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Conserved domains on  [gi|1958115121|gb|QQS60810|]
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sigma-70 family RNA polymerase sigma factor [Candidatus Falkowbacteria bacterium]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09210 super family cl35786
RNA polymerase sigma factor RpoD; Validated
 11-371 5.60e-150

RNA polymerase sigma factor RpoD; Validated


The actual alignment was detected with superfamily member PRK09210:

Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 427.86  E-value: 5.60e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  11 KALDDLVAKVRPRGFVTETEL---LQVFPQVENYIYDYeltLERLQRNSIRIIEDSGGfLDVDANVKKAgqltsilgsDK 87
Cdd:PRK09210   13 QVVKELIEKGKKRGTLTYDEIaekLIPFELDSDQIDDL---YERLEDAGISIVDEEGN-PSSAQVVEEE---------EE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  88 DRLKFDISELSA----DSIQMYLREIGKVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGsKGLSLLD 163
Cdd:PRK09210   80 EELDNDLSVPPGvkinDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVG-RGMLFLD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 164 LIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEI 243
Cdd:PRK09210  159 LIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEI 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 244 ASEMGETIDKVRYIIKISQDTISLETSVGEDDeDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMR 323
Cdd:PRK09210  239 AEEMDMPPEKVREILKIAQEPVSLETPIGEED-DSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLR 317

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 1958115121 324 FGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:PRK09210  318 FGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 11-371 5.60e-150

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 427.86  E-value: 5.60e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  11 KALDDLVAKVRPRGFVTETEL---LQVFPQVENYIYDYeltLERLQRNSIRIIEDSGGfLDVDANVKKAgqltsilgsDK 87
Cdd:PRK09210   13 QVVKELIEKGKKRGTLTYDEIaekLIPFELDSDQIDDL---YERLEDAGISIVDEEGN-PSSAQVVEEE---------EE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  88 DRLKFDISELSA----DSIQMYLREIGKVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGsKGLSLLD 163
Cdd:PRK09210   80 EELDNDLSVPPGvkinDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVG-RGMLFLD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 164 LIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEI 243
Cdd:PRK09210  159 LIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEI 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 244 ASEMGETIDKVRYIIKISQDTISLETSVGEDDeDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMR 323
Cdd:PRK09210  239 AEEMDMPPEKVREILKIAQEPVSLETPIGEED-DSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLR 317

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 1958115121 324 FGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:PRK09210  318 FGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 104-371 5.33e-147

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: 416.38  E-value: 5.33e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 104 MYLREIGKVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRK 183
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQG-RGLPLLDLIQEGNLGLMKAVEKFDPER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 184 GYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQD 263
Cdd:COG0568    80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLARE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 264 TISLETSVGeDDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDV 343
Cdd:COG0568   160 PVSLDAPVG-DDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGV 238

                         250       260
                  ....*....|....*....|....*...
gi 1958115121 344 TRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:COG0568   239 SRERVRQIEAKALRKLRHPLRSRKLRDY 266
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 134-371 1.31e-130

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 373.56  E-value: 1.31e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 134 AERKLIEANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIP 213
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTN-RGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 214 VHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGEdDEDSTLEDFIEDVKNVTPD 293
Cdd:TIGR02393  80 VHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGE-EEDSFLGDFIEDESIESPD 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958115121 294 RAAALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:TIGR02393 159 DAAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 138-209 4.58e-21

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: 85.72  E-value: 4.58e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958115121 138 LIEANLRLVVSIAKKFAGSkGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRT 209
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGD-GADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 302-360 2.29e-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: 52.88  E-value: 2.29e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958115121 302 KDYVHEIITQLTPREQKILEMRFGlldgVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQ 360
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 11-371 5.60e-150

