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Conserved domains on  [gi|333956851|gb|EGL74481|]
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RNA polymerase factor sigma-32 [Cronobacter sakazakii E899]

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: 549.01  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   1 MTKEMQTLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQ 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 161 LGVSSKDVREMESRMAAQDMTFDMSPDDDagDSQPMAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQI 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASLDAPIDDD--DEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 333956851 241 IRARWLDeDNKSTLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 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: 549.01  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   1 MTKEMQTLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQ 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 161 LGVSSKDVREMESRMAAQDMTFDMSPDDDagDSQPMAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQI 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASLDAPIDDD--DEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 333956851 241 IRARWLDeDNKSTLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 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 1.55e-170

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: 472.15  E-value: 1.55e-170
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   14 GNLDSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVSSKDVREME 172
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  173 SRMAAQDMTFDMSPDDDAGDSQpmAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARWLDEDnKS 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG--APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KL 237

                         250       260       270
                  ....*....|....*....|....*....|...
gi 333956851  253 TLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:TIGR02392 238 TLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-285 1.67e-112

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: 325.08  E-value: 1.67e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  18 SYIRAANAWPMLSADEERALAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVSSKDVREMEs 173
Cdd:COG0568   80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 174 RMAAQDMTFDMSPDDDaGDSQPMApvlFLQDKSsnfADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARW-LDEDNKS 252
Cdd:COG0568  155 RLAREPVSLDAPVGDD-EDSELGD---LLEDEE---APSPEEALEEELLREELREALDTLTEREREILRLRFgLDDGEPH 227

                        250       260       270
                 ....*....|....*....|....*....|...
gi 333956851 253 TLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:COG0568  228 TLEEIGKEFGVSRERVRQIEAKALRKLRHPLRS 260
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 53-123 1.37e-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: 75.32  E-value: 1.37e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 333956851   53 LILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 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 2.73e-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: 54.80  E-value: 2.73e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 333956851 224 DKLTDAMQGLDERSQQIIRARWLDEdnkSTLQELANRYGVSAERVRQLEKNAMKKLR 280
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEG---LSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_ASNC smart00344
helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase ...
 233-283 2.44e-03

helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli)


Pssm-ID: 214628 [Multi-domain]  Cd Length: 108  Bit Score: 36.72  E-value: 2.44e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 333956851   233 LDERSQQIIRArwLDEDNKSTLQELANRYGVSA----ERVRQLEKN-AMKKLRAAI 283
Cdd:smart00344   1 LDEIDRKILEE--LQKDARISLAELAKKVGLSPstvhNRVKRLEEEgVIKGYTAVL 54
 
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: 549.01  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   1 MTKEMQTLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQ 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 161 LGVSSKDVREMESRMAAQDMTFDMSPDDDagDSQPMAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQI 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASLDAPIDDD--DEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDI 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 333956851 241 IRARWLDeDNKSTLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 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 1.55e-170

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: 472.15  E-value: 1.55e-170
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   14 GNLDSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVSSKDVREME 172
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  173 SRMAAQDMTFDMSPDDDAGDSQpmAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARWLDEDnKS 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG--APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KL 237

                         250       260       270
                  ....*....|....*....|....*....|...
gi 333956851  253 TLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:TIGR02392 238 TLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-285 1.67e-112

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: 325.08  E-value: 1.67e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  18 SYIRAANAWPMLSADEERALAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVSSKDVREMEs 173
Cdd:COG0568   80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 174 RMAAQDMTFDMSPDDDaGDSQPMApvlFLQDKSsnfADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARW-LDEDNKS 252
Cdd:COG0568  155 RLAREPVSLDAPVGDD-EDSELGD---LLEDEE---APSPEEALEEELLREELREALDTLTEREREILRLRFgLDDGEPH 227

                        250       260       270
                 ....*....|....*....|....*....|...
gi 333956851 253 TLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:COG0568  228 TLEEIGKEFGVSRERVRQIEAKALRKLRHPLRS 260
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 17-285 4.48e-71

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 220.68  E-value: 4.48e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  17 DSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPE 96
Cdd:PRK07500   9 RSMIRSAMKAPYLEREEEHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  97 VGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREM 171
Cdd:PRK07500  89 REVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLaqadeELTKQEIHREIATALGVSLSDVEMM 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 172 ESRMAAQDMTFDMS-PDDDAGDSQPMApvlFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARWLDEDN 250
Cdd:PRK07500 169 DARLSGPDASLNAPqSEEDEGRSERMD---FLVDDSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDG 245

