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Conserved domains on  [gi|640455949|ref|WP_024906692|]
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MULTISPECIES: RNA polymerase sigma factor RpoH [Enterobacter]

Protein Classification

RNA polymerase sigma factor RpoH( domain architecture ID 11482333)

RNA polymerase sigma factor RpoH is involved in regulating the expression of heat shock genes; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Gene Ontology:  GO:0016987|GO:0003677|GO:0006352
PubMed:  3315851|3052291

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 1-285 0e+00

RNA polymerase factor sigma-32; Reviewed


:

Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 514.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   1 MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQ 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 161 LGVTSKDVREMESRMAAQDMTFdmSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDI 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASL--DAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 640455949 241 IRARWLDeDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK06596 239 IEARWLD-DDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282
 
Name Accession Description Interval E-value
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 1-285 0e+00

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 514.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   1 MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQ 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 161 LGVTSKDVREMESRMAAQDMTFdmSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDI 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASL--DAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 640455949 241 IRARWLDeDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK06596 239 IEARWLD-DDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 14-285 1.83e-159

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 444.42  E-value: 1.83e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   14 GNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVTSKDVREME 172
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  173 SRMAAQDMTFDMSSDDDASDSQpmAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARWLDEDnKS 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG--APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KL 237

                         250       260       270
                  ....*....|....*....|....*....|...
gi 640455949  253 TLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:TIGR02392 238 TLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-285 3.26e-96

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: 283.87  E-value: 3.26e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  18 SYIRAANTWPMLTAEEEKELAEKLHyQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVTSKDVREMEs 173
Cdd:COG0568   80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 174 RMAAQDMTFDmssdddasdsqpmAPVlyLQDKTSNFADGIEEDNWEDQAA--------NKLTHAMEGLDERSQDIIRARW 245
Cdd:COG0568  155 RLAREPVSLD-------------APV--GDDEDSELGDLLEDEEAPSPEEaleeellrEELREALDTLTEREREILRLRF 219

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 640455949 246 -LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:COG0568  220 gLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRS 260
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 53-123 2.14e-17

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 74.55  E-value: 2.14e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 640455949   53 LILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 224-280 8.21e-10

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: 53.65  E-value: 8.21e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 640455949 224 NKLTHAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEG---LSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 1-285 0e+00

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 514.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   1 MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQ 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 161 LGVTSKDVREMESRMAAQDMTFdmSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDI 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASL--DAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 640455949 241 IRARWLDeDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK06596 239 IEARWLD-DDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 14-285 1.83e-159

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 444.42  E-value: 1.83e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   14 GNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVTSKDVREME 172
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  173 SRMAAQDMTFDMSSDDDASDSQpmAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARWLDEDnKS 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG--APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KL 237

                         250       260       270
                  ....*....|....*....|....*....|...
gi 640455949  253 TLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:TIGR02392 238 TLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-285 3.26e-96

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: 283.87  E-value: 3.26e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  18 SYIRAANTWPMLTAEEEKELAEKLHyQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVTSKDVREMEs 173
Cdd:COG0568   80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 174 RMAAQDMTFDmssdddasdsqpmAPVlyLQDKTSNFADGIEEDNWEDQAA--------NKLTHAMEGLDERSQDIIRARW 245
Cdd:COG0568  155 RLAREPVSLD-------------APV--GDDEDSELGDLLEDEEAPSPEEaleeellrEELREALDTLTEREREILRLRF 219

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 640455949 246 -LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:COG0568  220 gLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRS 260
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 46-285 2.73e-57

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 185.24  E-value: 2.73e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  46 DLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 125
Cdd:PRK07500  38 DEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVR 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 126 VATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRMAAQDMTFDMSSDDDASDsqPMAPVL 200
Cdd:PRK07500 118 GGTSSAQKALFFNLRRLRARLaqadeELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEG--RSERMD 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 201 YLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARWLDEDNKsTLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK07500 196 FLVDDSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGA-TLEALGEELGISKERVRQIEARALEKLR 274


                 ....*
gi 640455949 281 AAIEA 285
Cdd:PRK07500 275 RALLS 279
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 44-285 4.73e-31