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 427.86  E-value: 5.60e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  11 KALDDLVAKVRPRGFVTETEL---LQVFPQVENYIYDYeltLERLQRNSIRIIEDSGGfLDVDANVKKAgqltsilgsDK 87
Cdd:PRK09210   13 QVVKELIEKGKKRGTLTYDEIaekLIPFELDSDQIDDL---YERLEDAGISIVDEEGN-PSSAQVVEEE---------EE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  88 DRLKFDISELSA----DSIQMYLREIGKVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGsKGLSLLD 163
Cdd:PRK09210   80 EELDNDLSVPPGvkinDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVG-RGMLFLD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 164 LIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEI 243
Cdd:PRK09210  159 LIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEI 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 244 ASEMGETIDKVRYIIKISQDTISLETSVGEDDeDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMR 323
Cdd:PRK09210  239 AEEMDMPPEKVREILKIAQEPVSLETPIGEED-DSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLR 317

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 1958115121 324 FGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:PRK09210  318 FGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 104-371 5.33e-147

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: 416.38  E-value: 5.33e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 104 MYLREIGKVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRK 183
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQG-RGLPLLDLIQEGNLGLMKAVEKFDPER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 184 GYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQD 263
Cdd:COG0568    80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLARE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 264 TISLETSVGeDDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDV 343
Cdd:COG0568   160 PVSLDAPVG-DDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGV 238

                         250       260
                  ....*....|....*....|....*...
gi 1958115121 344 TRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:COG0568   239 SRERVRQIEAKALRKLRHPLRSRKLRDY 266
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 98-371 6.11e-140

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 407.46  E-value: 6.11e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  98 SADSIQMYLREIGKVPLLTTEEEIELAKRKERG---------------------------DKDAERKLIEANLRLVVSIA 150
Cdd:PRK05901  209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGlyaeellaegekldpelrrdlqwigrdGKRAKNHLLEANLRLVVSLA 288

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 151 KKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQL 230
Cdd:PRK05901  289 KRYTN-RGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIEREL 367

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 231 IQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGeDDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIIT 310
Cdd:PRK05901  368 LQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIG-KEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLE 446

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958115121 311 QLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:PRK05901  447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDF 507
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 134-371 1.31e-130

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 373.56  E-value: 1.31e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 134 AERKLIEANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIP 213
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTN-RGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 214 VHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGEdDEDSTLEDFIEDVKNVTPD 293
Cdd:TIGR02393  80 VHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGE-EEDSFLGDFIEDESIESPD 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958115121 294 RAAALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:TIGR02393 159 DAAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 115-371 1.13e-125

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 374.52  E-value: 1.13e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 115 LTTEEEIELAKRKERGDKDAER---KLIEANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYA 191
Cdd:PRK05658  359 LTIEELKEINRQISKGEAKARRakkEMVEANLRLVISIAKKYT-NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 437

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 192 TWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSV 271
Cdd:PRK05658  438 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPI 517

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 272 GeDDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQI 351
Cdd:PRK05658  518 G-DDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 596

                         250       260
                  ....*....|....*....|
gi 1958115121 352 EYKTLEKIQKHSLIKKLKDY 371
Cdd:PRK05658  597 EAKALRKLRHPSRSRKLRSF 616
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 98-371 7.70e-108

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 318.98  E-value: 7.70e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  98 SADSIQMYLREIGKVPLLTTEEEIELAKRKERG---------------------------DKDAERKLIEANLRLVVSIA 150
Cdd:PRK07921   24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGlyaehlletrkrlsearkrdlaavvrdGEAARRHLLEANLRLVVSLA 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 151 KKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQL 230
Cdd:PRK07921  104 KRYTG-RGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREL 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 231 IQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGEdDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIIT 310
Cdd:PRK07921  183 HQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGS-DEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLA 261

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958115121 311 QLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:PRK07921  262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 100-358 1.04e-105