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 333956851 251 KsTLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK07500 246 A-TLEALGEELGISKERVRQIEARALEKLRRALLS 279
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 27-280 5.04e-32

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 121.25  E-value: 5.04e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  27 PMLSADEERALAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK09210 109 PLLTAEEEIELAKRIE-EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYAT 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 107 HWIKAEIHEYV---LRNWRI-VKVATT-----KAQRKLFfnlrktkQRLGwfNQDEVEMVARELGVSSKDVREMESrmAA 177
Cdd:PRK09210 188 WWIRQAITRAIadqARTIRIpVHMVETinkliRVQRQLL-------QELG--REPTPEEIAEEMDMPPEKVREILK--IA 256

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 178 QDMTFDMSP---DDDagdsqpmapvlflqdksSNFADGIEDD---NWEEHAA-----DKLTDAMQGLDERSQQIIRARW- 245
Cdd:PRK09210 257 QEPVSLETPigeEDD-----------------SHLGDFIEDQdatSPADHAAyellkEQLEDVLDTLTDREENVLRLRFg 319

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 333956851 246 LDEDNKSTLQELANRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK09210 320 LDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 44-285 5.38e-32

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: 118.00  E-value: 5.38e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  44 QGDLEAAKKLILSHLRFVVHIARNYAG-YGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI------HEY 116
Cdd:COG1191   11 EGDEEAREELIEEYLPLVKKIASRLAGrLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAIldylrdEDW 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 117 VLRNWRIVKVATTKAQRKLFfnlrktkQRLGWFNQDEvEmVARELGVSSKDVREMESRMAAQDMT-FDMSPDDDagdsqp 195
Cdd:COG1191   91 VPRSVRELARKIEEAIEELE-------QELGREPTDE-E-IAEELGISLEEVQEALEAANAYQLLsLDEPLEDG------ 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 196 mapvlflqdksSNFADGIEDDNWEEHAADK-----LTDAMQGLDERSQQIIRARWLDEDnksTLQELANRYGVSAERVRQ 270
Cdd:COG1191  156 -----------DDLLDLLESGDPEEELEHEelreaLAEAIEQLPERERLVLSLYYFEEL---TLKEIAEVLGVSESRVSR 221

                        250
                 ....*....|....*
gi 333956851 271 LEKNAMKKLRAAIEA 285
Cdd:COG1191  222 LHKKALARLREYLKE 236
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 27-280 5.95e-32

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 120.45  E-value: 5.95e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  27 PMLSADEERALAeKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK05657  66 PLLTAEEEVYFA-RRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 107 HWIKAEIHEYVLRNWRIVKV---------ATTKAQRKLFFNLRKtkqrlgwfnQDEVEMVARELGVSSKDVREMES---R 174
Cdd:PRK05657 145 WWIRQTIERAIMNQTRTIRLpvhvvkelnVYLRAARELEHKLDH---------EPSAEEIAELLDKPVDDVSRMLAlneR 215

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 175 MAAQDMTFDMSPDDDAGDsqpmapvlFLQDKSSNFADG-IEDDNWEEHAADKLTDamqgLDERSQQIIRARW-LDEDNKS 252
Cdd:PRK05657 216 ITSLDTPLGGDPEKSLLD--------ILADEQENGPEDtTQDDDMKQSIVKWLFE----LNDKQREVLARRFgLLGYEAA 283

                        250       260
                 ....*....|....*....|....*...
gi 333956851 253 TLQELANRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK05657 284 TLEDVAREIGLTRERVRQIQVEALRRLR 311
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 46-281 2.28e-26

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 105.20  E-value: 2.28e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  46 DLEAAKK-LILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIV 124
Cdd:PRK07921  83 DGEAARRhLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTI 162

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 125 K--VATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVARELGVSSKDVrEMESRMAAQDMTFDMspdddagdsqpmaPVlfL 202
Cdd:PRK07921 163 RlpVHLVEQVNKLARIKRELHQQLG--REATDEELAEESGIPEEKI-ADLLEHSRDPVSLDM-------------PV--G 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 203 QDKSSNFADGIEDDNW--EEHAA------DKLTDAMQGLDERSQQIIRARW-LDEDNKSTLQELANRYGVSAERVRQLEK 273
Cdd:PRK07921 225 SDEEAPLGDFIEDSEAtsAENAViagllhTDIRSVLATLDEREQQVIRLRFgLDDGQPRTLDQIGKLFGLSRERVRQIER 304


