NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1867924372|ref|WP_178992641|]
View 

sugar-binding transcriptional regulator [Paenarthrobacter nitroguajacolicus]

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];
11-315 9.88e-112

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


:

Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 325.93  E-value: 9.88e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  11 RAAQMYYLQDLTMDAIARELRTSRSTVSRLLSSARETGLVQVQIRSPFDTGPELESQIRNQYGV-DVHVVPVlDTLNEAE 89
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLkEVIVVPG-DSDDDEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  90 TLDRVAMQAARTIGPLVDSNAIIGVAWGATLSAVSRHLTRKVTHDSIVVQLNGAgnMQTTGITYASDIMRRFGSAYGARV 169
Cdd:COG2390    80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGG--LGEDVEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 170 EQFPVPAFFDHASTKTAMWNERSVQRILDLQARMSIAIFGVGSVDSDypSHVYAGGYLDEHDLTMLAADDVVGDVATVFF 249
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPD--STLARRGYLSEEELAELRAAGAVGDICGRFF 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1867924372 250 RSDGSSDGITLNERSTGPSHEQLRQVRRRICVVSGASKINGLQGALAAGLATDLILDEASARRLVS 315
Cdd:COG2390   236 DADGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
11-315 9.88e-112

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 325.93  E-value: 9.88e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  11 RAAQMYYLQDLTMDAIARELRTSRSTVSRLLSSARETGLVQVQIRSPFDTGPELESQIRNQYGV-DVHVVPVlDTLNEAE 89
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLkEVIVVPG-DSDDDEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  90 TLDRVAMQAARTIGPLVDSNAIIGVAWGATLSAVSRHLTRKVTHDSIVVQLNGAgnMQTTGITYASDIMRRFGSAYGARV 169
Cdd:COG2390    80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGG--LGEDVEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 170 EQFPVPAFFDHASTKTAMWNERSVQRILDLQARMSIAIFGVGSVDSDypSHVYAGGYLDEHDLTMLAADDVVGDVATVFF 249
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPD--STLARRGYLSEEELAELRAAGAVGDICGRFF 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1867924372 250 RSDGSSDGITLNERSTGPSHEQLRQVRRRICVVSGASKINGLQGALAAGLATDLILDEASARRLVS 315
Cdd:COG2390   236 DADGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 56-315 1.28e-60

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: 193.99  E-value: 1.28e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  56 SPFDTGPELESQIRNQYGVD-VHVVPVLDTLNEaETLDRVAMQAARTIGPLVDSNAIIGVAWGATLSAVSRHLTRKVTHD 134
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKeAIVVPGDSDEND-LVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPKSLRN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 135 SIVVQLNGagNMQTTGITYASDIMRRFGSAYGARVEQFPVPAFFDHASTKTAMWNERSVQRILDLQARMSIAIFGVGSVD 214
Cdd:pfam04198  80 LKFVPLIG--GLGRDGSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 215 SDypSHVYAGGYLDEHDLTMLAADDVVGDVATVFFRSDGSSDGITLNERSTGPSHEQLRQVRRRICVVSGASKINGLQGA 294
Cdd:pfam04198 158 EM--APLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAA 235

                         250       260
                  ....*....|....*....|.
gi 1867924372 295 LAAGLATDLILDEASARRLVS 315
Cdd:pfam04198 236 LRGGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 11-311 2.58e-26

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 105.96  E-value: 2.58e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  11 RAAQMYYLQDLTMDAIARELRTSRSTVSRLLSSARETGLVQVQIRSPFDTGPELESQIRNQYGvdVHVVPVLDTLNEAET 90
Cdd:PRK15418   20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFS--LQHIRVLPALADADI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  91 LDRVAMQAARTIGPLVDSNAIIGVAWGATLSAVSRHLTRKVTHDSI-VVQLNGAGNMQTTGItyasdimrrfGSAYGA-R 168
Cdd:PRK15418   98 GGRLGIGAAHMLMSLLQPQQLLAVGFGEATMNTLQHLSGFISSQQIrLVTLSGGVGPYMTGI----------GQLDAAcS 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 169 VEQFPVPAFFDHASTKTAMWNERSVQRILDLQARMSIAIFGVGSVDSDYPSHVYAGGYLDEHDLTMLAADDVVGDVATVF 248
Cdd:PRK15418  168 VSIIPAPLRASSAEIARTLRNENSVRDVMLAAQAADVAIVGIGAVNQKDDATILRSGYISQGEQLMIGRKGAVGDILGYF 247

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1867924372 249 FRSDGS-SDGITLNERSTGPSHEQLRQVRRRICVVSGASKINGLQGALAAGLATDLILDEASAR 311
Cdd:PRK15418  248 FDADGElVPDIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTAR 311
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 15-46 7.41e-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: 7.41e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1867924372  15 MYYLQDLTMDAIARELRTSRSTVSRLLSSARE 46
Cdd:cd06171    21 LRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-46 1.29e-03

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: 38.87  E-value: 1.29e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1867924372  11 RAAQMYYLQDLTMDAIARELRTSRSTVSRLLSSARE 46
Cdd:TIGR02937 117 EVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
11-315 9.88e-112