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: 115.69  E-value: 4.73e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAG-YGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI------HEY 116
Cdd:COG1191   11 EGDEEAREELIEEYLPLVKKIASRLAGrLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAIldylrdEDW 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 117 VLRNWRIVKVATTKAQRKLFfnlrktkQRLGWFNQDEvEmVARELGVTSKDVREMESRMAAqdmtfdmssdddasdsqpm 196
Cdd:COG1191   91 VPRSVRELARKIEEAIEELE-------QELGREPTDE-E-IAEELGISLEEVQEALEAANA------------------- 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 197 APVLYLQDKTSN---FADGIEEDNWEDQAANK-----LTHAMEGLDERSQDIIRARWLDEDnksTLQELADRYGVSAERV 268
Cdd:COG1191  143 YQLLSLDEPLEDgddLLDLLESGDPEEELEHEelreaLAEAIEQLPERERLVLSLYYFEEL---TLKEIAEVLGVSESRV 219

                        250
                 ....*....|....*..
gi 640455949 269 RQLEKNAMKKLRAAIEA 285
Cdd:COG1191  220 SRLHKKALARLREYLKE 236
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 44-280 4.43e-24

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 99.26  E-value: 4.43e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:PRK05657  82 RGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 124 VKV---------ATTKAQRKLFFNLRKtkqrlgwfnQDEVEMVARELGVTSKDVREMES---RMAAQDMTFdmssdddas 191
Cdd:PRK05657 162 IRLpvhvvkelnVYLRAARELEHKLDH---------EPSAEEIAELLDKPVDDVSRMLAlneRITSLDTPL--------- 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 192 DSQPMAPVL-YLQDKTSNFADgieeDNWEDQAANKLTHA-MEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERV 268
Cdd:PRK05657 224 GGDPEKSLLdILADEQENGPE----DTTQDDDMKQSIVKwLFELNDKQREVLARRFgLLGYEAATLEDVAREIGLTRERV 299

                        250
                 ....*....|..
gi 640455949 269 RQLEKNAMKKLR 280
Cdd:PRK05657 300 RQIQVEALRRLR 311
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 44-280 2.80e-22

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 94.67  E-value: 2.80e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYV---LRN 120
Cdd:PRK09210 125 EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIadqART 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 121 WRI-VKVATT-----KAQRKLFfnlrktkQRLGwfNQDEVEMVARELGVTSKDVREMESrmAAQdmtfdmssdddasdsQ 194
Cdd:PRK09210 205 IRIpVHMVETinkliRVQRQLL-------QELG--REPTPEEIAEEMDMPPEKVREILK--IAQ---------------E 258

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 195 PMA---PVLYLQDktSNFADGIEED---NWEDQAA-----NKLTHAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYG 262
Cdd:PRK09210 259 PVSletPIGEEDD--SHLGDFIEDQdatSPADHAAyellkEQLEDVLDTLTDREENVLRLRFgLDDGRTRTLEEVGKVFG 336

                        250
                 ....*....|....*...
gi 640455949 263 VSAERVRQLEKNAMKKLR 280
Cdd:PRK09210 337 VTRERIRQIEAKALRKLR 354
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 47-280 2.37e-20

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 89.93  E-value: 2.37e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  47 LEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK- 125
Cdd:PRK07598 174 LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRl 253

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 126 -VATT-------KAQRKLFFNLRKTKQrlgwfnqdeVEMVARELGVTSKDVREMESRMaaqdmtfdmssdddasdsqPMA 197
Cdd:PRK07598 254 pVHITeklnkikKAQRKISQEKGRTPT---------IEDIAQELEMTPTQVREVLLRV-------------------PRS 305

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 198 PVLYL---QDKTSNFADGIEEDNW--EDQA-----ANKLTHAMEGLDERSQDIIRARWLDEDNKS-TLQELADRYGVSAE 266
Cdd:PRK07598 306 VSLETkvgKDKDTELGDLLETDDIspEEMLmreslQRDLQHLLADLTSRERDVIRMRFGLADGHTySLAEIGRALDLSRE 385