                 ....*...
gi 333956851 274 NAMKKLRA 281
Cdd:PRK07921 305 EVMSKLRN 312
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
27-284 1.52e-24

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 98.87  E-value: 1.52e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  27 PMLSADEERALAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK08215  17 PVLKNEEMRELFERMQ-NGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 107 HWIKAEIHEYvLRNWRIVKVatTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVreMESRMAAQDMTFDM 184
Cdd:PRK08215  96 PMIIGEIRRY-LRDNNPIRV--SRSLRDIAYKALQVREKLINENSKEptVEEIAKELEVPREEV--VFALDAIQDPVSLF 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 185 SP-DDDAGDSqpmapvLFLQDKSSNfaDGIEDDNWEEHAAdkLTDAMQGLDERSQQIIRARWLDednKSTLQELANRYGV 263
Cdd:PRK08215 171 EPiYHDGGDP------IYVMDQISD--EKNKDENWLEEIA--LKEAMKKLNDREKLILNLRFFQ---GKTQMEVAEEIGI 237

                        250       260
                 ....*....|....*....|.
gi 333956851 264 SAERVRQLEKNAMKKLRAAIE 284
Cdd:PRK08215 238 SQAQVSRLEKAALKHMRKYIQ 258
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 27-280 3.53e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 95.83  E-value: 3.53e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  27 PMLSADEERALA----------EKLHYQGDLEAAKK----------------LILSHLRFVVHIARNYAGYGLPQADLIQ 80
Cdd:PRK05901 224 KLLNAEEEVELAkrieaglyaeELLAEGEKLDPELRrdlqwigrdgkraknhLLEANLRLVVSLAKRYTNRGLSFLDLIQ 303

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK-----VAT----TKAQRKLFfnlrktkQRLGWFNQ 151
Cdd:PRK05901 304 EGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRipvhmVETinklGRIERELL-------QELGREPT 376

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 152 DEvEMvARELGVSSKDVREMEsRMAAQDMTFDMSPDDDaGDSQpmapvlflqdkssnFADGIEDD---NWEEHAA----- 223
Cdd:PRK05901 377 PE-EL-AKEMGFTPEKVREIQ-KYNREPISLDKTIGKE-GDSQ--------------FGDFIEDSeavSPVDAVSftllq 438

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 333956851 224 DKLTDAMQGLDERSQQIIRARW-LDEDNKSTLQELANRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK05901 439 DQLQEVLETLSEREAGVIRMRFgLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
27-285 1.98e-20

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 87.72  E-value: 1.98e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  27 PMLSADEERALAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK05572  12 PQLKDEENKELIKKSQ-DGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 107 HWIKAEIHEYvLRNWRIVKVatTKAQRKLFFNLRKTKQRLG-WFNQD-EVEMVARELGVSSKDVremesrMAAQDMTFDM 184
Cdd:PRK05572  91 PMIIGEIQRF-LRDDGTVKV--SRSLKETANKIRKDKDELSkELGREpTIEELAEYLGVTPEEV------VLAQEASRSP 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 185 SP------DDDaGDsqpmaPVLFLqDKSSnfadgiedDNWEEHAADK--LTDAMQGLDERSQQIIRARWLDEDNKStlqE 256
Cdd:PRK05572 162 QSihetvhEND-GD-----PITLL-DQIA--------DQSEEDWFDKiaLKEAIRELDERERLIVYLRYFKDKTQS---E 223

                        250       260
                 ....*....|....*....|....*....
gi 333956851 257 LANRYGVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK05572 224 VAKRLGISQVQVSRLEKKILKQMKEKLDE 252
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
15-279 8.08e-20

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 85.77  E-value: 8.08e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  15 NLDSYIrAANAWPM-LSADEERALAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:PRK05803  17 FLVSYV-KNNSFPQpLSEEEERKYLELMK-EGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESF 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  94 NPEVGVRLVSFAVHWIKAEIheyvLRNWRivkvattkaqrklffNLRKTKQRLgwFNQDevemvarELGVsSKDVREMEs 173
Cdd:PRK05803  95 DAGKGTKLATYAARCIENEI----LMHLR---------------NLKKTKKEV--SLQD-------PIGV-DKEGNEIS- 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 174 rmaaqdmtfdmspdddagdsqpmapvlfLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARW-LDEDNKS 252
Cdd:PRK05803 145 ----------------------------LIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYgLGNGKEK 196