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 312.64  E-value: 1.04e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 100 DSIQMYLREIGKVPLLTTEEEIELA------------KRKERGDKD----------------------------AERKLI 139
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELArqvqqmmvleelREELEEQLGrepskeewaaaaglseaelrqrlrqgqrAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 140 EANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVET 219
Cdd:TIGR02997  81 KANLRLVVSVAKKYQN-RGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 220 INKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGeDDEDSTLEDFIEDvKNVTPDRAAALQ 299
Cdd:TIGR02997 160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVG-DEEDTELGDLLED-DGESPEEQVERE 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958115121 300 LLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEK 358
Cdd:TIGR02997 238 SLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK 296
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 100-371 1.20e-101

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 305.17  E-value: 1.20e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 100 DSIQMYLREIGKVPLLTTEEEIELA----------------------------------------KRKERGDKDAERKLI 139
Cdd:PRK07406   63 DSIRVYLQEIGRIRLLRPDEEIELArkiadlleleelreqfeselgrepsdkewaelvdmplpkfRRRLMLGRRAKEKMV 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 140 EANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVET 219
Cdd:PRK07406  143 QSNLRLVVSIAKKYMN-RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYET 221

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 220 INKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGEdDEDSTLEDFIEdVKNVTPDRAAALQ 299
Cdd:PRK07406  222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGK-EEDSRLGDFIE-ADGETPEDDVAKN 299

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958115121 300 LLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKHSLIKKLKDY 371
Cdd:PRK07406  300 LLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEY 371
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 88-361 1.02e-91

RNA polymerase sigma factor RpoS; 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 RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 131447 [Multi-domain]  Cd Length: 285  Bit Score: 276.61  E-value: 1.02e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  88 DRLKFDISELSADSIQMYLREIGKVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGSkGLSLLDLIQE 167
Cdd:TIGR02394   1 EFKKAETETRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNR-GLPLLDLIEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 168 GNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEM 247
Cdd:TIGR02394  80 GNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 248 GETIDKVRYIIKISQDTISLETSVGEDDEDSTLeDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRFGLL 327
Cdd:TIGR02394 160 DKPVEDVSRVLALNERITSLDAPLDDDSSKSLL-DTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLL 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1958115121 328 DGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:TIGR02394 239 GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 61-362 3.91e-88

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 268.75  E-value: 3.91e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  61 EDSGGFLDVDANVKKAGQLTSILGSDKDRLKFDISELSADSIQMYLREIGKVPLLTTEEEIELAKRKERGDKDAERKLIE 140
Cdd:PRK05657   14 FDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDFAARQRMIE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 141 ANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHMVETI 220
Cdd:PRK05657   94 SNLRLVVKIAKRYL-NRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKEL 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 221 NKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGEdDEDSTLEDFIEDVKNVTPDRAAALQL 300
Cdd:PRK05657  173 NVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGG-DPEKSLLDILADEQENGPEDTTQDDD 251

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958115121 301 LKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQKH 362
Cdd:PRK05657  252 MKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 97-361 5.44e-79

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 245.52  E-value: 5.44e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  97 LSADSIQMYLREIGKVPLLTTEEEI-----------------------------------------ELAKRKERGDKdAE 135
Cdd:PRK05949   15 FSADMVRTYLHEIGRVPLLTHEQEIvygkqvqqmmslleakealakklgrepslpewaeavnlsetELKQTLKQGKR-AK 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 136 RKLIEANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVH 215
Cdd:PRK05949   94 QKMIEANLRLVVAIAKKYQ-KRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIH 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 216 MVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGeDDEDSTLEDFIEDvKNVTPDRA 295
Cdd:PRK05949  173 ITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVG-DNQDTELSELLED-EGPSPDQY 250

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958115121 296 AALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:PRK05949  251 ITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 115-371 1.01e-76

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 242.47  E-value: 1.01e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 115 LTTEEeielAKRKERGDKDAERKLIEANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWW 194
Cdd:PRK07598  161 LTVEE----LEQIQKQGLRAKEHMIKANLRLVVSVAKKYQ-NRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 195 IRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGEd 274
Cdd:PRK07598  236 IRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGK- 314