                        250
                 ....*....|....
gi 640455949 267 RVRQLEKNAMKKLR 280
Cdd:PRK07598 386 RVRQIESKALQKLR 399
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 28-281 1.72e-19

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 86.32  E-value: 1.72e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  28 MLTAEE------------------EKELAEKLHYQGDLE-------AAKT-LILSHLRFVVHVARNYAGYGLPQADLIQE 81
Cdd:PRK07921  40 LLTAADevelakrieaglyaehllETRKRLSEARKRDLAavvrdgeAARRhLLEANLRLVVSLAKRYTGRGMPLLDLIQE 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  82 GNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK--VATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVAR 159
Cdd:PRK07921 120 GNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRlpVHLVEQVNKLARIKRELHQQLG--REATDEELAE 197

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 160 ELGVTSKDVREM--ESR-MAAQDMtfdmssdddasdsqpmaPVlyLQDKTSNFADGIEEDN---WEDQAANKLTHA---- 229
Cdd:PRK07921 198 ESGIPEEKIADLleHSRdPVSLDM-----------------PV--GSDEEAPLGDFIEDSEatsAENAVIAGLLHTdirs 258

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 640455949 230 -MEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK07921 259 vLATLDEREQQVIRLRFgLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 48-280 4.68e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 86.59  E-value: 4.68e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  48 EAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK-- 125
Cdd:PRK05901 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRip 350

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 126 ---VAT----TKAQRKLFfnlrktkQRLGWFNQDEvEMvARELGVTSKDVREMesRMAAQDmtfdmssdddasdsqpmaP 198
Cdd:PRK05901 351 vhmVETinklGRIERELL-------QELGREPTPE-EL-AKEMGFTPEKVREI--QKYNRE------------------P 401

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 199 V-LylqDKT------SNFADGIEEDNWE--DQAAN------KLTHAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYG 262
Cdd:PRK05901 402 IsL---DKTigkegdSQFGDFIEDSEAVspVDAVSftllqdQLQEVLETLSEREAGVIRMRFgLTDGQPKTLDEIGQVYG 478

                        250
                 ....*....|....*...
gi 640455949 263 VSAERVRQLEKNAMKKLR 280
Cdd:PRK05901 479 VTRERIRQIESKTLRKLR 496
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
44-285 1.92e-18

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 82.33  E-value: 1.92e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNWRI 123
Cdd:PRK05572  28 DGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGT 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 124 VKVatTKAQRKLFFNLRKTKQRLG-WFNQD-EVEMVARELGVTSKDVremesrMAAQDMTFDMSSDDDASDSQPMAPVlY 201
Cdd:PRK05572 107 VKV--SRSLKETANKIRKDKDELSkELGREpTIEELAEYLGVTPEEV------VLAQEASRSPQSIHETVHENDGDPI-T 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 202 LQDKtsnFADGIEEDnWEDQAAnkLTHAMEGLDERSQDIIRARWLDEDNKStlqELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK05572 178 LLDQ---IADQSEED-WFDKIA--LKEAIRELDERERLIVYLRYFKDKTQS---EVAKRLGISQVQVSRLEKKILKQMKE 248


                 ....
gi 640455949 282 AIEA 285
Cdd:PRK05572 249 KLDE 252
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
44-284 8.33e-18

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 80.76  E-value: 8.33e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNWRI 123
Cdd:PRK08215  33 NGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNP 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 124 VKVatTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVreMESRMAAQDmtfdmssdddasdsqPMA---P 198
Cdd:PRK08215 112 IRV--SRSLRDIAYKALQVREKLINENSKEptVEEIAKELEVPREEV--VFALDAIQD---------------PVSlfeP 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 199 V-------LYLQDKTSNfaDGIEEDNWEDQAAnkLTHAMEGLDERSQDIIRARWLDednKSTLQELADRYGVSAERVRQL 271
Cdd:PRK08215 173 IyhdggdpIYVMDQISD--EKNKDENWLEEIA--LKEAMKKLNDREKLILNLRFFQ---GKTQMEVAEEIGISQAQVSRL 245

                        250
                 ....*....|...
gi 640455949 272 EKNAMKKLRAAIE 284
Cdd:PRK08215 246 EKAALKHMRKYIQ 258
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 53-123 2.14e-17