                        250       260
                 ....*....|....*....|....*..
gi 333956851 253 TLQELANRYGVSAERVRQLEKNAMKKL 279
Cdd:PRK05803 197 TQREIAKALGISRSYVSRIEKRALKKL 223
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 33-280 2.24e-19

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 86.05  E-value: 2.24e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  33 EERALAEKLHyQGDlEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAE 112
Cdd:PRK05949  78 SETELKQTLK-QGK-RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQA 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 113 IHEYVLRNWRIVK--VATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVARELGVSSKDVREMESrMAAQDMTFDMSpdddA 190
Cdd:PRK05949 156 ITRAIAQQARTIRlpIHITEKLNKIKKTQRELSQKLG--RSATPAEIAKELELEPSQIREYLS-MARQPISLDVR----V 228

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 191 GDSQPMAPVLFLQDkssnfaDGIEDDNW--EEHAADKLTDAMQGLDERSQQIIRARWLDEDNKS-TLQELANRYGVSAER 267
Cdd:PRK05949 229 GDNQDTELSELLED------EGPSPDQYitQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKElSLAKVGERLNLSRER 302

                        250
                 ....*....|...
gi 333956851 268 VRQLEKNAMKKLR 280
Cdd:PRK05949 303 VRQLEHQALAHLR 315
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 48-280 1.27e-18

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 84.04  E-value: 1.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  48 EAAK-KLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKV 126
Cdd:PRK07405  80 EAAKrKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRL 159

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 127 ---------ATTKAQRKLffnlrktKQRLGwfNQDEVEMVARELGVSSKDVREMESRmAAQDMTFDMSpdddAGDSQPMA 197
Cdd:PRK07405 160 pihiteklnKIKKAQRQL-------SQQLG--RAATIGELAEELELTPKQVREYLER-ARQPLSLDLR----VGDNQDTE 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 198 PVLFLQDkssnfaDGIEDDNWEEHAADK--LTDAMQGLDERSQQIIRARW-LDEDNKSTLQELANRYGVSAERVRQLEKN 274
Cdd:PRK07405 226 LGELLED------TGASPEDFATQSSLQldLERLMEDLTPQQKEVIALRFgLEDGQPLTLAKIGERLNISRERVRQIERE 299


                 ....*.
gi 333956851 275 AMKKLR 280
Cdd:PRK07405 300 ALSKLR 305
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 39-280 2.13e-18

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 84.15  E-value: 2.13e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  39 EKLHYQGdLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVL 118
Cdd:PRK07598 167 EQIQKQG-LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIA 245

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 119 RNWRIVK--VATT-------KAQRKLFFNLRKTKQrlgwfnqdeVEMVARELGVSSKDVREMESRMAAQdmtfdMSPDDD 189
Cdd:PRK07598 246 TQSRTIRlpVHITeklnkikKAQRKISQEKGRTPT---------IEDIAQELEMTPTQVREVLLRVPRS-----VSLETK 311

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 190 AGdsqpmapvlflQDKSSNFADGIEDDNW---EEHAADKLTDAMQ----GLDERSQQIIRARWLDEDNKS-TLQELANRY 261
Cdd:PRK07598 312 VG-----------KDKDTELGDLLETDDIspeEMLMRESLQRDLQhllaDLTSRERDVIRMRFGLADGHTySLAEIGRAL 380

                        250
                 ....*....|....*....
gi 333956851 262 GVSAERVRQLEKNAMKKLR 280
Cdd:PRK07598 381 DLSRERVRQIESKALQKLR 399
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 29-283 1.05e-17

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 80.51  E-value: 1.05e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  29 LSADEERALAEKLHYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108
Cdd:PRK08583  10 LTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPT 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 109 IKAEIHEYvLRN--W-------------RIVKVA---TTKAQRklffnlrktkqrlgwfnQDEVEMVARELGVSSKDVRE 170
Cdd:PRK08583  90 IIGEIKRY-LRDktWsvhvprrikelgpKIKKAVdelTTELQR-----------------SPKISEIADRLGVSEEEVLE 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 171 -MESRMAAQDMTFDMSPDDDAGDSQpmapVLFLQdkssnfADGIEDDNWEEhaADK---LTDAMQGLDERSQQIIRARWL 246
Cdd:PRK08583 152 aMEMGKSYQALSVDHSIEADSDGST----VTLLD------IVGQQEDGYEL--TEQrmiLEKILPVLSDREKSIIQCTFI 219

