NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|736475933|ref|WP_034497564|]
View 

MULTISPECIES: sugar-binding transcriptional regulator [Rhizobium/Agrobacterium group]

Protein Classification

sugar-binding transcriptional regulator( domain architecture ID 11457260)

sugar-binding transcriptional regulator similar to Priestia megaterium central glycolytic genes regulator, in the absence of glucose, which represses the transcription of the gapA operon that encodes five key glycolytic enzymes

CATH:  1.10.10.60|3.40.50.1360
Gene Ontology:  GO:0030246|GO:0003677|GO:0006355
PubMed:  19232357
SCOP:  4002188

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
21-322 2.71e-114

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


:

Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 332.48  E-value: 2.71e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  21 RAAWLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKRSEVQIWINEGIEDFVSLAGQLEAAYGLDEAVIIPSPDkASAEG 100
Cdd:COG2390    1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDS-DDDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 101 TAKAVGLALGQFLSEAVPNGATIGVGWGRTMTASLSSFRPPRRENCKVVSLLGGIVAVHQTNPLDYTWRLASALGAECYM 180
Cdd:COG2390   80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGEDVEAQANEIARRLAEKLGGEYYL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 181 FLAPLLVDSVETKRALIEKCGLATLYDLAETLDLAIVSCGDIGPHSTSLSEGFISRETLRELIDAGCVCDTMFNFIDAEG 260
Cdd:COG2390  160 LPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDADG 239

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736475933 261 RSVDHPINQRAMAIDLDTLRKAKHIVLASGGAHRAIAIRATIKRIGCNTLITDEAAARALME 322
Cdd:COG2390  240 RIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
21-322 2.71e-114

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 332.48  E-value: 2.71e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  21 RAAWLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKRSEVQIWINEGIEDFVSLAGQLEAAYGLDEAVIIPSPDkASAEG 100
Cdd:COG2390    1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDS-DDDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 101 TAKAVGLALGQFLSEAVPNGATIGVGWGRTMTASLSSFRPPRRENCKVVSLLGGIVAVHQTNPLDYTWRLASALGAECYM 180
Cdd:COG2390   80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGEDVEAQANEIARRLAEKLGGEYYL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 181 FLAPLLVDSVETKRALIEKCGLATLYDLAETLDLAIVSCGDIGPHSTSLSEGFISRETLRELIDAGCVCDTMFNFIDAEG 260
Cdd:COG2390  160 LPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDADG 239

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736475933 261 RSVDHPINQRAMAIDLDTLRKAKHIVLASGGAHRAIAIRATIKRIGCNTLITDEAAARALME 322
Cdd:COG2390  240 RIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 68-322 5.36e-56

Putative sugar-binding domain; This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.


Pssm-ID: 427778  Cd Length: 256  Bit Score: 182.43  E-value: 5.36e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933   68 IEDFVSLAGQLEAAYGLDEAVIIPSPDKASAEgTAKAVGLALGQFLSEAVPNGATIGVGWGRTMTASLSSFRPPRRENCK 147
Cdd:pfam04198   3 VEGCLDLEQRLKEKFGLKEAIVVPGDSDENDL-VLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPKSLRNLK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  148 VVSLLGGIVAVHQTNPLDYTWRLASALGAECYMFLAPLLVDSVETKRALIEKCGLATLYDLAETLDLAIVSCGDIGPHST 227
Cdd:pfam04198  82 FVPLIGGLGRDGSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSASEMAP 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  228 SLSEGFISRETLRELIDAGCVCDTMFNFIDAEGRSVDHPINQRAMAIDLDTLRKAKHIVLASGGAHRAIAIRATIKRIGC 307
Cdd:pfam04198 162 LFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALRGGYI 241

                         250
                  ....*....|....*
gi 736475933  308 NTLITDEAAARALME 322
Cdd:pfam04198 242 NVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 21-324 7.23e-25

