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Conserved domains on  [gi|1709950839|ref|WP_143301623|]
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sigma-70 family RNA polymerase sigma factor, partial [Candidatus Entotheonella palauensis]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 1000435)

sigma-70 family RNA polymerase sigma factor similar to RNA polymerase sigma factor RpoD/SigA, which is the primary sigma factor during exponential growth; preferentially transcribes genes associated with fast growth, such as ribosomal operons, other protein-synthesis related genes, rRNA- and tRNA-encoding genes and prfB

CATH:  1.10.601.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003700|GO:0003677|GO:0006355
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK05658 super family cl35358
RNA polymerase sigma factor RpoD; Validated
 1-163 2.62e-74

RNA polymerase sigma factor RpoD; Validated


The actual alignment was detected with superfamily member PRK05658:

Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 233.53  E-value: 2.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKS 79
Cdd:PRK05658  455 TIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGdDEDSHLGDFIEDKNA 534

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK05658  535 ELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLR 614


                  ....
gi 1709950839 160 SFVD 163
Cdd:PRK05658  615 SFLD 618
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-163 2.62e-74

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 233.53  E-value: 2.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKS 79
Cdd:PRK05658  455 TIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGdDEDSHLGDFIEDKNA 534

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK05658  535 ELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLR 614


                  ....
gi 1709950839 160 SFVD 163
Cdd:PRK05658  615 SFLD 618
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-163 8.41e-74

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 221.85  E-value: 8.41e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIGE-GDTELGALIEDKKS 79
Cdd:COG0568   105 TIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDdEDSELGDLLEDEEA 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:COG0568   185 PSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLR 264


                  ....
gi 1709950839 160 SFVD 163
Cdd:COG0568   265 DYLD 268
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 10-86 3.68e-16

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 68.79  E-value: 3.68e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1709950839  10 EILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKSTSPLEAV 86
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGeEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 92-150 4.23e-13

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: 60.20  E-value: 4.23e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1709950839  92 RDKIHKMLNTLSPKEERILRMRFGLGdetpHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 81-150 7.04e-10

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: 54.66  E-value: 7.04e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  81 SPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGdetpHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:TIGR02937  90 SPEEELEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLR 155
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-163 2.62e-74

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 233.53  E-value: 2.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKS 79
Cdd:PRK05658  455 TIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGdDEDSHLGDFIEDKNA 534

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK05658  535 ELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLR 614


                  ....
gi 1709950839 160 SFVD 163
Cdd:PRK05658  615 SFLD 618
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-163 8.41e-74

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 221.85  E-value: 8.41e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIGE-GDTELGALIEDKKS 79
Cdd:COG0568   105 TIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDdEDSELGDLLEDEEA 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:COG0568   185 PSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLR 264


                  ....
gi 1709950839 160 SFVD 163
Cdd:COG0568   265 DYLD 268
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 1-163 2.06e-67

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 209.07  E-value: 2.06e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIGE-GDTELGALIEDKKS 79
Cdd:PRK09210  204 TIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEeDDSHLGDFIEDQDA 283

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK09210  284 TSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLK 363


                  ....
gi 1709950839 160 SFVD 163
Cdd:PRK09210  364 DFLE 367
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 1-163 4.91e-64

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 204.07  E-value: 4.91e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKS 79
Cdd:PRK05901  346 TIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGkEGDSQFGDFIEDSEA 425

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK05901  426 VSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLR 505


                  ....
gi 1709950839 160 SFVD 163
Cdd:PRK05901  506 DFLD 509
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 1-161 5.90e-48

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 157.97  E-value: 5.90e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKS 79
Cdd:PRK07921  161 TIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGsDEEAPLGDFIEDSEA 240

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK07921  241 TSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLR 320


                  ..
gi 1709950839 160 SF 161
Cdd:PRK07921  321 SY 322
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 1-162 2.93e-45

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 152.24  E-value: 2.93e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKS 79
Cdd:PRK07406  211 TIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGkEEDSRLGDFIEADGE 290

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TsPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK07406  291 T-PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLK 369


                  ...
gi 1709950839 160 SFV 162
Cdd:PRK07406  370 EYI 372
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 1-163 6.23e-40

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 139.23  E-value: 6.23e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEdKKS 79
Cdd:PRK07598  250 TIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGkDKDTELGDLLE-TDD 328

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK07598  329 ISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIR 408


                  ....
gi 1709950839 160 SFVD 163
Cdd:PRK07598  409 DYLE 412
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 1-162 1.16e-32

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 118.02  E-value: 1.16e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIGEG-DTELGALIEDKkS 79
Cdd:PRK05949  166 TIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNqDTELSELLEDE-G 244