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 333956851 247 deDNKSTlQELANRYGVSAERVRQLEKNAMKKLRAAI 283
Cdd:PRK08583 220 --ENLSQ-KETGERLGISQMHVSRLQRQAIKKLREAA 253
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 53-123 1.37e-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: 75.32  E-value: 1.37e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 333956851   53 LILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
27-123 6.89e-16

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 74.89  E-value: 6.89e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  27 PMLSADEERALAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK08301  32 PPLSKEEEEYLLNKLP-KGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 110

                         90
                 ....*....|....*..
gi 333956851 107 HWIKAEIHEYVLRNWRI 123
Cdd:PRK08301 111 RCIENEILMYLRRNNKV 127
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 49-280 1.74e-15

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 75.59  E-value: 1.74e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  49 AAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI--------------- 113
Cdd:PRK07406 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAItraiadqsrtirlpv 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 114 HEYVLRNwRIVKVATTKAQRklfFNLRKTKQRLGwfnqDEVEMVARELgvsskdvremesRMAAQDMTFDMSPDDDAGds 193
Cdd:PRK07406 217 HLYETIS-RIKKTTKVLSQE---FGRKPTEEEIA----ESMEMTIEKL------------RFIAKSAQLPISLETPIG-- 274

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 194 qpmapvlflQDKSSNFADGIEDD-NWEEHAADK------LTDAMQGLDERSQQIIRARW-LDEDNKSTLQELANRYGVSA 265
Cdd:PRK07406 275 ---------KEEDSRLGDFIEADgETPEDDVAKnllredLEGVLATLSPRERDVLRLRYgLDDGRMKTLEEIGQIFNVTR 345

                        250
                 ....*....|....*
gi 333956851 266 ERVRQLEKNAMKKLR 280
Cdd:PRK07406 346 ERIRQIEAKALRKLR 360
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 48-283 1.00e-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: 1.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851   48 EAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEvgVRLVSFAVHWIKAEIHEYvlrnwrivkva 127
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDY----------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  128 ttkaqrklffnLRKTKQRLGWFNQDEVEmvarelgvsskdvremesrmaaqdmtfdmspdddagdsqpmapvlflqdksS 207
Cdd:TIGR02937  68 -----------LRRKRRLRRELDLLEEL---------------------------------------------------L 85

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 333956851  208 NFADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARWLDEdnkSTLQELANRYGVSAERVRQLEKNAMKKLRAAI 283
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEG---LSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 63-284 4.21e-13

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 67.49  E-value: 4.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  63 HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVAttKAQRKLFFNLRKT 142
Cdd:PRK07122  55 HIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP--RRLKELHLRLGRA 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 143 ----KQRLGwfNQDEVEMVARELGVSSKDVRE-MESRMAAQDMTFDMSPDDDAGDSQPMAPVLflqdkssnfadGIED-- 215
Cdd:PRK07122 133 taelSQRLG--RAPTASELAAELGMDREEVVEgLVAGSAYNTLSIDSGGGSGDDDARAIADTL-----------GDVDag 199

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 216 -DNWEEHAAdkLTDAMQGLDERSQQIIRARWLDednKSTLQELANRYGVSAERVRQLEKNAMKKLRAAIE 284
Cdd:PRK07122 200 lDQIENREA--LRPLLAALPERERTVLVLRFFE---SMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 229-281 6.17e-13

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 62.06  E-value: 6.17e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 333956851  229 AMQGLDERSQQIIRARWLDEdnkSTLQELANRYGVSAERVRQLEKNAMKKLRA 281
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEG---LTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 48-280 1.81e-12

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 67.13  E-value: 1.81e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  48 EAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI-------------- 113
Cdd:PRK05658 380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAItrsiadqartirip 459

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 114 -H--EYVlrNwRIVKVAttkaqrklffnlRKTKQRLGwfNQDEVEMVARELGVSSKDVRE----------MEsrmaaqdm 180
Cdd:PRK05658 460 vHmiETI--N-KLNRIS------------RQMLQEIG--REPTPEELAERLGMPEDKVRKvlkiakepisLE-------- 514