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 102.11  E-value: 7.23e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  21 RAAWLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKRSEVQIWINEGIEDFVSLAGQLEAAYGLDEAVIIPSPDKASAEG 100
Cdd:PRK15418  20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPALADADIGG 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 101 TakaVGLALGQFLSEAVPNGATIGVGWGRTMTASL---SSFrpPRRENCKVVSLLGGiVAVHQTNpldytwrlASALGAE 177
Cdd:PRK15418 100 R---LGIGAAHMLMSLLQPQQLLAVGFGEATMNTLqhlSGF--ISSQQIRLVTLSGG-VGPYMTG--------IGQLDAA 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 178 C--YMFLAPLLVDSVETKRALIEKCGLATLYDLAETLDLAIVSCGDIGP--HSTSLSEGFISRETLRELIDAGCVCDTMF 253
Cdd:PRK15418 166 CsvSIIPAPLRASSAEIARTLRNENSVRDVMLAAQAADVAIVGIGAVNQkdDATILRSGYISQGEQLMIGRKGAVGDILG 245

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736475933 254 NFIDAEGRSV-DHPINQRAMAIDLDTLRKAKHIVLASGGAHRAIAIRATIKRIGCNTLITDEAAARALMELV 324
Cdd:PRK15418 246 YFFDADGELVpDIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAILALL 317
transpos_IS630 NF033545
IS630 family transposase;
19-70 2.20e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 42.24  E-value: 2.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 736475933  19 RLRAAWLYYNQGMTQKDVAEKLGISRSTVIRLLdeamKRsevqiWINEGIED 70
Cdd:NF033545   1 RRARILLLAAEGLSITEIAERLGVSRSTVYRWL----KR-----FNEGGLEG 43
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 24-57 4.90e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 40.02  E-value: 4.90e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 736475933   24 WLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:TIGR02937 120 VLRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 19-50 7.19e-04

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 37.15  E-value: 7.19e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 736475933  19 RLRAAWLyyNQGMTQKDVAEKLGISRSTVIRL 50
Cdd:cd00093    3 RLKELRK--EKGLTQEELAEKLGVSRSTISRI 32
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
29-50 1.02e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.73  E-value: 1.02e-03
                           10        20
                   ....*....|....*....|..
gi 736475933    29 QGMTQKDVAEKLGISRSTVIRL 50
Cdd:smart00530   9 KGLTQEELAEKLGVSRSTLSRI 30
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
21-322 2.71e-114

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 332.48  E-value: 2.71e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  21 RAAWLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKRSEVQIWINEGIEDFVSLAGQLEAAYGLDEAVIIPSPDkASAEG 100
Cdd:COG2390    1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDS-DDDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 101 TAKAVGLALGQFLSEAVPNGATIGVGWGRTMTASLSSFRPPRRENCKVVSLLGGIVAVHQTNPLDYTWRLASALGAECYM 180
Cdd:COG2390   80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGEDVEAQANEIARRLAEKLGGEYYL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 181 FLAPLLVDSVETKRALIEKCGLATLYDLAETLDLAIVSCGDIGPHSTSLSEGFISRETLRELIDAGCVCDTMFNFIDAEG 260
Cdd:COG2390  160 LPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDADG 239

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736475933 261 RSVDHPINQRAMAIDLDTLRKAKHIVLASGGAHRAIAIRATIKRIGCNTLITDEAAARALME 322
Cdd:COG2390  240 RIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 68-322 5.36e-56

Putative sugar-binding domain; This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.


