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Conserved domains on  [gi|739087660|ref|WP_036958742|]
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MULTISPECIES: LysR family transcriptional regulator [Providencia]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11487634)

LysR family transcriptional regulator LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-289 0e+00

DNA-binding transcriptional repressor LrhA; Provisional


:

Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 531.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   1 MPAAKRPIFNLELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARR 80
Cdd:PRK15092   1 MINANRPIINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  81 ILRLNDEACLSLVYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVG 160
Cdd:PRK15092  81 ILRFNDEACSSLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 161 YPKIVLRVSPSLWYCGKHFSFNLEQPLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGIMARSI 240
Cdd:PRK15092 161 FPALNLRTSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPV 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 739087660 241 ELSGEDLRILGEDEGLPVLPAIRYNLYLNSKSPTKAAQILFNSLKNEQT 289
Cdd:PRK15092 241 EMMSPDLRVLGESEGLPPLPDTEYLLCRDPNSNNELAQVIFQAMESYHN 289
 
Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-289 0e+00

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 531.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   1 MPAAKRPIFNLELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARR 80
Cdd:PRK15092   1 MINANRPIINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  81 ILRLNDEACLSLVYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVG 160
Cdd:PRK15092  81 ILRFNDEACSSLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 161 YPKIVLRVSPSLWYCGKHFSFNLEQPLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGIMARSI 240
Cdd:PRK15092 161 FPALNLRTSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPV 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 739087660 241 ELSGEDLRILGEDEGLPVLPAIRYNLYLNSKSPTKAAQILFNSLKNEQT 289
Cdd:PRK15092 241 EMMSPDLRVLGESEGLPPLPDTEYLLCRDPNSNNELAQVIFQAMESYHN 289
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 100-284 4.52e-94

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: 275.75  E-value: 4.52e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 100 VLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVGYPKIVLRVSPSLWYCGKHF 179
Cdd:cd08439    1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 180 SFNLEQPLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGIMARSIELSGEDLRILGEDEGLPVL 259
Cdd:cd08439   81 ILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGESEGLPPL 160

                        170       180
                 ....*....|....*....|....*
gi 739087660 260 PAIRYNLYLNSKSPTKAAQILFNSL 284
Cdd:cd08439  161 PDTGYTLCLDPNRPSELAQAFFEAL 185
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-248 2.05e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 135.76  E-value: 2.05e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEAC- 89
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  90 -LSLVYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIST--EEHVGYPKIVL 166
Cdd:COG0583   81 eLRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLgpPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 167 RVSPSLWYCGKhfSFNLEQPLPLVvldepstyremminhleqqqipwriaymaTTLSGARAAVRAGLGIMARSIELSGED 246
Cdd:COG0583  161 GEERLVLVASP--DHPLARRAPLV-----------------------------NSLEALLAAVAAGLGIALLPRFLAADE 209


                 ..
gi 739087660 247 LR 248
Cdd:COG0583  210 LA 211
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 12-287 8.43e-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: 103.47  E-value: 8.43e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  12 ELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACLS 91
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  92 L--VYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAI----STEEHVGY-P-- 162
Cdd:NF040786  82 FdrYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFtgtkLEKKRLVYtPfy 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 163 --KIVLRVSPSL-WYCGKHFSFNLE--QPLPLVVLDEPS-TYREMMiNHLEQQQIP---WRIAYMATTLSGARAAVRAGL 233
Cdd:NF040786 162 kdRLVLITPNGTeKYRMLKEEISISelQKEPFIMREEGSgTRKEAE-KALKSLGISledLNVVASLGSTEAIKQSVEAGL 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 234 GImarSI--ELSGEDLRILGEDE--GLPVLPAIR--YNLYLNSKSPTKAAQILFNSLKNE 287
Cdd:NF040786 241 GI---SVisELAAEKEVERGRVLifPIPGLPKNRdfYLVYNKNRQLSPTAEAFLQFVKER 297
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-235 1.04e-18