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 74.55  E-value: 2.14e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 640455949   53 LILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 49-280 6.72e-17

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 79.83  E-value: 6.72e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  49 AAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVkvat 128
Cdd:PRK07406 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTI---- 212

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 129 tkaqrKLFFNLRKTKQRLgwfnQDEVEMVARELGVTSKDvREMESRMaaqDMTFDMSSDDDASDSQPMA---PVLYLQDk 205
Cdd:PRK07406 213 -----RLPVHLYETISRI----KKTTKVLSQEFGRKPTE-EEIAESM---EMTIEKLRFIAKSAQLPISletPIGKEED- 278

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 206 tSNFADGIEED--NWEDQAA-NKLTHAMEG----LDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMK 277
Cdd:PRK07406 279 -SRLGDFIEADgeTPEDDVAkNLLREDLEGvlatLSPRERDVLRLRYgLDDGRMKTLEEIGQIFNVTRERIRQIEAKALR 357


                 ...
gi 640455949 278 KLR 280
Cdd:PRK07406 358 KLR 360
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 44-280 4.43e-14

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 71.03  E-value: 4.43e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDlEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:PRK05949  88 QGK-RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQART 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 124 VK--VATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVARELGVTSKDVREMESrMAAQDMTFdmssDDDASDSQPMAPVLY 201
Cdd:PRK05949 167 IRlpIHITEKLNKIKKTQRELSQKLG--RSATPAEIAKELELEPSQIREYLS-MARQPISL----DVRVGDNQDTELSEL 239

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 202 LQDktsnfaDGIEEDNWEDQAA--NKLTHAMEGLDERSQDIIRARWLDEDNKS-TLQELADRYGVSAERVRQLEKNAMKK 278
Cdd:PRK05949 240 LED------EGPSPDQYITQELlrQDLNNLLAELTPQQREVLTLRFGLEDGKElSLAKVGERLNLSRERVRQLEHQALAH 313


                 ..
gi 640455949 279 LR 280
Cdd:PRK05949 314 LR 315
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 48-283 1.11e-13

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: 67.37  E-value: 1.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949   48 EAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEvgVRLVSFAVHWIKAEIHEYvlrnwrivkva 127
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDY----------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  128 ttkaqrklffnLRKTKQRLGWFNQDEVEmvarelgvtskdvremesrmaaqdmtfdmssdddasdsqpmapvlylqdktS 207
Cdd:TIGR02937  68 -----------LRRKRRLRRELDLLEEL---------------------------------------------------L 85

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 640455949  208 NFADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLRAAI 283
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEG---LSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
44-279 3.47e-13

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 67.28  E-value: 3.47e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIheyvLRNWRi 123
Cdd:PRK05803  45 EGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEI----LMHLR- 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 124 vkvattkaqrklffNLRKTKQRLgwFNQDevemvarELGVtSKDVREMEsrmaaqdmtfdmssdddasdsqpmapvlyLQ 203
Cdd:PRK05803 120 --------------NLKKTKKEV--SLQD-------PIGV-DKEGNEIS-----------------------------LI 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 204 DKTSNfadgiEEDNWEDQAAN-----KLTHAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMK 277
Cdd:PRK05803 147 DILGS-----EEDDVIEQVELkmeveKLYKKIDILDEREKEVIEMRYgLGNGKEKTQREIAKALGISRSYVSRIEKRALK 221


                 ..
gi 640455949 278 KL 279
Cdd:PRK05803 222 KL 223
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 43-283 1.53e-12

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 65.87  E-value: 1.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  43 YQ--GDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRN 120
Cdd:PRK08583  22 YQenQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRY-LRD 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 121 --W-------------RIVKVA---TTKAQRklffnlrktkqrlgwfnQDEVEMVARELGVTSKDVRE-MESRMAAQdmt 181
Cdd:PRK08583 101 ktWsvhvprrikelgpKIKKAVdelTTELQR-----------------SPKISEIADRLGVSEEEVLEaMEMGKSYQ--- 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 182 fdmssdddasdsqpmapVLYLQDKTSNFADGI----------EEDNWEDqaANK---LTHAMEGLDERSQDIIRARWLde 248
Cdd:PRK08583 161 -----------------ALSVDHSIEADSDGStvtlldivgqQEDGYEL--TEQrmiLEKILPVLSDREKSIIQCTFI-- 219