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 275 DEDSTLEDFIEdVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYK 354
Cdd:PRK07598  315 DKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESK 393

                         250
                  ....*....|....*..
gi 1958115121 355 TLEKIQKHSLIKKLKDY 371
Cdd:PRK07598  394 ALQKLRQPKRRNRIRDY 410
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 94-361 7.46e-75

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 234.65  E-value: 7.46e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  94 ISELSADSIQMYLREIGKVPLLTTEEEIELAKRKER---------------GDKD------------------------- 133
Cdd:PRK07405    2 TAKTSTDLVRTYLREIGRVPLLTHEEEILYGKQVQRlvalqeireelaeelGREPtdaewakaaklseeelrsaiaegea 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 134 AERKLIEANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIP 213
Cdd:PRK07405   82 AKRKMVEANLRLVVSVAKKYL-KRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLP 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 214 VHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGeDDEDSTLEDFIEDvKNVTPD 293
Cdd:PRK07405  161 IHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVG-DNQDTELGELLED-TGASPE 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958115121 294 RAAALQLLKDYVHEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:PRK07405  239 DFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 101-361 3.03e-50

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 169.97  E-value: 3.03e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 101 SIQMYLREIGKVPLLTTEEEIELAKR-KERGDKDAERKLIEANLRLVVSIAKKFAGSkGLSLLDLIQEGNIGLFRAVEKF 179
Cdd:PRK06596   15 NLDAYIQAVNKIPMLTAEEEYMLAKRlREHGDLEAAKQLVLSHLRFVVHIARGYRGY-GLPQADLIQEGNIGLMKAVKRF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 180 EYRKGYKFSTYATWWIRQAItrsladQS---RTIRIpVHMVETINkfqhiQRQLIQDLGR-----EPL-PEE---IASEM 247
Cdd:PRK06596   94 DPEVGVRLVSFAVHWIKAEI------HEyilRNWRI-VKVATTKA-----QRKLFFNLRKakkrlGWLnPEEvemVAEEL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 248 GETIDKVRYI-IKISQDTISLETSVGEDDEDST-LEDFIEDvKNVTPDRAAA----LQLLKDYVHEIITQLTPREQKILE 321
Cdd:PRK06596  162 GVSEEEVREMeSRLSGQDASLDAPIDDDDEESGaPQDYLED-KSSDPADVLEednwEDQRRALLADALEGLDERSRDIIE 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1958115121 322 MRFgLLDGVShTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:PRK06596  241 ARW-LDDDKS-TLQELAAEYGVSAERVRQIEKNAMKKLKA 278
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 100-361 2.98e-46

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: 158.98  E-value: 2.98e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 100 DSIQMYLREIGKVPLLTTEEEIELAKR-KERGDKDAERKLIEANLRLVVSIAKKFAGSkGLSLLDLIQEGNIGLFRAVEK 178
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRlREHGDLDAAKKLVLSHLRFVVKIARGYRGY-GLPQADLIQEGNIGLMKAVKR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 179 FEYRKGYKFSTYATWWIRQAITRSLAdqsRTIRIpVHMVETINkfqhiQRQL-------IQDLGREPLPEE---IASEMG 248
Cdd:TIGR02392  80 FDPERGVRLVSFAVHWIKAEIHEYIL---RNWRL-VKVATTKA-----QRKLffnlrkmKKRLQGWLNPEEveaIAEELG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 249 ETIDKVRYI-IKISQDTISLETSVGEDDEDST-LEDFIEDvKNVTPDRAAA----LQLLKDYVHEIITQLTPREQKILEM 322
Cdd:TIGR02392 151 VSEREVREMeSRLSGQDMSLNASIDDDEDDGGaPIAYLVD-KRSDPEDTLEeeqwEELQRQALANALGSLDARSRRIIEA 229