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: 82.34  E-value: 1.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   99 GVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIST--EEHVGYPKIVLRVSPSLWYCG 176
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRgpPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 739087660  177 KHFSFNLEQPL--------PLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGI 235
Cdd:pfam03466  82 PDHPLARGEPVsledladePLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGI 148
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 11-87 5.18e-12

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 65.14  E-value: 5.18e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDE 87
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDS 77
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-157 2.31e-11

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 63.01  E-value: 2.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRqGRNKALTDSGTQLLSYARRILRLNDE--A 88
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAEllA 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 739087660   89 CLSLVYEEIDGVLKIGSPDDTANTILPDLLARFSgAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEE 157
Cdd:TIGR03298  80 ELPGLAPGAPTRLTIAVNADSLATWFLPALAPVL-AREGVLLDLVVEDQDHTAELLRSGEVLGAVTTEA 147
 
Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-289 0e+00

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 531.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   1 MPAAKRPIFNLELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARR 80
Cdd:PRK15092   1 MINANRPIINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  81 ILRLNDEACLSLVYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVG 160
Cdd:PRK15092  81 ILRFNDEACSSLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 161 YPKIVLRVSPSLWYCGKHFSFNLEQPLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGIMARSI 240
Cdd:PRK15092 161 FPALNLRTSPTLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPV 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 739087660 241 ELSGEDLRILGEDEGLPVLPAIRYNLYLNSKSPTKAAQILFNSLKNEQT 289
Cdd:PRK15092 241 EMMSPDLRVLGESEGLPPLPDTEYLLCRDPNSNNELAQVIFQAMESYHN 289
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 100-284 4.52e-94

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: 275.75  E-value: 4.52e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 100 VLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVGYPKIVLRVSPSLWYCGKHF 179
Cdd:cd08439    1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 180 SFNLEQPLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGIMARSIELSGEDLRILGEDEGLPVL 259
Cdd:cd08439   81 ILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGESEGLPPL 160

                        170       180
                 ....*....|....*....|....*
gi 739087660 260 PAIRYNLYLNSKSPTKAAQILFNSL 284
Cdd:cd08439  161 PDTGYTLCLDPNRPSELAQAFFEAL 185
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-248 2.05e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 135.76  E-value: 2.05e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEAC- 89
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  90 -LSLVYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIST--EEHVGYPKIVL 166
Cdd:COG0583   81 eLRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLgpPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 167 RVSPSLWYCGKhfSFNLEQPLPLVvldepstyremminhleqqqipwriaymaTTLSGARAAVRAGLGIMARSIELSGED 246
Cdd:COG0583  161 GEERLVLVASP--DHPLARRAPLV-----------------------------NSLEALLAAVAAGLGIALLPRFLAADE 209


                 ..
gi 739087660 247 LR 248
Cdd:COG0583  210 LA 211
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 12-287 8.43e-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: 103.47  E-value: 8.43e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  12 ELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACLS 91
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  92 L--VYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAI----STEEHVGY-P-- 162
Cdd:NF040786  82 FdrYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFtgtkLEKKRLVYtPfy 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 163 --KIVLRVSPSL-WYCGKHFSFNLE--QPLPLVVLDEPS-TYREMMiNHLEQQQIP---WRIAYMATTLSGARAAVRAGL 233
Cdd:NF040786 162 kdRLVLITPNGTeKYRMLKEEISISelQKEPFIMREEGSgTRKEAE-KALKSLGISledLNVVASLGSTEAIKQSVEAGL 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 234 GImarSI--ELSGEDLRILGEDE--GLPVLPAIR--YNLYLNSKSPTKAAQILFNSLKNE 287
Cdd:NF040786 241 GI---SVisELAAEKEVERGRVLifPIPGLPKNRdfYLVYNKNRQLSPTAEAFLQFVKER 297
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-235 1.04e-18

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: 82.34  E-value: 1.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   99 GVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIST--EEHVGYPKIVLRVSPSLWYCG 176
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRgpPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 739087660  177 KHFSFNLEQPL--------PLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGI 235
Cdd:pfam03466  82 PDHPLARGEPVsledladePLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGI 148
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 16-258 3.11e-18

