFSL 266
Cdd:cd08439  154 SEGLPPLPDTGYTL 167
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-247 1.31e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.95  E-value: 1.31e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   4 FDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFD 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  84 EVRG--QAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVmnlsSGPFRPASGD 161
Cdd:COG0583   81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR----LGPPPDPGLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 162 ARwVLRREPLSWVASPAmaellpeplplvllpddcmmHQIAVRSLDeqrvpyvlvhsASGVAGLQSMLAAGLGVGCLCAS 241
Cdd:COG0583  157 AR-PLGEERLVLVASPD--------------------HPLARRAPL-----------VNSLEALLAAVAAGLGIALLPRF 204


                 ....*.
gi 749307175 242 AIGDGL 247
Cdd:COG0583  205 LAADEL 210
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-266 1.89e-31

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 118.98  E-value: 1.89e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK15092  12 DLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  85 VRGQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMNlssgpfRPASGDaRW 164
Cdd:PRK15092  92 LMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTH------RPSSFP-AL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 165 VLRREPLSWVASPAMAELLPEPLPLVLLPDDCMMHQIAVRSLDEQRVPYVLVHSASGVAGLQSMLAAGLGVGCLCASAIG 244
Cdd:PRK15092 165 NLRTSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMS 244

                        250       260
                 ....*....|....*....|..
gi 749307175 245 DGLVRLGAKYRLPALPDAVFSL 266
Cdd:PRK15092 245 PDLRVLGESEGLPPLPDTEYLL 266
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-147 1.89e-26

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: 105.01  E-value: 1.89e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNE---AA 81
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEkleEE 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 749307175  82 FDEVRGQaIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVV 147
Cdd:NF040786  82 FDRYGKE-SKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT 146
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-147 4.62e-23

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 96.24  E-value: 4.62e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   4 FDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEA--- 80
Cdd:CHL00180   5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEEtcr 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 749307175  81 AFDEVR-GQaiKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVV 147
Cdd:CHL00180  85 ALEDLKnLQ--RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIV 150
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-146 4.78e-23

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 95.79  E-value: 4.78e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRivALNEaaFDEV 85
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARR--ALQD--LEAG 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 749307175  86 RgQAI-------KGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGV 146
Cdd:PRK11242  79 R-RAIhdvadlsRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGI 145
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 8.41e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.28  E-value: 8.41e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 749307175    6 LDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAG 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-126 7.20e-19

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 84.47  E-value: 7.20e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   4 FDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFD 83
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 749307175  84 EVRGQAIKGELRVAITD---YYRTHEVAGMLARLRECYPQLSLHVS 126
Cdd:PRK10094  82 ELQQVNDGVERQVNIVInnlLYNPQAVAQLLAWLNERYPFTQFHIS 127
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
4-98 1.18e-17

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 80.97  E-value: 1.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   4 FDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSkRGVEPTPAGSRLLQHARRIVALNEAAFD 83
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVRLLEAELLG 80

                         90
                 ....*....|....*.
gi 749307175  84 EVRGQAIKGE-LRVAI 98
Cdd:PRK03635  81 ELPALDGTPLtLSIAV 96
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 93-266 1.27e-16

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 75.83  E-value: 1.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  93 ELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMnlssgpfRPASGDARWVLRREPLS 172
Cdd:cd08439    1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALIT-------HPPPGASATILRRSPTV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 173 WVASPAMAELLPEPLPLVLLPDDCMMHQIAVRSLDEQRVPYVLVHSASGVAGLQSMLAAGLGVGCLCASAIGDGLVRLGA 252
Cdd:cd08439   74 WYCAAGYILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGE 153

                        170
                 ....*....|....
gi 749307175 253 KYRLPALPDAVFSL 266
Cdd:cd08439  154 SEGLPPLPDTGYTL 167
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-80 4.47e-16