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHpsRSNNLR 159
Cdd:PRK05949  245 PSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVK 322


                  ...
gi 1709950839 160 SFV 162
Cdd:PRK05949  323 EYL 325
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 1-160 3.87e-31

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 113.90  E-value: 3.87e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKS 79
Cdd:PRK05657  161 TIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGgDPEKSLLDILADEQE 240

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLKHPSRSNNLR 159
Cdd:PRK05657  241 NGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320


                  .
gi 1709950839 160 S 160
Cdd:PRK05657  321 I 321
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 1-150 2.43e-28

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 106.77  E-value: 2.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIGEG-DTELGALIEDKkS 79
Cdd:PRK07405  156 TIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNqDTELGELLEDT-G 234

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1709950839  80 TSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK07405  235 ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 3-150 1.20e-21

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: 87.19  E-value: 1.20e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   3 RIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAK--RTVSLENHIGEGDTelgaLIEDKKST 80
Cdd:COG1191    90 WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD----LLDLLESG 165

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709950839  81 SPLEAVINRDLRDKIHKMLNTLSPKEERILRMRF--GLgdetphTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:COG1191   166 DPEEELEHEELREALAEAIEQLPERERLVLSLYYfeEL------TLKEIAEVLGVSESRVSRLHKKALARLR 231
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 42-150 1.33e-17

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 77.14  E-value: 1.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  42 HVEKVKNTLNVAKRTV------------SLENHIGEGDTELGALI---EDKKStSPLEAVINRDL----RDKIHKMLNTL 102
Cdd:PRK06596  153 EVEMVAEELGVSEEEVremesrlsgqdaSLDAPIDDDDEESGAPQdylEDKSS-DPADVLEEDNWedqrRALLADALEGL 231

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1709950839 103 SPKEERILRMRFgLgDETPHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK06596  232 DERSRDIIEARW-L-DDDKSTLQELAAEYGVSAERVRQIEKNAMKKLK 277
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
3-151 2.10e-17

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 76.24  E-value: 2.10e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   3 RIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLN--VAKRTVSLENHIGEGDTELG--ALIEDKK 78
Cdd:PRK07670   99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNegFFANLLSIDEKTHDQDDGENvsVTIRDDK 178

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1709950839  79 STSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGlgDETphTLEEVGQIFGVSRERIRQIEAQALRKLKH 151
Cdd:PRK07670  179 TPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK--EEL--TLTEIGQVLNLSTSRISQIHSKALFKLKK 247
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 10-86 3.68e-16

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 68.79  E-value: 3.68e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1709950839  10 EILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIG-EGDTELGALIEDKKSTSPLEAV 86
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGeEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 99-151 4.03e-14

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: 62.83  E-value: 4.03e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1709950839  99 LNTLSPKEERILRMRFGlgdeTPHTLEEVGQIFGVSRERIRQIEAQALRKLKH 151
Cdd:pfam04545   2 LASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 92-150 4.23e-13

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: 60.20  E-value: 4.23e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1709950839  92 RDKIHKMLNTLSPKEERILRMRFGLGdetpHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 17-150 6.31e-13

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 64.32  E-value: 6.31e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  17 RSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLN--VAKRTVSLEN--HIGEGDTE--LGALIEDKKSTSPLEAVINRD 90
Cdd:PRK06288  122 RAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDlwFGGDEGDEvsLMDTLESPAALNPDEIAEREE 201

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709950839  91 LRDKIHKMLNTLSPKEERILRMRF--GLgdetphTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK06288  202 IKRVIVEAIKTLPEREKKVLILYYyeDL------TLKEIGKVLGVTESRISQLHTKAVLQLR 257
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 23-150 2.59e-12

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 62.75  E-value: 2.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  23 MVELGRKPLPEEIAKDTGL---HVEKVKNTLNVAKrtVSLENHIGEGDTELGALIEDKKSTSPLEAVINRD------LRD 93
Cdd:PRK07500  142 DEELTKQEIHREIATALGVslsDVEMMDARLSGPD--ASLNAPQSEEDEGRSERMDFLVDDSPLPDEQVESsidgerRRR 219

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1709950839  94 KIHKMLNTLSPKEERILRMRfGLGDEtPHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK07500  220 WLTQALQTLNERELRIIRER-RLRED-GATLEALGEELGISKERVRQIEARALEKLR 274
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 81-150 7.04e-10

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: 54.66  E-value: 7.04e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  81 SPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGdetpHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:TIGR02937  90 SPEEELEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLR 155
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 25-150 3.05e-09