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1958115121 323 RFglLDGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:TIGR02392 230 RW--LDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 119-362 3.09e-43

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: 149.97  E-value: 3.09e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 119 EEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQA 198
Cdd:COG1191     1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 199 ITRSLADQSrtiRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQ--DTISLETSVGEDDe 276
Cdd:COG1191    81 ILDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGD- 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 277 dstleDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRF--GLldgvshTLEEVGAEFDVTRERIRQIEYK 354
Cdd:COG1191   157 -----DLLDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYfeEL------TLKEIAEVLGVSESRVSRLHKK 225


                  ....*...
gi 1958115121 355 TLEKIQKH 362
Cdd:COG1191   226 ALARLREY 233
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 111-361 6.49e-37

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 134.78  E-value: 6.49e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 111 KVPLLTTEEEIELAKR-KERGDKDAERKLIEANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFST 189
Cdd:PRK07500   17 KAPYLEREEEHALAYRwKDHRDEDALHRIISAHMRLVISMAGKFR-RFGLPMNDLIQEGYVGLLEAAARFEPDREVRFST 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 190 YATWWIRQAItrsladQSRTIRiPVHMVET----------INkFQHIQRQLIQD---LGREPLPEEIASEMGETIDKVRY 256
Cdd:PRK07500   96 YATWWIRASI------QDYILR-NWSIVRGgtssaqkalfFN-LRRLRARLAQAdeeLTKQEIHREIATALGVSLSDVEM 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 257 I-IKISQDTISLETSVGEDDEDSTLE-DFIEDVKNVTPDRAAAL---QLLKDYVHEIITQLTPREQKILEMRfgLLDGVS 331
Cdd:PRK07500  168 MdARLSGPDASLNAPQSEEDEGRSERmDFLVDDSPLPDEQVESSidgERRRRWLTQALQTLNERELRIIRER--RLREDG 245

                         250       260       270
                  ....*....|....*....|....*....|
gi 1958115121 332 HTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:PRK07500  246 ATLEALGEELGISKERVRQIEARALEKLRR 275
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 131-361 3.67e-34

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 125.80  E-value: 3.67e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 131 DKDAERKLIEANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTI 210
Cdd:TIGR02980   1 DKEAREKLVELNLPLVRSIARRFR-NRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 211 RIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQD--TISLETSVGEDDEDS-TLEDFIEDV 287
Cdd:TIGR02980  80 RVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVEALEAGNAyqALSLDASIEDDDGDPiALLDTLGDE 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958115121 288 KNvtpdraaALQLLKDY--VHEIITQLTPREQKILEMRFglldGVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:TIGR02980 160 DD-------ALETVEDRlaLKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
111-362 5.78e-30

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 115.43  E-value: 5.78e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 111 KVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTY 190
Cdd:PRK08215   15 KLPVLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNN-RGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTY 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 191 ATWWIRQAITRSLADQSrTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETS 270
Cdd:PRK08215   94 AVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEP 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 271 VGEDDEDST-LEDFIEDVKNVTPDRAAALQLlkdyvHEIITQLTPREQKILEMRFglLDGvsHTLEEVGAEFDVTRERIR 349
Cdd:PRK08215  173 IYHDGGDPIyVMDQISDEKNKDENWLEEIAL-----KEAMKKLNDREKLILNLRF--FQG--KTQMEVAEEIGISQAQVS 243

                         250
                  ....*....|...
gi 1958115121 350 QIEYKTLEKIQKH 362
Cdd:PRK08215  244 RLEKAALKHMRKY 256
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 138-361 1.83e-28

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 110.44  E-value: 1.83e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 138 LIEANLRLVVSIAKKFAG--SKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAI---TRSLADQSRTIRI 212
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVglPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 213 PVHMVEtinkfqHIQRQLIQDLGREPLPEEIASEMGETIDKVR----YIIKISQdtISLETSVGEDDEDSTLEDFIEDVK 288
Cdd:TIGR02479  81 KARKLE------RAIRELEARLGREPTEEEIAEELGMDLKEYRqalnEINALSL--VSLDELLESGDDGGSLIDRIEDDK 152