Pssm-ID: 427778  Cd Length: 256  Bit Score: 182.43  E-value: 5.36e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933   68 IEDFVSLAGQLEAAYGLDEAVIIPSPDKASAEgTAKAVGLALGQFLSEAVPNGATIGVGWGRTMTASLSSFRPPRRENCK 147
Cdd:pfam04198   3 VEGCLDLEQRLKEKFGLKEAIVVPGDSDENDL-VLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPKSLRNLK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  148 VVSLLGGIVAVHQTNPLDYTWRLASALGAECYMFLAPLLVDSVETKRALIEKCGLATLYDLAETLDLAIVSCGDIGPHST 227
Cdd:pfam04198  82 FVPLIGGLGRDGSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSASEMAP 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  228 SLSEGFISRETLRELIDAGCVCDTMFNFIDAEGRSVDHPINQRAMAIDLDTLRKAKHIVLASGGAHRAIAIRATIKRIGC 307
Cdd:pfam04198 162 LFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALRGGYI 241

                         250
                  ....*....|....*
gi 736475933  308 NTLITDEAAARALME 322
Cdd:pfam04198 242 NVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 21-324 7.23e-25

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 102.11  E-value: 7.23e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933  21 RAAWLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKRSEVQIWINEGIEDFVSLAGQLEAAYGLDEAVIIPSPDKASAEG 100
Cdd:PRK15418  20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPALADADIGG 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 101 TakaVGLALGQFLSEAVPNGATIGVGWGRTMTASL---SSFrpPRRENCKVVSLLGGiVAVHQTNpldytwrlASALGAE 177
Cdd:PRK15418 100 R---LGIGAAHMLMSLLQPQQLLAVGFGEATMNTLqhlSGF--ISSQQIRLVTLSGG-VGPYMTG--------IGQLDAA 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736475933 178 C--YMFLAPLLVDSVETKRALIEKCGLATLYDLAETLDLAIVSCGDIGP--HSTSLSEGFISRETLRELIDAGCVCDTMF 253
Cdd:PRK15418 166 CsvSIIPAPLRASSAEIARTLRNENSVRDVMLAAQAADVAIVGIGAVNQkdDATILRSGYISQGEQLMIGRKGAVGDILG 245

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736475933 254 NFIDAEGRSV-DHPINQRAMAIDLDTLRKAKHIVLASGGAHRAIAIRATIKRIGCNTLITDEAAARALMELV 324
Cdd:PRK15418 246 YFFDADGELVpDIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAILALL 317
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 25-57 3.97e-06

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 47.13  E-value: 3.97e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 736475933  25 LYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:COG1191  197 LYYFEELTLKEIAEVLGVSESRVSRLHKKALAR 229
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 2-51 4.64e-06

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 47.54  E-value: 4.64e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 736475933   2 AKLRRETHTAYSEAASLRLRAAWLYYnQGMTQKDVAEKLGISRSTVIRLL 51
Cdd:COG3415   11 RDLEKLLRKTKDAREARRLRAVLLLA-EGLSVREIAERLGVSRSTVYRWL 59
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 25-57 1.27e-05

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 42.03  E-value: 1.27e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 736475933   25 LYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:pfam04545  15 LRYGEGLTLEEIGERLGISRERVRQIEKRALRK 47
PRK04217 PRK04217
hypothetical protein; Provisional
 12-57 7.88e-05

hypothetical protein; Provisional


Pssm-ID: 235258  Cd Length: 110  Bit Score: 41.40  E-value: 7.88e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 736475933  12 YSEAASLRLraawLYYnQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:PRK04217  45 YEEFEALRL----VDY-EGLTQEEAGKRMGVSRGTVWRALTSARKK 85
HTH_23 pfam13384
Homeodomain-like domain;
19-70 1.02e-04

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 39.17  E-value: 1.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 736475933   19 RLRAAWLYYnQGMTQKDVAEKLGISRSTVIRLLDEamkrsevqiWINEGIED 70
Cdd:pfam13384   7 RARALLLLA-EGLSVKEIAELLGVSRRTVYRWLKR---------YNEEGLEG 48
transpos_IS630 NF033545
IS630 family transposase;
19-70 2.20e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 42.24  E-value: 2.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 736475933  19 RLRAAWLYYNQGMTQKDVAEKLGISRSTVIRLLdeamKRsevqiWINEGIED 70
Cdd:NF033545   1 RRARILLLAAEGLSITEIAERLGVSRSTVYRWL----KR-----FNEGGLEG 43
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
19-50 2.25e-04