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 325.93  E-value: 9.88e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  11 RAAQMYYLQDLTMDAIARELRTSRSTVSRLLSSARETGLVQVQIRSPFDTGPELESQIRNQYGV-DVHVVPVlDTLNEAE 89
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLkEVIVVPG-DSDDDEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  90 TLDRVAMQAARTIGPLVDSNAIIGVAWGATLSAVSRHLTRKVTHDSIVVQLNGAgnMQTTGITYASDIMRRFGSAYGARV 169
Cdd:COG2390    80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGG--LGEDVEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 170 EQFPVPAFFDHASTKTAMWNERSVQRILDLQARMSIAIFGVGSVDSDypSHVYAGGYLDEHDLTMLAADDVVGDVATVFF 249
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPD--STLARRGYLSEEELAELRAAGAVGDICGRFF 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1867924372 250 RSDGSSDGITLNERSTGPSHEQLRQVRRRICVVSGASKINGLQGALAAGLATDLILDEASARRLVS 315
Cdd:COG2390   236 DADGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 56-315 1.28e-60

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: 193.99  E-value: 1.28e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  56 SPFDTGPELESQIRNQYGVD-VHVVPVLDTLNEaETLDRVAMQAARTIGPLVDSNAIIGVAWGATLSAVSRHLTRKVTHD 134
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKeAIVVPGDSDEND-LVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPKSLRN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 135 SIVVQLNGagNMQTTGITYASDIMRRFGSAYGARVEQFPVPAFFDHASTKTAMWNERSVQRILDLQARMSIAIFGVGSVD 214
Cdd:pfam04198  80 LKFVPLIG--GLGRDGSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 215 SDypSHVYAGGYLDEHDLTMLAADDVVGDVATVFFRSDGSSDGITLNERSTGPSHEQLRQVRRRICVVSGASKINGLQGA 294
Cdd:pfam04198 158 EM--APLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAA 235

                         250       260
                  ....*....|....*....|.
gi 1867924372 295 LAAGLATDLILDEASARRLVS 315
Cdd:pfam04198 236 LRGGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 11-311 2.58e-26

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 105.96  E-value: 2.58e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  11 RAAQMYYLQDLTMDAIARELRTSRSTVSRLLSSARETGLVQVQIRSPFDTGPELESQIRNQYGvdVHVVPVLDTLNEAET 90
Cdd:PRK15418   20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFS--LQHIRVLPALADADI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372  91 LDRVAMQAARTIGPLVDSNAIIGVAWGATLSAVSRHLTRKVTHDSI-VVQLNGAGNMQTTGItyasdimrrfGSAYGA-R 168
Cdd:PRK15418   98 GGRLGIGAAHMLMSLLQPQQLLAVGFGEATMNTLQHLSGFISSQQIrLVTLSGGVGPYMTGI----------GQLDAAcS 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372 169 VEQFPVPAFFDHASTKTAMWNERSVQRILDLQARMSIAIFGVGSVDSDYPSHVYAGGYLDEHDLTMLAADDVVGDVATVF 248
Cdd:PRK15418  168 VSIIPAPLRASSAEIARTLRNENSVRDVMLAAQAADVAIVGIGAVNQKDDATILRSGYISQGEQLMIGRKGAVGDILGYF 247

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1867924372 249 FRSDGS-SDGITLNERSTGPSHEQLRQVRRRICVVSGASKINGLQGALAAGLATDLILDEASAR 311
Cdd:PRK15418  248 FDADGElVPDIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTAR 311
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 14-44 1.26e-04

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: 42.50  E-value: 1.26e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1867924372  14 QMYYLQDLTMDAIARELRTSRSTVSRLLSSA 44
Cdd:COG1191   196 SLYYFEELTLKEIAEVLGVSESRVSRLHKKA 226
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 15-46 7.41e-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: 7.41e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1867924372  15 MYYLQDLTMDAIARELRTSRSTVSRLLSSARE 46
Cdd:cd06171    21 LRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-46 1.29e-03

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: 38.87  E-value: 1.29e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1867924372  11 RAAQMYYLQDLTMDAIARELRTSRSTVSRLLSSARE 46
Cdd:TIGR02937 117 EVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152
Sig-70_gmx1 TIGR03001
RNA polymerase sigma-70 factor, Myxococcales family 1; This group of sigma factors are members ...
 3-77 2.41e-03

RNA polymerase sigma-70 factor, Myxococcales family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.


Pssm-ID: 188267 [Multi-domain]  Cd Length: 244  Bit Score: 38.90  E-value: 2.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867924372   3 RSRHSDALRAA----------------QMYYLQDLTMDAIARELRTSRSTVSRLLSSARETGL----VQVQIRSPFDtGP 62
Cdd:TIGR03001 144 RERYRQDFRQAlrealaalsererhllRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARERLLertrRRLAERLKLS-SP 222

                          90
                  ....*....|....*...
gi 1867924372  63 ELES---QIRNQYGVDVH 77
Cdd:TIGR03001 223 ELESllgLVRSRLDVSLS 240
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 6-59 3.48e-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: 35.26  E-value: 3.48e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1867924372   6 HSDALRAaqMYYLQDLTMDAIARELRTSRSTVSRLLSSARETGLVQVQiRSPFD 59
Cdd:pfam12802   7 QFRVLLA--LARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVERE-PSPAD 57
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 7-46 6.00e-03

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: 37.28  E-value: 6.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1867924372   7 SDALRAA-QMYYLQDLTMDAIARELRTSRSTVSRLLSSARE 46
Cdd:COG1595   129 PPRQREVlVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 14-46 9.01e-03

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: 33.94  E-value: 9.01e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1867924372  14 QMYYLQDLTMDAIARELRTSRSTVSRLLSSARE 46
Cdd:pfam04545  14 VLRYGEGLTLEEIGERLGISRERVRQIEKRALR 46
 
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