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 76.55  E-value: 4.47e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 749307175   4 FDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSkRGVEPTPAGSRLLQHARRiVALNEA 80
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQ-VALLEA 76
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 5-145 6.22e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 73.27  E-value: 6.22e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK09906   2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLR 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 749307175  85 VRGQA-IKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLG 145
Cdd:PRK09906  82 ARKIVqEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVG 143
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-147 4.23e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 70.87  E-value: 4.23e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRskrgveptpAGSRLL--QHAR----RIVALNE 79
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDR---------VGKRLVvnEHGRllypRALALLE 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 749307175  80 AAFD-EVRGQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVV 147
Cdd:PRK10837  76 QAVEiEQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLI 144
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-144 1.35e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 69.66  E-value: 1.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK15421   3 EVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQA 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  85 VrGQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDL 144
Cdd:PRK15421  83 C-NEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL 141
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 5-175 1.44e-13

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 69.71  E-value: 1.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK11233   2 NFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  85 VR--GQAIKGELRVAITDYYRTHEVA-GMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMNLssgpfRPASGD 161
Cdd:PRK11233  82 VHnvGQALSGQVSIGLAPGTAASSLTmPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEH-----SPVAGL 156

                        170
                 ....*....|....
gi 749307175 162 ARWVLRREPLSWVA 175
Cdd:PRK11233 157 SSQPLLKEDLFLVG 170
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-125 2.81e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 68.88  E-value: 2.81e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   3 GFDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRL---LQHArrIVALNE 79
Cdd:PRK10086  13 GWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwaLKSS--LDTLNQ 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 749307175  80 AAFDeVRGQAIKGELRVaitdyYRTHEVAG-----MLARLRECYPQLSLHV 125
Cdd:PRK10086  91 EILD-IKNQELSGTLTV-----YSRPSIAQcwlvpRLADFTRRYPSISLTI 135
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 6-147 1.45e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 66.55  E-value: 1.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAG-SLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRS-KRGVEPTPAGSRLLQHARRIvaLNEA--- 80
Cdd:PRK12682   3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERI--LREVgni 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 749307175  81 -AFDEVRGQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVV 147
Cdd:PRK12682  81 kRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA 148
PRK12680 PRK12680
LysR family transcriptional regulator;
6-154 1.49e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 66.95  E-value: 1.49e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAG-SLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEP-TPAGSRLLQHARRIV--ALNEAA 81
Cdd:PRK12680   3 LTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESvTPAGVEVIERARAVLseANNIRT 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 749307175  82 FDEVRGQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMNLSSGP 154
Cdd:PRK12680  83 YAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEP 155
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-75 4.95e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 64.96  E-value: 4.95e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 749307175  14 AVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIV 75
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
PRK09986 PRK09986
LysR family transcriptional regulator;
5-146 4.50e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 62.05  E-value: 4.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK09986   8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLAR 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 749307175  85 VR--GQAIKGELRVAITDYYRTHEVAGMLARLRECYPQL--SLHvSAMKSADIEAAHAKgQIDLGV 146
Cdd:PRK09986  88 VEqiGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVewLLR-ELSPSMQMAALERR-ELDAGI 151
cysB PRK12681
HTH-type transcriptional regulator CysB;
6-144 4.79e-11

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 62.22  E-value: 4.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAG-SLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRS-KRGVEPTPAGSRLLQHARRIValneaafd 83
Cdd:PRK12681   3 LQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSgKHLTQVTPAGEEIIRIAREIL-------- 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 749307175  84 eVRGQAIK-----------GELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDL 144
Cdd:PRK12681  75 -SKVESIKsvagehtwpdkGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADF 145
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-266 6.45e-11

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: 60.38  E-value: 6.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   92 GELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMnlssGPFRPASGDARwVLRREPL 171
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR----GPPDDPGLEAR-PLGEEPL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  172 SWVASPAMAELLPEPLPLV--------LLPDDCMMHQIAVRSLDEQRVPYVLVHSASGVAGLQSMLAAGLGVGCLCASAI 243
Cdd:pfam03466  77 VLVAPPDHPLARGEPVSLEdladepliLLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180
                  ....*....|....*....|...
gi 749307175  244 GDGLVRLGAKYRLPALPDAVFSL 266
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPREL 179
PRK09791 PRK09791
LysR family transcriptional regulator;
6-86 1.10e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 60.93  E-value: 1.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDEV 85
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86