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 39.06  E-value: 2.25e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 736475933  19 RLRAAwlyynQGMTQKDVAEKLGISRSTVIRL 50
Cdd:COG1476   11 ELRKE-----RGLTQEELAELLGVSRQTISAI 37
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 19-69 2.66e-04

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 38.34  E-value: 2.66e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 736475933   19 RLRAAwLYYNQGMTQKDVAEKLGISRSTVirlldeamkRSEVQIWINEGIE 69
Cdd:pfam13518   2 RLKIV-LLALEGESIKEAARLFGISRSTV---------YRWIRRYREGGLE 42
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 24-57 4.90e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 40.02  E-value: 4.90e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 736475933   24 WLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:TIGR02937 120 VLRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 19-50 7.19e-04

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 37.15  E-value: 7.19e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 736475933  19 RLRAAWLyyNQGMTQKDVAEKLGISRSTVIRL 50
Cdd:cd00093    3 RLKELRK--EKGLTQEELAEKLGVSRSTISRI 32
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-57 8.22e-04

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 39.59  E-value: 8.22e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 736475933   4 LRRETHTAYSEA-ASL--RLRAA-WLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:COG1595  113 EAEELLEALLAAlERLppRQREVlVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKK 170
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 25-57 8.28e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 37.08  E-value: 8.28e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 736475933  25 LYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:cd06171   21 LRFGEGLSYEEIAEILGISRSTVRQRLHRALKK 53
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
29-50 1.02e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.73  E-value: 1.02e-03
                           10        20
                   ....*....|....*....|..
gi 736475933    29 QGMTQKDVAEKLGISRSTVIRL 50
Cdd:smart00530   9 KGLTQEELAEKLGVSRSTLSRI 30
COG2512 COG2512
Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain ...
 31-81 1.38e-03

Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain [General function prediction only];


Pssm-ID: 442002 [Multi-domain]  Cd Length: 80  Bit Score: 36.82  E-value: 1.38e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 736475933  31 MTQKDVAEKLGISRSTVIRLLDEAMKRSEVQIwINEGIEDFVSLAGQLEAA 81
Cdd:COG2512   31 MTQSEIVKETGWSKSKVSRLLSRLEERGLIEK-ERVGRENVVELPEDEPEA 80
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 23-57 1.57e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 36.41  E-value: 1.57e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 736475933   23 AWLYYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:pfam12802  12 LALARNPGLTVAELARRLGISKQTVSRLVKRLEAK 46
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
19-50 1.58e-03

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.90  E-value: 1.58e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 736475933  19 RLRAAWLyyNQGMTQKDVAEKLGISRSTVIRL 50
Cdd:COG1396   11 RLRELRK--ARGLTQEELAERLGVSRSTISRI 40
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 4-69 1.58e-03

ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.


Pssm-ID: 272946 [Multi-domain]  Cd Length: 187  Bit Score: 38.90  E-value: 1.58e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 736475933    4 LRRETHTAYSEAAS-LRLRAawlyyNQGMTQKDVAEKLGISRSTVIRLLDEAMKRSEVQIWINEGIE 69
Cdd:TIGR00180  98 IQREDLSPIEEAQAyKRLLE-----KFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASG 159
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
31-69 1.69e-03

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 36.45  E-value: 1.69e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 736475933  31 MTQKDVAEKLGISRSTVIRLLDE--------------AMKRSEVQIWINEGIE 69
Cdd:COG3311    9 LRLKEVAELLGVSRSTIYRLIKKgefpkpvklggrsvRWRESEVEAWLAARIA 61
DUF134 pfam02001
Protein of unknown function DUF134; This family of archaeal proteins has no known function. A ...
 14-57 1.82e-03

Protein of unknown function DUF134; This family of archaeal proteins has no known function. A study suggests that some members may be G-quadruplex binding proteins.