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 82.70  E-value: 3.11e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  16 LRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILR--------LNDE 87
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQdleagrraIHDV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  88 ACLSlvyeeiDGVLKIG-SPDDTANTILPdLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEhVGYPKIV- 165
Cdd:PRK11242  86 ADLS------RGSLRLAmTPTFTAYLIGP-LIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAP-VHSPEIEa 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 166 ---------LRVSPSLWYCGKHFSFNLEQ--PLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGL- 233
Cdd:PRK11242 158 qplftetlaLVVGRHHPLAARRKALTLDElaDEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRl 237

                        250       260
                 ....*....|....*....|....*.
gi 739087660 234 -GIMARSIELSGEDLRILGEDEGLPV 258
Cdd:PRK11242 238 aTLLPAAIAREHDGLCAIPLDPPLPQ 263
rbcR CHL00180
LysR transcriptional regulator; Provisional
 13-153 1.76e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 80.83  E-value: 1.76e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  13 LDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACLSL 92
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739087660  93 VY-EEID-GVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAI 153
Cdd:CHL00180  87 EDlKNLQrGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI 149
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
13-71 2.22e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 2.22e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 739087660   13 LDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSG 71
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 101-278 3.14e-17

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: 78.03  E-value: 3.14e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 101 LKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTE---------EHVGYPKIVLRVSPS 171
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALpvddpglesEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 172 -LWYCGKHFSFNLEQPLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGI--MARSI--ELSGED 246
Cdd:cd05466   82 hPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIalLPESAveELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 739087660 247 LRILGEDEglpvlPAIRYNLYL---NSKSPTKAAQ 278
Cdd:cd05466  162 LVVLPLED-----PPLSRTIGLvwrKGRYLSPAAR 191
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-134 9.00e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 70.42  E-value: 9.00e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  16 LRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACLSLVYE 95
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQ 98

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 739087660  96 EIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIV 134
Cdd:PRK10086  99 ELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILT 137
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 11-87 5.18e-12

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 65.14  E-value: 5.18e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDE 87
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDS 77
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 30-165 5.31e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 65.01  E-value: 5.31e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  30 AAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRN-KALTDSGTQLLSYARRILR-LNDEACLSLVYEEID-GVLKIGSP 106
Cdd:PRK12682  21 EAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRlKGLTEPGKAVLDVIERILReVGNIKRIGDDFSNQDsGTLTIATT 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 739087660 107 DDTANTILPDLLARFSGAYP--NLimdIIVKRSPF-LMSMLEDNELDLAISTEEHVGYPKIV 165
Cdd:PRK12682 101 HTQARYVLPRVVAAFRKRYPkvNL---SLHQGSPDeIARMVISGEADIGIATESLADDPDLA 159
cbl PRK12679
HTH-type transcriptional regulator Cbl;
38-165 8.09e-12

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 64.45  E-value: 8.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  38 TQSAVSQQMQRLESLIGKELFVRQG-RNKALTDSGTQLLSYARRIL-------RLNDeaclsLVYEEIDGVLKIGSPDDT 109
Cdd:PRK12679  29 SQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILneasnvrRLAD-----LFTNDTSGVLTIATTHTQ 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 739087660 110 ANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVGYPKIV 165
Cdd:PRK12679 104 ARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLV 159
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
11-82 9.40e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 64.44  E-value: 9.40e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRIL 82
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 11-152 9.65e-12

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 64.41  E-value: 9.65e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACL 90
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 739087660  91 ---SLVYEEIdgVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLA 152
Cdd:PRK09906  81 rarKIVQEDR--QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVG 143
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-153 1.26e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 63.71  E-value: 1.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  16 LRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACLSLVYE 95
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRAR 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 739087660  96 EIDGVLKIG-SPDDTANTILPDlLARFSGAYPNliMDIIVKRSPFLMSMLEDnELDLAI 153
Cdd:PRK11139  91 SAKGALTVSlLPSFAIQWLVPR-LSSFNEAHPD--IDVRLKAVDRLEDFLRD-DVDVAI 145
PRK09791 PRK09791
LysR family transcriptional regulator;
9-155 1.61e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 63.63  E-value: 1.61e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   9 FNLELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRI---LRLN 85
Cdd:PRK09791   3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIleeLRAA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739087660  86 DEACLSLVyEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRspfLMSM---LEDNELDLAIST 155
Cdd:PRK09791  83 QEDIRQRQ-GQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQ---LVSMineLRQGELDFTINT 151
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-157 2.31e-11