                 .
gi 749307175  86 R 86
Cdd:PRK09791  87 R 87
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-150 2.29e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 60.01  E-value: 2.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   1 MRGFDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARR-IVALNE 79
Cdd:PRK11013   1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRsYYGLDR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 749307175  80 --AAFDEVRgQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMNL 150
Cdd:PRK11013  81 ivSAAESLR-EFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETL 152
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-96 1.06e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 57.93  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRI-VALNEAAfDE 84
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIfDQLAEAT-RK 86

                         90
                 ....*....|..
gi 749307175  85 VRGQAIKGELRV 96
Cdd:PRK11139  87 LRARSAKGALTV 98
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-123 1.39e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.85  E-value: 1.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIvaLNEAafDEV 85
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRM--LHEV--QDV 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 749307175  86 RGQAIK------GELRVAITDYYRTHEVAGMLARLRECYPQLSL 123
Cdd:PRK10632  80 HEQLYAfnntpiGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSV 123
cbl PRK12679
HTH-type transcriptional regulator Cbl;
20-146 2.06e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 57.51  E-value: 2.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  20 SLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVR-SKRGVEPTPAGSRLLQHARRIvaLNEAAfdEVRGQA------IKG 92
Cdd:PRK12679  18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERI--LNEAS--NVRRLAdlftndTSG 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 749307175  93 ELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGV 146
Cdd:PRK12679  94 VLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGI 147
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-120 3.93e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 55.98  E-value: 3.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  29 HLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIvaLNE-----AAFDEVrGQAIKGELRV--AITDY 101
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQT--LLQwqqlrHTLDQQ-GPSLSGELSLfcSVTAA 78

                         90
                 ....*....|....*....
gi 749307175 102 YrTHeVAGMLARLRECYPQ 120
Cdd:PRK11716  79 Y-SH-LPPILDRFRAEHPL 95
PRK09801 PRK09801
LysR family transcriptional regulator;
9-149 1.91e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 54.66  E-value: 1.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   9 LRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDEVRGQ 88
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 749307175  89 AIK--GELRVAIT-DYYRTHeVAGMLARLRECYPQLSLHVSAMksaDIEAAHAKGQIDLGVVMN 149
Cdd:PRK09801  91 KTRpeGMIRIGCSfGFGRSH-IAPAITELMRNYPELQVHFELF---DRQIDLVQDNIDLDIRIN 150
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
6-74 1.98e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 54.21  E-value: 1.98e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 749307175   6 LDQLRTFAAVADAG-SLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVR-SKRGVEPTPAGSRLLQHARRI 74
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERI 73
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
5-85 5.61e-08

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 52.71  E-value: 5.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK03601   2 DTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKE 81


                 .
gi 749307175  85 V 85
Cdd:PRK03601  82 V 82
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 5-127 7.21e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.69  E-value: 7.21e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDE 84
Cdd:PRK14997   3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 749307175  85 VRGQAI--KGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSA 127
Cdd:PRK14997  83 IAALQVepRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEA 127
PRK10341 PRK10341
transcriptional regulator TdcA;
8-75 8.54e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 52.56  E-value: 8.54e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 749307175   8 QLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIV 75
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESIT 78
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 6-146 1.02e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.35  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   6 LDQLRTFAAVADAG-SLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRS-KRGVEPTPAGSRLLQHARRIvaLNEA--- 80
Cdd:PRK12683   3 FQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERM--LLDAenl 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 749307175  81 --AFDEVRGQAiKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGV 146
Cdd:PRK12683  81 rrLAEQFADRD-SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI 147
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-238 2.09e-07

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: 50.29  E-value: 2.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  93 ELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMnlssGPFRPASGDARwVLRREPLS 172
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA----LPVDDPGLESE-PLFEEPLV 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 749307175 173 WVASPAMAELLPEPLPLV--------LLPDDCMMHQIAVRSLDEQRVPYVLVHSASGVAGLQSMLAAGLGVGCL 238
Cdd:cd05466   76 LVVPPDHPLAKRKSVTLAdladepliLFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALL 149
nhaR PRK11062
transcriptional activator NhaR; Provisional
 12-85 6.85e-07