Pssm-ID: 280223  Cd Length: 98  Bit Score: 37.21  E-value: 1.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 736475933   14 EAASLRLRAawlYYNqgMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:pfam02001  39 EAEAIRLVD---YED--MSQDDAAAKMGISKATLWRLLTAARKK 77
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 30-87 2.14e-03

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 36.71  E-value: 2.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 736475933  30 GMTQKDVAEKLGISRSTVIRLL--------DEAMKRSEV-----QIWINegiedfvslagqLEAAYGLDEA 87
Cdd:COG3093   22 GLSQTELAKALGVSRQRISEILngkraitaDTALRLARAfgtsaEFWLN------------LQAAYDLWLA 80
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 29-50 3.02e-03

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 35.21  E-value: 3.02e-03
                          10        20
                  ....*....|....*....|..
gi 736475933   29 QGMTQKDVAEKLGISRSTVIRL 50
Cdd:pfam01381   8 LGLSQEELAEKLGVSRSTISKI 29
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
1-58 3.19e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 36.44  E-value: 3.19e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 736475933   1 MAKLRREthtaYSEAasLRLRAAWLYYNQGMTQKDVAEKLGISRSTV---IRLLDEAMKRS 58
Cdd:COG2963    1 MSKKRRR----YSPE--FKAEAVRLVLEGGASVAEVARELGISPSTLyrwVRQYREGGLGG 55
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 27-51 4.02e-03

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 34.61  E-value: 4.02e-03
                         10        20
                 ....*....|....*....|....*
gi 736475933  27 YNQGMTQKDVAEKLGISRSTVIRLL 51
Cdd:cd00569   18 LAAGESVAEIARELGVSRSTLYRYL 42
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
25-56 4.27e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 34.72  E-value: 4.27e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 736475933   25 LYYNQGMTQKDVAEKLGISRSTVIRLLDEAMK 56
Cdd:pfam13412  10 LQENPRISQRELAERLGLSPSTVNRRLKRLEE 41
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
27-47 4.34e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 35.96  E-value: 4.34e-03
                         10        20
                 ....*....|....*....|.
gi 736475933  27 YNQGMTQKDVAEKLGISRSTV 47
Cdd:COG2522   25 VERGLSQSEIAKLLGITQAAV 45
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 23-53 5.00e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 426012 [Multi-domain]  Cd Length: 59  Bit Score: 34.83  E-value: 5.00e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 736475933   23 AWLYYNQGMTQKDVAEKLGISRSTVIRLLDE 53
Cdd:pfam01047  10 RILYEHGPLTVSELAEKLGVSKSTVTRVLDR 40
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
27-51 5.08e-03

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 34.25  E-value: 5.08e-03
                          10        20
                  ....*....|....*....|....*
gi 736475933   27 YNQGMTQKDVAEKLGISRSTVIRLL 51
Cdd:pfam02796  18 LEEGISIKQIAKIFGISRSTVYRYL 42
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 18-57 6.19e-03

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 37.59  E-value: 6.19e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 736475933   18 LRLRaawlyYNQGMTQKDVAEKLGISRSTVIRLLDEAMKR 57
Cdd:TIGR02980 187 LLLR-----FFEDKTQSEIAERLGISQMHVSRLLRRALKK 221
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 4-51 7.09e-03

Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441084 [Multi-domain]  Cd Length: 241  Bit Score: 37.27  E-value: 7.09e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 736475933   4 LRRETHTAYSEAASLRLRAAwlyyNQGMTQKDVAEKLGISRSTVIRLL 51
Cdd:COG1475   98 LQREDLNPLEEARAYQRLLE----EFGLTQEEIAERLGKSRSEVSNLL 141
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
31-51 8.99e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 33.95  E-value: 8.99e-03
                           10        20
                   ....*....|....*....|.
gi 736475933    31 MTQKDVAEKLGISRSTVIRLL 51
Cdd:smart00419   9 LTRQEIAELLGLTRETVSRTL 29
 
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