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 63.01  E-value: 2.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRqGRNKALTDSGTQLLSYARRILRLNDE--A 88
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAEllA 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 739087660   89 CLSLVYEEIDGVLKIGSPDDTANTILPDLLARFSgAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEE 157
Cdd:TIGR03298  80 ELPGLAPGAPTRLTIAVNADSLATWFLPALAPVL-AREGVLLDLVVEDQDHTAELLRSGEVLGAVTTEA 147
PRK09986 PRK09986
LysR family transcriptional regulator;
11-153 4.24e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 62.43  E-value: 4.24e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRlNDEACL 90
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLD-NAEQSL 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739087660  91 SLVyEEI----DGVLKIGSPDDTANTILPDLLARFSGAYPNLIMdIIVKRSPFL-MSMLEDNELDLAI 153
Cdd:PRK09986  86 ARV-EQIgrgeAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEW-LLRELSPSMqMAALERRELDAGI 151
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-134 5.35e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 62.10  E-value: 5.35e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRqGRNKALTDSGTQLLSYARRILRLNDEACL 90
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 739087660  91 SLVYEEIDGV-LKIGSPDDTANTILPDLLARFSGAYPnLIMDIIV 134
Cdd:PRK03635  81 ELPALDGTPLtLSIAVNADSLATWFLPALAPVLARSG-VLLDLVV 124
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
14-156 5.92e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 61.57  E-value: 5.92e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  14 DLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACLSLV 93
Cdd:PRK03601   4 ELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVA 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739087660  94 YEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTE 156
Cdd:PRK03601  84 HTSQHNELSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLITTE 146
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-156 1.24e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 60.76  E-value: 1.24e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  10 NLELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRqGRNKALTDSGTQLLSYARRIlRLNDEAC 89
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-ALLEADL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 739087660  90 LSLVYEEIDG--VLKIGSPDDTANTILPDLLARFSgAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTE 156
Cdd:PRK13348  79 LSTLPAERGSppTLAIAVNADSLATWFLPALAAVL-AGERILLELIVDDQDHTFALLERGEVVGCVSTQ 146
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
30-165 1.33e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 61.15  E-value: 1.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  30 AAAESVCRTQSAVSQQMQRLESLIGKELFVRQG-RNKALTDSGTQLLSYARRILRlndeaclslvyeEIDGVLKIGspDD 108
Cdd:PRK12684  21 EAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERILQ------------EVENLKRVG--KE 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 739087660 109 TAN------TI----------LPDLLARFSGAYPNLIMDIIvKRSPFLMS-MLEDNELDLAISTEEHVGYPKIV 165
Cdd:PRK12684  87 FAAqdqgnlTIatthtqaryaLPAAIKEFKKRYPKVRLSIL-QGSPTQIAeMVLHGQADLAIATEAIADYKELV 159
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 31-196 1.66e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 60.83  E-value: 1.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  31 AAESVCRTQSAVSQQMQRLESLIGKELFVRQG-RNKALTDSGTQLLSYARRILRlnDEACLSLVYEEI----DGVLKIGS 105
Cdd:PRK12683  22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLL--DAENLRRLAEQFadrdSGHLTVAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 106 PDDTANTILPDLLARFSGAYPNLIMdIIVKRSPF-LMSMLEDNELDLAISTEEHVGYPKIVlrvspSLWYCGKHFSFNLE 184
Cdd:PRK12683 100 THTQARYALPKVVRQFKEVFPKVHL-ALRQGSPQeIAEMLLNGEADIGIATEALDREPDLV-----SFPYYSWHHVVVVP 173