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 640455949 249 DNKSTlQELADRYGVSAERVRQLEKNAMKKLRAAI 283
Cdd:PRK08583 220 ENLSQ-KETGERLGISQMHVSRLQRQAIKKLREAA 253
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 229-281 1.57e-12

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: 60.90  E-value: 1.57e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 640455949  229 AMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEG---LTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 18-280 1.45e-11

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 63.62  E-value: 1.45e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  18 SYIRAANTWPMLTAE--------------------------------------EEKELAEKLHYQGDLEAAK-TLILSHL 58
Cdd:PRK07405  12 TYLREIGRVPLLTHEeeilygkqvqrlvalqeireelaeelgreptdaewakaAKLSEEELRSAIAEGEAAKrKMVEANL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  59 RFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKV---------ATT 129
Cdd:PRK07405  92 RLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLpihiteklnKIK 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 130 KAQRKLffnlrktKQRLGwfNQDEVEMVARELGVTSKDVREMESRmaaqdmtfdmssdddasDSQPMAPVLYLQD-KTSN 208
Cdd:PRK07405 172 KAQRQL-------SQQLG--RAATIGELAEELELTPKQVREYLER-----------------ARQPLSLDLRVGDnQDTE 225

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 209 FADGIEEDNW--EDQAA-----NKLTHAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK07405 226 LGELLEDTGAspEDFATqsslqLDLERLMEDLTPQQKEVIALRFgLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 63-284 1.72e-11

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 62.87  E-value: 1.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  63 HVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVAttKAQRKLFFNLRKT 142
Cdd:PRK07122  55 HIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP--RRLKELHLRLGRA 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 143 ----KQRLGwfNQDEVEMVARELGVTSKDVRE-MESRMAAQDMTFDMSSDDDASDSQPMAPVLYLQDktsnfadgIEEDN 217
Cdd:PRK07122 133 taelSQRLG--RAPTASELAAELGMDREEVVEgLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVD--------AGLDQ 202

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 640455949 218 WEDQAAnkLTHAMEGLDERSQDIIRARWLDednKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 284
Cdd:PRK07122 203 IENREA--LRPLLAALPERERTVLVLRFFE---SMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
44-123 6.19e-11

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 61.02  E-value: 6.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:PRK08301  48 KGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKV 127
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 77-279 7.47e-11

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 61.09  E-value: 7.47e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  77 DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEY---------VLRNWRIVKVATTKAQRKLffnlrktKQRLG 147
Cdd:PRK07408  55 DLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYlrdksptvrIPRRWQELQRQAKKVRQEL-------RQELG 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 148 wfNQDEVEMVARELGVTSKDVREMesRMAAQDMTfdmssdddasdsqPM---APVLYLQDKTSNFADGIEEDNW------ 218
Cdd:PRK07408 128 --RQPTDQEIAQALDISLEEWQEI--KLALQNRT-------------PLsldAPVNQDEDGSTSLGDLLPDPRYrsfqla 190

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640455949 219 -EDQAanKLTHAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERV-RQLEK--NAMKKL 279
Cdd:PRK07408 191 qEDRI--RLQQALAQLEERTREVLEFVFLHD---LTQKEAAERLGISPVTVsRRVKKglDQLKKL 250
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 48-93 4.23e-10

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 60.19  E-value: 4.23e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 640455949  48 EAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:PRK05658 380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 425
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 46-285 7.17e-10