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 181 tfdmSP--DDDagDSQpmapvlflqdkssnFADGIEDDNWE---EHAA-----DKLTDAMQGLDERSQQIIRARWLDEDN 250
Cdd:PRK05658 515 ----TPigDDE--DSH--------------LGDFIEDKNAElpiDAAIqeslrEATTDVLASLTPREAKVLRMRFGIDMN 574

                        250       260       270
                 ....*....|....*....|....*....|.
gi 333956851 251 KS-TLQELANRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK05658 575 TDhTLEEVGKQFDVTRERIRQIEAKALRKLR 605
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 77-281 6.82e-12

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 63.71  E-value: 6.82e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  77 DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN-W--RIVKvattKAQRKLFFNLRKTKQRLGWfNQDE 153
Cdd:PRK06986  40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdWvpRSVR----RNAREVAQAIRQLEQELGR-EPTD 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 154 VEmVARELGVSSKDVREMesRMAAQdmTFDMSPDDDAGDSQPMAPVLFLQDKSSNFADGIEDDNWEEhaadKLTDAMQGL 233
Cdd:PRK06986 115 TE-VAEKLGLSLEEYREM--LLDTN--ISQLFSIDELRGEHGDSILVTEDHQDEDPLQQLEDEELRE----ALVEAIESL 185

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 333956851 234 DERSQQIIRARWLDEDNkstLQELANRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK06986 186 PEREQLVLSLYYQEELN---LKEIGAVLGVSESRVSQIHSQAIKRLRA 230
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 77-279 1.33e-11

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 63.02  E-value: 1.33e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  77 DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEY---------VLRNWRIVKVATTKAQRKLffnlrktKQRLG 147
Cdd:PRK07408  55 DLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYlrdksptvrIPRRWQELQRQAKKVRQEL-------RQELG 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 148 wfNQDEVEMVARELGVSSKDVREMesRMAAQDMTFdMSPDddagdsqpmAPVLFLQDKSSNFADGIEDDNW-------EE 220
Cdd:PRK07408 128 --RQPTDQEIAQALDISLEEWQEI--KLALQNRTP-LSLD---------APVNQDEDGSTSLGDLLPDPRYrsfqlaqED 193

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 333956851 221 HAadKLTDAMQGLDERSQQIIRARWLDEdnkSTLQELANRYGVSAERV-RQLEK--NAMKKL 279
Cdd:PRK07408 194 RI--RLQQALAQLEERTREVLEFVFLHD---LTQKEAAERLGISPVTVsRRVKKglDQLKKL 250
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 46-285 4.29e-11

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 61.94  E-value: 4.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  46 DLEAAKKLILSHLRFVVHIARNYAGyGLPQ----ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNW 121
Cdd:PRK05911  21 EIEYRDVLIEFYLPLVKNVAHRLIS-GMPShvktEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDD-LRKQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 122 RIVKVATTKAQRKLffnlrktkqrlgwfnQDEVEMVARELGVSSKDVREMEsrmaaqdmTFDMSPDDDAG---DSQPmAP 198
Cdd:PRK05911  99 DWVPRSVHQKANKL---------------ADAMDSLRQSLGKEPTDGELCE--------YLNISQQELSGwfsSARP-AL 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 199 VLFLQDKSSNFADGIEDDNWEEHAADK-----------------LTDAMQGLDERSQQIIRARWLDEdnkSTLQELANRY 261
Cdd:PRK05911 155 ILSLNEEFPCQSDDEAGLALEERIADEraetgydvvdkkefssiLAEAILALEEKERKVMALYYYEE---LVLKEIGKIL 231

                        250       260
                 ....*....|....*....|....
gi 333956851 262 GVSAERVRQLEKNAMKKLRAAIEA 285
Cdd:PRK05911 232 GVSESRVSQIHSKALLKLRATLSA 255
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 224-280 2.73e-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: 54.80  E-value: 2.73e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 333956851 224 DKLTDAMQGLDERSQQIIRARWLDEdnkSTLQELANRYGVSAERVRQLEKNAMKKLR 280
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEG---LSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 32-281 5.28e-10

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 58.55  E-value: 5.28e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  32 DEERALAEKLHYQGDLEAAKKLILSHLRFVVHIArNYAGYGLP----QADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVH 107
Cdd:PRK06288  15 QDETELWREYKKTGDPKIREYLILKYSPLVKYVA-GRIAVGMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVT 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 108 WIKAEIHEYvLR--NW--RIVKVATTKAQRKLFFnlrkTKQRLGWfNQDEVEmVARELGVSSKDVREMESRMAAQDMTfd 183
Cdd:PRK06288  94 RIRGAIFDE-LRsiDWipRSVRQKARQIERAIAM----LEARLGR-TPSDEE-IADELGISLEEYNSLLSKLSGTSVV-- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 184 mSPDDdagdsqpmapVLFLQDKSSNFA--DGIED---DNWEEHAAD-----KLTDAMQGLDERSQQIIRARWLDEdnkST 253
Cdd:PRK06288 165 -SLND----------LWFGGDEGDEVSlmDTLESpaaLNPDEIAEReeikrVIVEAIKTLPEREKKVLILYYYED---LT 230

                        250       260
                 ....*....|....*....|....*...
gi 333956851 254 LQELANRYGVSAERVRQLEKNAMKKLRA 281
Cdd:PRK06288 231 LKEIGKVLGVTESRISQLHTKAVLQLRA 258
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
32-104 1.18e-06

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 47.98  E-value: 1.18e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 333956851  32 DEEraLAEKLHyQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEvgvRLVSF 104
Cdd:PRK08295  11 DEE--LVELAR-SGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKD---KLSSF 77
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
33-284 3.40e-06

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 47.35  E-value: 3.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  33 EERALAEKLHYQGDLEAAKKLILSHLRFV-VHIARNYAGygLPQA----DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVH 107
Cdd:PRK07670   7 EEQKLWDRWKEERDPDAADELIRRYMPLVhYHVQRISVG--LPKSvskdDLKSLGMLGLYDALEKFDPSRDLKFDTYASF 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 108 WIKAEIHEYVLRNWRIVKVATTKAqRKLFFNLRKTKQRLGwfNQDEVEMVARELGVSSKDV-REMESRMAAQDMTFDMSP 186
Cdd:PRK07670  85 RIRGAIIDGLRKEDWLPRSMREKT-KKVEAAIEKLEQRYM--RNVTPKEVAAELGMTEEEVeATMNEGFFANLLSIDEKT 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 187 DDDagDSQPMAPVLFLQDKSSNfadgIEDDNWEEHAADKLTDAMQGLDERSQQIIRARWLDEdnkSTLQELANRYGVSAE 266
Cdd:PRK07670 162 HDQ--DDGENVSVTIRDDKTPT----PEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEE---LTLTEIGQVLNLSTS 232

                        250
                 ....*....|....*...
gi 333956851 267 RVRQLEKNAMKKLRAAIE 284
Cdd:PRK07670 233 RISQIHSKALFKLKKLLE 250
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
77-280 1.77e-04

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 41.77  E-value: 1.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851  77 DLIQEGNIGLMKAVRRFN-PEVGvrLVSFAVHWIKAEI-HEYVLRNWRIVKVATTKAQRKLFfnLRKTKQRLGwfNQDEV 154
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGhPDEQ--FAAYAVHRIRGAIlDELRELDWRPRRLRQKTHKTNDA--IREIAKRLG--HEPNF 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956851 155 EMVARELGVSSKDVREMESRMAAQDMTfdmSPDDDAGDSQPMAPvlfLQDKssnfadGIEDDNWEEhaaDKLTDAMQGLD 234
Cdd:PRK12427 121 EEISAELNLTAEEYQEYLLLENAGTLE---SLDELLALEAHNDI---LQSR------DLEENIIIE---DNLKQALSQLD 185

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 333956851 235 ERSQQIIRARWLDEDNkstLQELANRYGVSAERVRQLEKNAMKKLR 280
Cdd:PRK12427 186 EREQLILHLYYQHEMS---LKEIALVLDLTEARICQLNKKIAQKIK 228
HTH_ASNC smart00344
helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase ...
 233-283 2.44e-03

helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli)


Pssm-ID: 214628 [Multi-domain]  Cd Length: 108  Bit Score: 36.72  E-value: 2.44e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 333956851   233 LDERSQQIIRArwLDEDNKSTLQELANRYGVSA----ERVRQLEKN-AMKKLRAAI 283
Cdd:smart00344   1 LDEIDRKILEE--LQKDARISLAELAKKVGLSPstvhNRVKRLEEEgVIKGYTAVL 54
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 210-285 6.72e-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: 36.90  E-value: 6.72e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 333956851 210 ADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARWLDEDnksTLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 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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