                        170
                 ....*....|..
gi 739087660 185 QPLPLVVLDEPS 196
Cdd:PRK12683 174 KGHPLTGRENLT 185
cysB PRK12681
HTH-type transcriptional regulator CysB;
30-156 4.50e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 59.53  E-value: 4.50e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  30 AAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRN-KALTDSGTQLLSYARRILRlNDEACLSLVYEEID---GVLKIGS 105
Cdd:PRK12681  21 ATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHlTQVTPAGEEIIRIAREILS-KVESIKSVAGEHTWpdkGSLYIAT 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 739087660 106 PDDTANTILPDLLARFSGAYPN--LIMDiivKRSPFLMS-MLEDNELDLAISTE 156
Cdd:PRK12681 100 THTQARYALPPVIKGFIERYPRvsLHMH---QGSPTQIAeAAAKGNADFAIATE 150
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
40-126 4.79e-10

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 59.06  E-value: 4.79e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  40 SAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRIL--------RLNDEAclslvyEEIDGVLKIGSPDDTAN 111
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLlqwqqlrhTLDQQG------PSLSGELSLFCSVTAAY 79

                         90
                 ....*....|....*
gi 739087660 112 TILPDLLARFSGAYP 126
Cdd:PRK11716  80 SHLPPILDRFRAEHP 94
PRK12680 PRK12680
LysR family transcriptional regulator;
11-153 6.78e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 56.17  E-value: 6.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  11 LELDLLRTFIAVVDGA-TFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRN-KALTDSGTQLLSYARRILrlnDEA 88
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSlESVTPAGVEVIERARAVL---SEA 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  89 CLSLVY-----EEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAI 153
Cdd:PRK12680  78 NNIRTYaanqrRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAI 147
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 101-282 1.31e-08

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: 54.03  E-value: 1.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 101 LKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIsTEEHVGYPKI----------VLRVSP 170
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL-VEGPVDHPDLivepfaedelVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 171 SL-WYCGKHFSFNLEQPLPLVVLDEPSTYREMM---INHLEQQQIPWRIAYMATTLSGARAAVRAGLGI-----MARSIE 241
Cdd:cd08420   81 DHpLAGRKEVTAEELAAEPWILREPGSGTREVFeraLAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGIsilsrLAVRKE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 739087660 242 LSGEDLRILgedeGLPVLPAIR--YNLYLNSKSPTKAAQILFN 282
Cdd:cd08420  161 LELGRLVAL----PVEGLRLTRpfSLIYHKDKYLSPAAEAFLE 199
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
11-170 1.73e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 54.64  E-value: 1.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  11 LELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEAcL 90
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA-L 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  91 SLVYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEhvgYPKIVLRVSP 170
Cdd:PRK15421  81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDI---LPRSGLHYSP 157
PRK10341 PRK10341
transcriptional regulator TdcA;
16-155 1.84e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.48  E-value: 1.84e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  16 LRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILR--------LNDE 87
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRemknmvneINGM 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739087660  88 ACLSLVYeeidgvLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIST 155
Cdd:PRK10341  92 SSEAVVD------VSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGT 153
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 20-153 2.38e-08

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 54.27  E-value: 2.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  20 IAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILR----LNDEAclSLVYE 95
Cdd:PRK11151  10 VALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLRevkvLKEMA--SQQGE 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 739087660  96 EIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAI 153
Cdd:PRK11151  88 TMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAI 145
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 16-268 3.95e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 53.54  E-value: 3.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  16 LRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEacLSLVYE 95
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVE--IEQLFR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  96 EIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAI-----STEEHVGYP----KIVL 166
Cdd:PRK10837  86 EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLiegpcHSPELISEPwledELVV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 167 RVSPSLWYCGKHFSFNLEQPLPLVVLDEPSTYREmMINHLEQQQIP-WRIAyMATTLSGA-RAAVRAGLGIMARSIELSG 244
Cdd:PRK10837 166 FAAPDSPLARGPVTLEQLAAAPWILRERGSGTRE-IVDYLLLSHLPrFELA-MELGNSEAiKHAVRHGLGISCLSRRVIA 243