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 49.62  E-value: 6.85e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 749307175  12 FAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIVALNEAAFDEV 85
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEMLDIV 85
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 5-147 2.07e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.10  E-value: 2.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   5 DLDQLrtfAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARRIV----ALNEA 80
Cdd:PRK11151   5 DLEYL---VALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLrevkVLKEM 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 749307175  81 AFDEvrGQAIKGELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVV 147
Cdd:PRK11151  82 ASQQ--GETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIL 146
leuO PRK09508
leucine transcriptional activator; Reviewed
 1-61 1.68e-05

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 45.40  E-value: 1.68e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 749307175   1 MRGFDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPT 61
Cdd:PRK09508  19 LRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPT 79
PRK11482 PRK11482
DNA-binding transcriptional regulator;
1-73 1.70e-04

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 42.40  E-value: 1.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 749307175   1 MRGFDLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTPAGSRLLQHARR 73
Cdd:PRK11482  26 LRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQ 98
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
5-62 4.47e-04

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 41.34  E-value: 4.47e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 749307175   5 DLDQLRTFAAVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGVEPTP 62
Cdd:PRK10216   9 DLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTP 66
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
14-95 5.86e-04

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 38.65  E-value: 5.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  14 AVADAGSLTAAAPLLHLSQSTVSEQVRKLEMRAGVPLFVRSKRGV-----EPTPAGSRLLQHARRIVALNEAAFDEvRGQ 88
Cdd:COG2005   29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTGGKggggaRLTPEGRRLLALYRRLEAEAQRALAA-LFE 107


                 ....*..
gi 749307175  89 AIKGELR 95
Cdd:COG2005  108 ELFALLR 114
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 110-147 1.92e-03

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: 38.63  E-value: 1.92e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 749307175 110 MLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVV 147
Cdd:cd08420   18 LLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLV 55
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-180 3.67e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 37.55  E-value: 3.67e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 749307175 107 VAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVmnlsSGPFRPASGDARWV-LRREPLSWVASPAMA 180
Cdd:cd08427   15 LPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIV----VEPPFPLPKDLVWTpLVREPLVLIAPAELA 85
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
8-84 3.69e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.87  E-value: 3.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175   8 QLRTFAAVADAGSLTAA--APLLHLSQSTVSEQVRKLEmRAGvplFVRSKRG--------VEPTPAGSRLLQHARRIV-A 76
Cdd:COG1846   40 QFRVLAALAEAGGLTQSelAERLGLTKSTVSRLLDRLE-EKG---LVEREPDpedrravlVRLTEKGRALLEEARPALeA 115


                 ....*...
gi 749307175  77 LNEAAFDE 84
Cdd:COG1846  116 LLAELLAG 123
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 93-177 3.77e-03

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: 37.58  E-value: 3.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  93 ELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVvmnlssGPFRPASGDARW-VLRREPL 171
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAI------GVFPELPPGLRSqPLFEDRF 74


                 ....*.
gi 749307175 172 SWVASP 177
Cdd:cd08417   75 VCVARK 80
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-284 5.41e-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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 37.19  E-value: 5.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 107 VAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVMNLSSGPFRPASGDARWVLRREPLSWVASPAMAELLPEP 186
Cdd:cd08423   15 LPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTRVPLLDDPLDLVLPADHPLAGREE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175 187 LPLVLLPDD--------CMMHQIAVRSLDEQ-RVPYVlVHSASGVAGLQSMLAAGLGVGCLCASAIG---DGLVRLgaky 254
Cdd:cd08423   95 VALADLADEpwiagcpgSPCHRWLVRACRAAgFTPRI-AHEADDYATVLALVAAGLGVALVPRLALGarpPGVVVR---- 169

                        170       180       190
                 ....*....|....*....|....*....|.
gi 749307175 255 RLPALPD-AVFSLTPPMPGERETVAQAREVL 284
Cdd:cd08423  170 PLRPPPTrRIYAAVRAGAARRPAVAAALEAL 200
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-178 5.80e-03

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: 37.10  E-value: 5.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749307175  93 ELRVAITDYYRTHEVAGMLARLRECYPQLSLHVSAMKSADIEAAHAKGQIDLGVVmnlssGPFRPASGDARWVLRREPLs 172
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFV-----RPPPDPPGLASRPLLREPL- 74


                 ....*.
gi 749307175 173 WVASPA 178
Cdd:cd08414   75 VVALPA 80
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH