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Conserved domains on  [gi|2087637625|dbj|GJG71444|]
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RNA polymerase sigma factor RpoH [Enterobacter hormaechei]

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: 513.57  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625   1 MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQ 80
Cdd:PRK06596    1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596   81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 161 LGVSSKDVREMESRMAAQDMTFdmSADDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDERSQDI 240
Cdd:PRK06596  161 LGVSEEEVREMESRLSGQDASL--DAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2087637625 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: 513.57  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625   1 MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQ 80
Cdd:PRK06596    1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596   81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 161 LGVSSKDVREMESRMAAQDMTFdmSADDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDERSQDI 240
Cdd:PRK06596  161 LGVSEEEVREMESRLSGQDASL--DAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2087637625 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 2.46e-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: 444.03  E-value: 2.46e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  14 GNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVSSKDVREME 172
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 173 SRMAAQDMTFDMSADDDASDSQpmAPVLYLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDERSQDIIRARWLDEDnKS 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG--APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KL 237

                         250       260       270
                  ....*....|....*....|....*....|...
gi 2087637625 253 TLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:TIGR02392 238 TLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-285 7.99e-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: 283.10  E-value: 7.99e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  18 SYIRAANTWPMLTAEEEKELAEKLHyQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVSSKDVREMEs 173
Cdd:COG0568    80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 174 RMAAQDMTFDmsadddasdsqpmAPVlyLQDKTSNFADGIEEDNWEDQAA--------NKLTFAMEGLDERSQDIIRARW 245
Cdd:COG0568   155 RLAREPVSLD-------------APV--GDDEDSELGDLLEDEEAPSPEEaleeellrEELREALDTLTEREREILRLRF 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 2087637625 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 2087637625  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 2.25e-09

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: 52.49  E-value: 2.25e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2087637625 224 NKLTFAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLR 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: 513.57  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625   1 MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQ 80
Cdd:PRK06596    1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596   81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 161 LGVSSKDVREMESRMAAQDMTFdmSADDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDERSQDI 240
Cdd:PRK06596  161 LGVSEEEVREMESRLSGQDASL--DAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2087637625 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 2.46e-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: 444.03  E-value: 2.46e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  14 GNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVSSKDVREME 172
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 173 SRMAAQDMTFDMSADDDASDSQpmAPVLYLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDERSQDIIRARWLDEDnKS 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG--APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KL 237

                         250       260       270
                  ....*....|....*....|....*....|...
gi 2087637625 253 TLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:TIGR02392 238 TLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-285 7.99e-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: 283.10  E-value: 7.99e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  18 SYIRAANTWPMLTAEEEKELAEKLHyQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVSSKDVREMEs 173
Cdd:COG0568    80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 174 RMAAQDMTFDmsadddasdsqpmAPVlyLQDKTSNFADGIEEDNWEDQAA--------NKLTFAMEGLDERSQDIIRARW 245
Cdd:COG0568   155 RLAREPVSLD-------------APV--GDDEDSELGDLLEDEEAPSPEEaleeellrEELREALDTLTEREREILRLRF 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 2087637625 246 -LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:COG0568   220 gLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRS 260
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 46-285 1.03e-57

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 186.39  E-value: 1.03e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  46 DLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 125
Cdd:PRK07500   38 DEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVR 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 126 VATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAAQDMTFDMSADDDASDsqPMAPVL 200
Cdd:PRK07500  118 GGTSSAQKALFFNLRRLRARLaqadeELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEG--RSERMD 195

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 201 YLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDERSQDIIRARWLDEDNKsTLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK07500  196 FLVDDSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGA-TLEALGEELGISKERVRQIEARALEKLR 274


                  ....*
gi 2087637625 281 AAIEA 285
Cdd:PRK07500  275 RALLS 279
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 44-285 3.09e-30

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: 113.38  E-value: 3.09e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAG-YGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI------HEY 116
Cdd:COG1191    11 EGDEEAREELIEEYLPLVKKIASRLAGrLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAIldylrdEDW 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 117 VLRNWRIVKVATTKAQRKLFfnlrktkQRLGWFNQDEvEmVARELGVSSKDVREMESRMAAqdmtfdmsadddasdsqpm 196
Cdd:COG1191    91 VPRSVRELARKIEEAIEELE-------QELGREPTDE-E-IAEELGISLEEVQEALEAANA------------------- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 197 APVLYLQDKTSN---FADGIEEDNWEDQAANK-----LTFAMEGLDERSQDIIRARWLDEDnksTLQELADRYGVSAERV 268
Cdd:COG1191   143 YQLLSLDEPLEDgddLLDLLESGDPEEELEHEelreaLAEAIEQLPERERLVLSLYYFEEL---TLKEIAEVLGVSESRV 219

                         250
                  ....*....|....*..
gi 2087637625 269 RQLEKNAMKKLRAAIEA 285
Cdd:COG1191   220 SRLHKKALARLREYLKE 236
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 44-280 8.70e-23

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 95.41  E-value: 8.70e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:PRK05657   82 RGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 124 VKV---------ATTKAQRKLFFNLRKtkqrlgwfnQDEVEMVARELGVSSKDVREMES---RMAAQDMTF----DMSAD 187
Cdd:PRK05657  162 IRLpvhvvkelnVYLRAARELEHKLDH---------EPSAEEIAELLDKPVDDVSRMLAlneRITSLDTPLggdpEKSLL 232

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 188 DDASDSQPMAPVLYLQDktsnfaDGIEE--DNWEDQaankltfamegLDERSQDIIRARW-LDEDNKSTLQELADRYGVS 264
Cdd:PRK05657  233 DILADEQENGPEDTTQD------DDMKQsiVKWLFE-----------LNDKQREVLARRFgLLGYEAATLEDVAREIGLT 295

                         250
                  ....*....|....*.
gi 2087637625 265 AERVRQLEKNAMKKLR 280
Cdd:PRK05657  296 RERVRQIQVEALRRLR 311
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 44-280 9.79e-22

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 93.13  E-value: 9.79e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYV---LRN 120
Cdd:PRK09210  125 EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIadqART 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 121 WRI-VKVATT-----KAQRKLFfnlrktkQRLGwfNQDEVEMVARELGVSSKDVREMESrmAAQdmtfdmsadddasdsQ 194
Cdd:PRK09210  205 IRIpVHMVETinkliRVQRQLL-------QELG--REPTPEEIAEEMDMPPEKVREILK--IAQ---------------E 258

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 195 PMA---PVLYLQDktSNFADGIEED---NWEDQAA-----NKLTFAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYG 262
Cdd:PRK09210  259 PVSletPIGEEDD--SHLGDFIEDQdatSPADHAAyellkEQLEDVLDTLTDREENVLRLRFgLDDGRTRTLEEVGKVFG 336

                         250
                  ....*....|....*...
gi 2087637625 263 VSAERVRQLEKNAMKKLR 280
Cdd:PRK09210  337 VTRERIRQIEAKALRKLR 354
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 28-281 1.31e-18

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 84.01  E-value: 1.31e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  28 MLTAEE------------------EKELAEKLHYQGDLE-------AAKT-LILSHLRFVVHVARNYAGYGLPQADLIQE 81
Cdd:PRK07921   40 LLTAADevelakrieaglyaehllETRKRLSEARKRDLAavvrdgeAARRhLLEANLRLVVSLAKRYTGRGMPLLDLIQE 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  82 GNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK--VATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVAR 159
Cdd:PRK07921  120 GNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRlpVHLVEQVNKLARIKRELHQQLG--REATDEELAE 197

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 160 ELGVSSKDVREM--ESR-MAAQDMtfdmsadddasdsqpmaPVlyLQDKTSNFADGIEEDNWEDQAA--------NKLTF 228
Cdd:PRK07921  198 ESGIPEEKIADLleHSRdPVSLDM-----------------PV--GSDEEAPLGDFIEDSEATSAENaviagllhTDIRS 258

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2087637625 229 AMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK07921  259 VLATLDEREQQVIRLRFgLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 47-280 1.48e-18

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 84.92  E-value: 1.48e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  47 LEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK- 125
Cdd:PRK07598  174 LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRl 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 126 -VATT-------KAQRKLFFNLRKTKQrlgwfnqdeVEMVARELGVSSKDVREMESRMaaqdmtfdmsadddasdsqPMA 197
Cdd:PRK07598  254 pVHITeklnkikKAQRKISQEKGRTPT---------IEDIAQELEMTPTQVREVLLRV-------------------PRS 305

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 198 PVLYL---QDKTSNFADGIEEDNW--EDQA-----ANKLTFAMEGLDERSQDIIRARWLDEDNKS-TLQELADRYGVSAE 266
Cdd:PRK07598  306 VSLETkvgKDKDTELGDLLETDDIspEEMLmreslQRDLQHLLADLTSRERDVIRMRFGLADGHTySLAEIGRALDLSRE 385

                         250
                  ....*....|....
gi 2087637625 267 RVRQLEKNAMKKLR 280
Cdd:PRK07598  386 RVRQIESKALQKLR 399
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 48-280 4.46e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 83.89  E-value: 4.46e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  48 EAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK-- 125
Cdd:PRK05901  271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRip 350

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 126 ---VAT----TKAQRKLFfnlrktkQRLGWFNQDEvEMvARELGVSSKDVREMesRMAAQDmtfdmsadddasdsqpmaP 198
Cdd:PRK05901  351 vhmVETinklGRIERELL-------QELGREPTPE-EL-AKEMGFTPEKVREI--QKYNRE------------------P 401

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 199 V-LylqDKT------SNFADGIEEDNWE--DQAAN------KLTFAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYG 262
Cdd:PRK05901  402 IsL---DKTigkegdSQFGDFIEDSEAVspVDAVSftllqdQLQEVLETLSEREAGVIRMRFgLTDGQPKTLDEIGQVYG 478

                         250
                  ....*....|....*...
gi 2087637625 263 VSAERVRQLEKNAMKKLR 280
Cdd:PRK05901  479 VTRERIRQIESKTLRKLR 496
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
44-285 9.59e-18

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 80.40  E-value: 9.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNWRI 123
Cdd:PRK05572   28 DGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGT 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 124 VKVatTKAQRKLFFNLRKTKQRLG-WFNQD-EVEMVARELGVSSKDVremesrMAAQDMTFDMSADDDASDSQPMAPVlY 201
Cdd:PRK05572  107 VKV--SRSLKETANKIRKDKDELSkELGREpTIEELAEYLGVTPEEV------VLAQEASRSPQSIHETVHENDGDPI-T 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 202 LQDKtsnFADGIEEDnWEDQAAnkLTFAMEGLDERSQDIIRARWLDEDNKStlqELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK05572  178 LLDQ---IADQSEED-WFDKIA--LKEAIRELDERERLIVYLRYFKDKTQS---EVAKRLGISQVQVSRLEKKILKQMKE 248


                  ....
gi 2087637625 282 AIEA 285
Cdd:PRK05572  249 KLDE 252
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
44-284 1.42e-17

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 79.99  E-value: 1.42e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNWRI 123
Cdd:PRK08215   33 NGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNP 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 124 VKVatTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVreMESRMAAQDmtfdmsadddasdsqPMA---P 198
Cdd:PRK08215  112 IRV--SRSLRDIAYKALQVREKLINENSKEptVEEIAKELEVPREEV--VFALDAIQD---------------PVSlfeP 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 199 V-------LYLQDKTSNfaDGIEEDNWEDQAAnkLTFAMEGLDERSQDIIRARWLDednKSTLQELADRYGVSAERVRQL 271
Cdd:PRK08215  173 IyhdggdpIYVMDQISD--EKNKDENWLEEIA--LKEAMKKLNDREKLILNLRFFQ---GKTQMEVAEEIGISQAQVSRL 245

                         250
                  ....*....|...
gi 2087637625 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 2087637625  53 LILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 49-280 7.91e-17

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 79.44  E-value: 7.91e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  49 AAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVkvat 128
Cdd:PRK07406  137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTI---- 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 129 tkaqrKLFFNLRKTKQRLgwfnQDEVEMVARELGVSSKDvREMESRMaaqDMTFDMSADDDASDSQPMA---PVLYLQDk 205
Cdd:PRK07406  213 -----RLPVHLYETISRI----KKTTKVLSQEFGRKPTE-EEIAESM---EMTIEKLRFIAKSAQLPISletPIGKEED- 278

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 206 tSNFADGIEED--NWEDQAA-NKLTFAMEG----LDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMK 277
Cdd:PRK07406  279 -SRLGDFIEADgeTPEDDVAkNLLREDLEGvlatLSPRERDVLRLRYgLDDGRMKTLEEIGQIFNVTRERIRQIEAKALR 357


                  ...
gi 2087637625 278 KLR 280
Cdd:PRK07406  358 KLR 360
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 44-280 1.58e-13

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 69.49  E-value: 1.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDlEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:PRK05949   88 QGK-RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQART 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 124 VK--VATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVARELGVSSKDVREMESrMAAQDMTFdmsaDDDASDSQPMAPVLY 201
Cdd:PRK05949  167 IRlpIHITEKLNKIKKTQRELSQKLG--RSATPAEIAKELELEPSQIREYLS-MARQPISL----DVRVGDNQDTELSEL 239

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 202 LQDktsnfaDGIEEDNWEDQAA--NKLTFAMEGLDERSQDIIRARWLDEDNKS-TLQELADRYGVSAERVRQLEKNAMKK 278
Cdd:PRK05949  240 LED------EGPSPDQYITQELlrQDLNNLLAELTPQQREVLTLRFGLEDGKElSLAKVGERLNLSRERVRQLEHQALAH 313


                  ..
gi 2087637625 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 4.02e-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: 65.83  E-value: 4.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  48 EAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEvgVRLVSFAVHWIKAEIHEYvlrnwrivkva 127
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDY----------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 128 ttkaqrklffnLRKTKQRLGWFNQDEVEmvarelgvsskdvremesrmaaqdmtfdmsadddasdsqpmapvlylqdktS 207
Cdd:TIGR02937  68 -----------LRRKRRLRRELDLLEEL---------------------------------------------------L 85

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2087637625 208 NFADGIEEDNWEDQAANKLTFAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLRAAI 283
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEG---LSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
44-279 7.54e-13

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 66.51  E-value: 7.54e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIheyvLRNWRi 123
Cdd:PRK05803   45 EGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEI----LMHLR- 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 124 vkvattkaqrklffNLRKTKQRLgwFNQDevemvarELGVsSKDVREMEsrmaaqdmtfdmsadddasdsqpmapvlyLQ 203
Cdd:PRK05803  120 --------------NLKKTKKEV--SLQD-------PIGV-DKEGNEIS-----------------------------LI 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 204 DKTSNfadgiEEDNWEDQAANKLTF-----AMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMK 277
Cdd:PRK05803  147 DILGS-----EEDDVIEQVELKMEVeklykKIDILDEREKEVIEMRYgLGNGKEKTQREIAKALGISRSYVSRIEKRALK 221


                  ..
gi 2087637625 278 KL 279
Cdd:PRK05803  222 KL 223
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 229-281 1.43e-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: 1.43e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2087637625 229 AMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEG---LTLEEIGERLGISRERVRQIEKRALRKLRK 50
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 2087637625  43 YQ--GDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRN 120
Cdd:PRK08583   22 YQenQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRY-LRD 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 121 --W-------------RIVKVA---TTKAQRklffnlrktkqrlgwfnQDEVEMVARELGVSSKDVRE-MESRMAAQdmt 181
Cdd:PRK08583  101 ktWsvhvprrikelgpKIKKAVdelTTELQR-----------------SPKISEIADRLGVSEEEVLEaMEMGKSYQ--- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 182 fdmsadddasdsqpmapVLYLQDKTSNFADGI---------EEDNWEDQAANKLTF--AMEGLDERSQDIIRARWLdeDN 250
Cdd:PRK08583  161 -----------------ALSVDHSIEADSDGStvtlldivgQQEDGYELTEQRMILekILPVLSDREKSIIQCTFI--EN 221

                         250       260       270
                  ....*....|....*....|....*....|...
gi 2087637625 251 KSTlQELADRYGVSAERVRQLEKNAMKKLRAAI 283
Cdd:PRK08583  222 LSQ-KETGERLGISQMHVSRLQRQAIKKLREAA 253
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 63-284 1.66e-11

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 62.87  E-value: 1.66e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  63 HVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVAttKAQRKLFFNLRKT 142
Cdd:PRK07122   55 HIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP--RRLKELHLRLGRA 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 143 ----KQRLGwfNQDEVEMVARELGVSSKDVRE-MESRMAAQDMTFDMSADDDASDSQPMAPVLYLQDktsnfadgIEEDN 217
Cdd:PRK07122  133 taelSQRLG--RAPTASELAAELGMDREEVVEgLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVD--------AGLDQ 202

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2087637625 218 WEDQAAnkLTFAMEGLDERSQDIIRARWLDednKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 284
Cdd:PRK07122  203 IENREA--LRPLLAALPERERTVLVLRFFE---SMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
44-123 6.62e-11

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 61.02  E-value: 6.62e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:PRK08301   48 KGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKV 127
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 18-280 1.02e-10

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 61.31  E-value: 1.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  18 SYIRAANTWPMLTAE--------------------------------------EEKELAEKLHYQGDLEAAK-TLILSHL 58
Cdd:PRK07405   12 TYLREIGRVPLLTHEeeilygkqvqrlvalqeireelaeelgreptdaewakaAKLSEEELRSAIAEGEAAKrKMVEANL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  59 RFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKV---------ATT 129
Cdd:PRK07405   92 RLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLpihiteklnKIK 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 130 KAQRKLffnlrktKQRLGwfNQDEVEMVARELGVSSKDVREMESRmaaqdmtfdmsadddasDSQPMAPVLYLQD-KTSN 208
Cdd:PRK07405  172 KAQRQL-------SQQLG--RAATIGELAEELELTPKQVREYLER-----------------ARQPLSLDLRVGDnQDTE 225

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 209 FADGIEEDNW--EDQAA-----NKLTFAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK07405  226 LGELLEDTGAspEDFATqsslqLDLERLMEDLTPQQKEVIALRFgLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 77-279 1.08e-10

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 60.70  E-value: 1.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  77 DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEY---------VLRNWRIVKVATTKAQRKLffnlrktKQRLG 147
Cdd:PRK07408   55 DLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYlrdksptvrIPRRWQELQRQAKKVRQEL-------RQELG 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 148 wfNQDEVEMVARELGVSSKDVREMesRMAAQDMTfdmsadddasdsqPM---APVLYLQDKTSNFADGIEEDNW------ 218
Cdd:PRK07408  128 --RQPTDQEIAQALDISLEEWQEI--KLALQNRT-------------PLsldAPVNQDEDGSTSLGDLLPDPRYrsfqla 190

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2087637625 219 -EDQAanKLTFAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERV-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 2087637625  48 EAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:PRK05658  380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 425
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 224-280 2.25e-09

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: 52.49  E-value: 2.25e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2087637625 224 NKLTFAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEG---LSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 46-285 2.52e-09

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 56.55  E-value: 2.52e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  46 DLEAAKTLILSHLRFVVHVARNYAGyGLPQ----ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNW 121
Cdd:PRK05911   21 EIEYRDVLIEFYLPLVKNVAHRLIS-GMPShvktEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDD-LRKQ 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 122 RIVKVATTKAQRKLffnlrktkqrlgwfnQDEVEMVARELGVSSKDVREMES-RMAAQDMTfdmsadDDASDSQPmAPVL 200
Cdd:PRK05911   99 DWVPRSVHQKANKL---------------ADAMDSLRQSLGKEPTDGELCEYlNISQQELS------GWFSSARP-ALIL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 201 YLQDKTSNFADG-----IEEDNWEDQA------------ANKLTFAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGV 263
Cdd:PRK05911  157 SLNEEFPCQSDDeaglaLEERIADERAetgydvvdkkefSSILAEAILALEEKERKVMALYYYEE---LVLKEIGKILGV 233

                         250       260
                  ....*....|....*....|..
gi 2087637625 264 SAERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK05911  234 SESRVSQIHSKALLKLRATLSA 255
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 77-281 1.89e-08

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 53.70  E-value: 1.89e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  77 DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN-W--RIVKvattKAQRKLFFNLRKTKQRLGWfNQDE 153
Cdd:PRK06986   40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdWvpRSVR----RNAREVAQAIRQLEQELGR-EPTD 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 154 VEmVARELGVSSKDVREM-----ESRMAAQDmtfdmsaddDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDqaanKLTF 228
Cdd:PRK06986  115 TE-VAEKLGLSLEEYREMlldtnISQLFSID---------ELRGEHGDSILVTEDHQDEDPLQQLEDEELRE----ALVE 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2087637625 229 AMEGLDERSQDIIRARWLDEDNkstLQELADRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK06986  181 AIESLPEREQLVLSLYYQEELN---LKEIGAVLGVSESRVSQIHSQAIKRLRA 230
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 45-281 1.66e-07

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 51.23  E-value: 1.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  45 GDLEAAKTLILSHLRFVVHVArNYAGYGLP----QADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLR- 119
Cdd:PRK06288   28 GDPKIREYLILKYSPLVKYVA-GRIAVGMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDE-LRs 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 120 -NW--RIVKVATTKAQRKLFFnlrkTKQRLGWfNQDEVEmVARELGVSSKDVREMESRMAAQDMTFDMSADDDASDSQPM 196
Cdd:PRK06288  106 iDWipRSVRQKARQIERAIAM----LEARLGR-TPSDEE-IADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEV 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 197 APVLYLQDKTSNFADGIEEDnweDQAANKLTFAMEGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAM 276
Cdd:PRK06288  180 SLMDTLESPAALNPDEIAER---EEIKRVIVEAIKTLPEREKKVLILYYYED---LTLKEIGKVLGVTESRISQLHTKAV 253


                  ....*
gi 2087637625 277 KKLRA 281
Cdd:PRK06288  254 LQLRA 258
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
44-104 4.28e-06

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 46.44  E-value: 4.28e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2087637625  44 QGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEvgvRLVSF 104
Cdd:PRK08295   20 SGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKD---KLSSF 77
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
77-280 2.09e-03

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 38.69  E-value: 2.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625  77 DLIQEGNIGLMKAVRRFN-PEVGvrLVSFAVHWIKAEI-HEYVLRNWRIVKVATTKAQRKLFfnLRKTKQRLGwfNQDEV 154
Cdd:PRK12427   47 DMEQIALMGLLEALRRYGhPDEQ--FAAYAVHRIRGAIlDELRELDWRPRRLRQKTHKTNDA--IREIAKRLG--HEPNF 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087637625 155 EMVARELGVSSKDVREMESRMAAQDMTfdmsadddasdsqpmapvlYLQDKTSNFADGI--EEDNWEDQAANK--LTFAM 230
Cdd:PRK12427  121 EEISAELNLTAEEYQEYLLLENAGTLE-------------------SLDELLALEAHNDilQSRDLEENIIIEdnLKQAL 181

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2087637625 231 EGLDERSQDIIRARWLDEDNkstLQELADRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK12427  182 SQLDEREQLILHLYYQHEMS---LKEIALVLDLTEARICQLNKKIAQKIK 228
 
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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