                        250       260
                 ....*....|....*....|....*
gi 739087660 245 EDLRiLGEDEGLPV-LPAIRYNLYL 268
Cdd:PRK10837 244 DQLQ-AGTLVEVAVpLPRLMRTLYR 267
PRK09801 PRK09801
LysR family transcriptional regulator;
16-156 3.35e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 50.80  E-value: 3.35e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  16 LRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRIL----RLNDEacLS 91
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILtqyqRLVDD--VT 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 739087660  92 LVYEEIDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDI-IVKRSpflMSMLEDN-ELDLAISTE 156
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFeLFDRQ---IDLVQDNiDLDIRINDE 152
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 101-278 8.78e-07

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 48.31  E-value: 8.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 101 LKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHV--GYPKIVLRVS-PSLWYCGK 177
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLpeDIAFEPLARLpPYVWLPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 178 HfsfnleqPL--------------PLVVLDEPSTyREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGI------MA 237
Cdd:cd08412   82 H-------PLagkdevsladlaaePLILLDLPHS-REYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYsllndrPY 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 739087660 238 RSIELSGEDLRILGEDEGLPVLPAIRynLYLNSKSPTKAAQ 278
Cdd:cd08412  154 RPWSYDGKRLVRRPLADPVPPLRLGL--AWRRGARLTRAAR 192
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 109-278 9.00e-07

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: 48.27  E-value: 9.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 109 TANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIsteehVGYP--------------KIVLRVSPSLWY 174
Cdd:cd08419    9 TAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAI-----MGRPpedldlvaepfldnPLVVIAPPDHPL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 175 CGKHfSFNLEQ--PLPLVVLDEPSTYREMMINHLEQQQIPWRIaYMatTLSGARA---AVRAGLGIMARSI-----ELSG 244
Cdd:cd08419   84 AGQK-RIPLERlaREPFLLREPGSGTRLAMERFFAEHGVTLRV-RM--ELGSNEAikqAVMAGLGLSVLSLhtlalELAT 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 739087660 245 EDLRILgEDEGLPVLpaiR--YNLYLNSKSPTKAAQ 278
Cdd:cd08419  160 GRLAVL-DVEGFPIR---RqwYVVHRKGKRLSPAAQ 191
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 101-268 1.17e-06

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: 47.94  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 101 LKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEhVGYPKIVLRVSPSL-WYCGKHF 179
Cdd:cd08415    2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLP-LDHPGLESEPLASGrAVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 180 SFNLEQ----------PLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGImarSI-------EL 242
Cdd:cd08415   81 GHPLARkdvvtpadlaGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGV---AIvdpltaaGY 157

                        170       180
                 ....*....|....*....|....*.
gi 739087660 243 SGEDLRIlgedegLPVLPAIRYNLYL 268
Cdd:cd08415  158 AGAGLVV------RPFRPAIPFEFAL 177
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 16-130 1.52e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 48.91  E-value: 1.52e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  16 LRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEACLSL--V 93
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVhnV 85

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 739087660  94 YEEIDGVLKIG-SPDDTANTILPDLLARFSGAYPNLIM 130
Cdd:PRK11233  86 GQALSGQVSIGlAPGTAASSLTMPLLQAVRAEFPGIVL 123
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
19-133 2.38e-06

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 48.22  E-value: 2.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  19 FIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEaclslVYEEI- 97
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQD-----VHEQLy 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 739087660  98 ------DGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDII 133
Cdd:PRK10632  85 afnntpIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLV 126
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 100-235 4.02e-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: 46.38  E-value: 4.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 100 VLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIS----TEEHVG-YP----KIVLRVSP 170
Cdd:cd08434    1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCspvpDEPDIEwIPlfteELVLVVPK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 739087660 171 S--LwycGKHFSFNLEQ--PLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGI 235
Cdd:cd08434   81 DhpL---AGRDSVDLAElaDEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGV 146
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 100-160 1.44e-05

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: 44.90  E-value: 1.44e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 739087660 100 VLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVG 160
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELP 61
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 19-132 2.93e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 44.98  E-value: 2.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660  19 FIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDEA--CLSLVYEE 96
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAqdAIAALQVE 89