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 53.70  E-value: 3.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  25 ELGRKPLPEEIAKDTGLHVEKVKNTLNV--AKRTVSLENHIGEGDTELGaLIEDKKSTSPLEAVINRDLRDKIHKMLNTL 102
Cdd:PRK06986  107 ELGREPTDTEVAEKLGLSLEEYREMLLDtnISQLFSIDELRGEHGDSIL-VTEDHQDEDPLQQLEDEELREALVEAIESL 185

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1709950839 103 SPKEERILRMRFglgdETPHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK06986  186 PEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 79-150 4.09e-06

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: 44.60  E-value: 4.09e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709950839  79 STSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGLGdetpHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:COG1595   105 AADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEG----LSYAEIAEILGISEGTVKSRLSRARKKLR 172
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
86-150 8.56e-06

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 44.08  E-value: 8.56e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  86 VINRDLRDKIHKML-----NTLSPKEERILRMRFGLGDETPHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK08301  158 IIYKDIEDEVDRKLlkkalKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 2-150 9.23e-06

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 44.00  E-value: 9.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   2 IRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTL--NVAKRTVSLENHIGEGDTELGALIEDKKS 79
Cdd:PRK07122  116 VKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLvaGSAYNTLSIDSGGGSGDDDARAIADTLGD 195

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709950839  80 TSP-LEAVINrdlRDKIHKMLNTLSPKEERILRMRFGLGdetpHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK07122  196 VDAgLDQIEN---REALRPLLAALPERERTVLVLRFFES----MTQTQIAERVGISQMHVSRLLAKTLARLR 260
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 4-150 8.56e-05

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 41.53  E-value: 8.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   4 IPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRT--VSL-ENHIGEGDTELGALIE----D 76
Cdd:PRK05911  101 VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPAliLSLnEEFPCQSDDEAGLALEeriaD 180

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1709950839  77 KKSTSPLEAVINRDLRDKIHKMLNTLSPKEERILRMRFGlgDETphTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK05911  181 ERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY--EEL--VLKEIGKILGVSESRVSQIHSKALLKLR 250
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
2-150 1.87e-04

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 40.32  E-value: 1.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   2 IRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHI--GEGDT-ELGALIEDKK 78
Cdd:PRK08215  112 IRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIyhDGGDPiYVMDQISDEK 191

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1709950839  79 ST--SPLEaviNRDLRDKIHKmlntLSPKEERILRMRFGLGdetpHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK08215  192 NKdeNWLE---EIALKEAMKK----LNDREKLILNLRFFQG----KTQMEVAEEIGISQAQVSRLEKAALKHMR 254
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
1-150 2.76e-04

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 39.95  E-value: 2.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAKRTVSLENHIGEGDTELGALIeDKKST 80
Cdd:PRK05572  106 TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLL-DQIAD 184

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709950839  81 SPLEAVInrdlrDKI--HKMLNTLSPKEERILRMRFgLGDETPhtlEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK05572  185 QSEEDWF-----DKIalKEAIRELDERERLIVYLRY-FKDKTQ---SEVAKRLGISQVQVSRLEKKILKQMK 247
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 1-150 2.83e-03

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 36.98  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVEKVKNTLNVAK--RTVSLENHIgEGDtelgaliEDKK 78
Cdd:PRK08583  104 SVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSI-EAD-------SDGS 175

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1709950839  79 STSPLEAVINR----DLRDK---IHKMLNTLSPKEERILRMRFglgdETPHTLEEVGQIFGVSRERIRQIEAQALRKLK 150
Cdd:PRK08583  176 TVTLLDIVGQQedgyELTEQrmiLEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLR 250
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 68-148 3.02e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 36.37  E-value: 3.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839  68 TELgALIEDKKSTSPLE-AVINRDLRdKIHKMLNTLSPKEerilRMRFGLG--DETPHTleEVGQIFGVSRERIRQIEAQ 144
Cdd:PRK12523   87 AEL-ALVPEAEQPSPEEqHLILEDLK-AIDRLLGKLSSKA----RAAFLYNrlDGMGHA--EIAERLGVSVSRVRQYLAQ 158


                  ....
gi 1709950839 145 ALRK 148
Cdd:PRK12523  159 GLRQ 162
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 1-81 5.51e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 36.05  E-value: 5.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709950839   1 TIRIPVHMIEILNKVVRSSQTLMVELGRKPLPEEIAKDTGLHVE---KVKntLNVAKRT-VSLE---NHIGEGDTELGAL 73
Cdd:PRK07408  101 TVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEewqEIK--LALQNRTpLSLDapvNQDEDGSTSLGDL 178


                  ....*...
gi 1709950839  74 IEDKKSTS 81
Cdd:PRK07408  179 LPDPRYRS 186
 
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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