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 58.09  E-value: 7.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  46 DLEAAKTLILSHLRFVVHVARNYAGyGLPQ----ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNW 121
Cdd:PRK05911  21 EIEYRDVLIEFYLPLVKNVAHRLIS-GMPShvktEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDD-LRKQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 122 RIVKVATTKAQRKLFFNLRKTKQRLGwfnqdevemvaRElgVTSKDVREMeSRMAAQDMTfdmssdDDASDSQPmAPVLY 201
Cdd:PRK05911  99 DWVPRSVHQKANKLADAMDSLRQSLG-----------KE--PTDGELCEY-LNISQQELS------GWFSSARP-ALILS 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 202 LQDKTSNFADG-----IEEDNWEDQA------------ANKLTHAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVS 264
Cdd:PRK05911 158 LNEEFPCQSDDeaglaLEERIADERAetgydvvdkkefSSILAEAILALEEKERKVMALYYYEE---LVLKEIGKILGVS 234

                        250       260
                 ....*....|....*....|.
gi 640455949 265 AERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK05911 235 ESRVSQIHSKALLKLRATLSA 255
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 224-280 8.21e-10

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: 53.65  E-value: 8.21e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 640455949 224 NKLTHAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEG---LSYEEIAEILGISRSTVRQRLHRALKKLR 55
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 77-281 1.42e-08

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 54.08  E-value: 1.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  77 DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN-W--RIVKvattKAQRKLFFNLRKTKQRLGWfNQDE 153
Cdd:PRK06986  40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdWvpRSVR----RNAREVAQAIRQLEQELGR-EPTD 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 154 VEmVARELGVTSKDVREM-----ESRMAAQDmtfdmssddDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDqaanKLTH 228
Cdd:PRK06986 115 TE-VAEKLGLSLEEYREMlldtnISQLFSID---------ELRGEHGDSILVTEDHQDEDPLQQLEDEELRE----ALVE 180

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 640455949 229 AMEGLDERSQDIIRARWLDEDNkstLQELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK06986 181 AIESLPEREQLVLSLYYQEELN---LKEIGAVLGVSESRVSQIHSQAIKRLRA 230
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 45-281 2.11e-07

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 50.84  E-value: 2.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  45 GDLEAAKTLILSHLRFVVHVArNYAGYGLP----QADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLR- 119
Cdd:PRK06288  28 GDPKIREYLILKYSPLVKYVA-GRIAVGMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDE-LRs 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 120 -NW--RIVKVATTKAQRKLFFnlrkTKQRLGWfNQDEVEmVARELGVTSKDVREMESRMAAQDMTFDMSSDDDASDSQPM 196
Cdd:PRK06288 106 iDWipRSVRQKARQIERAIAM----LEARLGR-TPSDEE-IADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEV 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 197 APVLYLQDKTSNFADGIEEDnweDQAANKLTHAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAM 276
Cdd:PRK06288 180 SLMDTLESPAALNPDEIAER---EEIKRVIVEAIKTLPEREKKVLILYYYED---LTLKEIGKVLGVTESRISQLHTKAV 253


                 ....*
gi 640455949 277 KKLRA 281
Cdd:PRK06288 254 LQLRA 258
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
44-104 3.69e-06

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 46.83  E-value: 3.69e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 640455949  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEvgvRLVSF 104
Cdd:PRK08295  20 SGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKD---KLSSF 77
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
77-280 3.02e-04

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 41.39  E-value: 3.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949  77 DLIQEGNIGLMKAVRRFN-PEVGvrLVSFAVHWIKAEI-HEYVLRNWRIVKVATTKAQRKLFfnLRKTKQRLGwfNQDEV 154
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGhPDEQ--FAAYAVHRIRGAIlDELRELDWRPRRLRQKTHKTNDA--IREIAKRLG--HEPNF 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640455949 155 EMVARELGVTSKDVREMESRMAAQDMTfdmssdddasdsqpmapvlYLQDKTSNFADGI--EEDNWEDQAANK--LTHAM 230
Cdd:PRK12427 121 EEISAELNLTAEEYQEYLLLENAGTLE-------------------SLDELLALEAHNDilQSRDLEENIIIEdnLKQAL 181

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 640455949 231 EGLDERSQDIIRARWLDEDNkstLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK12427 182 SQLDEREQLILHLYYQHEMS---LKEIALVLDLTEARICQLNKKIAQKIK 228
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 210-285 1.94e-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: 38.44  E-value: 1.94e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 640455949 210 ADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARWLDEDnksTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:COG1595  105 AADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGL---SYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
 
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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