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 739087660  97 IDGVLKIGSPDDTANTILPDLLARFSGAYPNLIMDI 132
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
leuO PRK09508
leucine transcriptional activator; Reviewed
 10-84 3.99e-05

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 44.24  E-value: 3.99e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 739087660  10 NLELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRL 84
Cdd:PRK09508  21 MVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQL 95
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-235 5.71e-05

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: 43.28  E-value: 5.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 110 ANTILPDLLARFSGAYPNL---IMDIIVKRspfLMSMLEDNELDLAISTEEHVGyPKIVLR---------VSPSLWYCGK 177
Cdd:cd08440   11 AATLLPPVLAAFRRRHPGIrvrLRDVSAEQ---VIEAVRSGEVDFGIGSEPEAD-PDLEFEpllrdpfvlVCPKDHPLAR 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 178 HFSFNLEQ--PLPLVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGI 235
Cdd:cd08440   87 RRSVTWAElaGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGV 146
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 100-162 7.49e-05

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: 42.65  E-value: 7.49e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739087660 100 VLKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVGYP 162
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQP 63
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 21-83 8.21e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 43.39  E-value: 8.21e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739087660  21 AVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILR 83
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK 74
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-159 8.78e-05

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 42.61  E-value: 8.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 739087660 100 VLKIGSPDDTANTILPDLLARFSGAYPNliMDIIVKRS-PFLMS-MLEDNELDLAISTEEHV 159
Cdd:cd08464    1 TFRIGLSDDVESWLAPPLLAALRAEAPG--VRLVFRQVdPFNVGdMLDRGEIDLAIGVFGEL 60
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-250 5.33e-04

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: 40.25  E-value: 5.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 101 LKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAISTEEHVGYPkivlrvspslwycgKHFS 180
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLP--------------KDLV 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 181 FN--LEQPLPLVVLDE--PSTYREMMINH------------------LEQQQIPWRIAYMATTLSGARAAVRAGLGI--- 235
Cdd:cd08427   68 WTplVREPLVLIAPAElaGDDPRELLATQpfirydrsawggrlvdrfLRRQGIRVREVMELDSLEAIAAMVAQGLGVaiv 147

                        170
                 ....*....|....*.
gi 739087660 236 -MARSIELSGEDLRIL 250
Cdd:cd08427  148 pDIAVPLPAGPRVRVL 163
PRK11482 PRK11482
DNA-binding transcriptional regulator;
5-107 6.95e-04

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 40.48  E-value: 6.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660   5 KRPIF----NLELDLLRTFIAVVDGATFAAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARR 80
Cdd:PRK11482  19 KPQIFrtlrNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQ 98

                         90       100
                 ....*....|....*....|....*...
gi 739087660  81 ILrlndeaclslvyEEIDGVLKI-GSPD 107
Cdd:PRK11482  99 GL------------ESILGALDItGSYD 114
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 101-235 1.62e-03

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: 39.01  E-value: 1.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087660 101 LKIGSPDDTANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIST--EEHVGYPKIVLRVSPSLwycgkh 178
Cdd:cd08457    2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADgpLEERQGFLIETRSLPAV------ 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 739087660 179 FSFNLEQPLP--------------LVVLDEPSTYREMMINHLEQQQIPWRIAYMATTLSGARAAVRAGLGI 235
Cdd:cd08457   76 VAVPMGHPLAqldvvspqdlagerIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGI 146
nhaR PRK11062
transcriptional activator NhaR; Provisional
 29-87 4.01e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 38.07  E-value: 4.01e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 739087660  29 AAAAESVCRTQSAVSQQMQRLESLIGKELFVRQGRNKALTDSGTQLLSYARRILRLNDE 87
Cdd:PRK11062  22 VGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQE 80
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-154 4.08e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 37.67  E-value: 4.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 739087660 109 TANTILPDLLARFSGAYPNLIMDIIVKRSPFLMSMLEDNELDLAIS 154
Cdd:cd08426   10 LAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLA 55
 
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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