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958115121 289 NVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRF--GLldgvshTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:TIGR02479 153 SEDPEEELEREELREALAEAIESLSEREQLVLSLYYyeEL------NLKEIGEVLGLTESRVSQIHSQALKKLRA 221
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 121-361 5.80e-26

RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131931 [Multi-domain]  Cd Length: 231  Bit Score: 104.03  E-value: 5.80e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 121 IELAKRkerGDKDAERKLIEANLRLVVSIAKKFAgSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAIT 200
Cdd:TIGR02885   2 IKLAQN---GDKEARDKLIECNLRLVWSIVKRFL-NRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 201 RSLADQSrTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGEDDEDS-T 279
Cdd:TIGR02885  78 RFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPiY 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 280 LEDFIEDVKNVTPDRAAALQLlkdyvHEIITQLTPREQKILEMRFglldGVSHTLEEVGAEFDVTRERIRQIEYKTLEKI 359
Cdd:TIGR02885 157 LLDQIADKGSEDSDWLEKIAL-----KEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKM 227


                  ..
gi 1958115121 360 QK 361
Cdd:TIGR02885 228 KE 229
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
111-362 8.50e-24

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 98.51  E-value: 8.50e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 111 KVPLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTY 190
Cdd:PRK05572   10 KKPQLKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLN-RGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTY 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 191 ATWWIRQAITRSLADQSrTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETS 270
Cdd:PRK05572   89 AVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHET 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 271 VGEDDEDS-TLEDFI-EDVKNVTPDRAAalqllkdyVHEIITQLTPREQKILEMRFgLLDgvsHTLEEVGAEFDVTRERI 348
Cdd:PRK05572  168 VHENDGDPiTLLDQIaDQSEEDWFDKIA--------LKEAIRELDERERLIVYLRY-FKD---KTQSEVAKRLGISQVQV 235

                         250
                  ....*....|....
gi 1958115121 349 RQIEYKTLEKIQKH 362
Cdd:PRK05572  236 SRLEKKILKQMKEK 249
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
115-361 9.00e-23

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 95.40  E-value: 9.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 115 LTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGSkGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYAtww 194
Cdd:PRK05803   31 LSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENT-GEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA--- 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 195 irqaitrsladqSRTIRIPVHMvetinkfqHIqRQLiqdlgreplpeeiasemgetidkvryiiKISQDTISLETSVGED 274
Cdd:PRK05803  107 ------------ARCIENEILM--------HL-RNL----------------------------KKTKKEVSLQDPIGVD 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 275 DEDS--TLEDFIEDVKNVTPDRA-AALQLLKDYvhEIITQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQI 351
Cdd:PRK05803  138 KEGNeiSLIDILGSEEDDVIEQVeLKMEVEKLY--KKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRI 215

                         250
                  ....*....|
gi 1958115121 352 EYKTLEKIQK 361
Cdd:PRK05803  216 EKRALKKLFK 225
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 138-209 4.58e-21

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: 85.72  E-value: 4.58e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958115121 138 LIEANLRLVVSIAKKFAGSkGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRT 209
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGD-GADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 137-324 6.48e-21

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 90.75  E-value: 6.48e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 137 KLIEANLRLVVSIAKKFAGSKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHM 216
Cdd:PRK07408   29 QLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 217 VETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQ--DTISLETSVGEDDEDST-LEDFIEDVknvtpd 293
Cdd:PRK07408  109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQnrTPLSLDAPVNQDEDGSTsLGDLLPDP------ 182

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1958115121 294 RAAALQL-LKDYVH--EIITQLTPREQKILEMRF 324
Cdd:PRK07408  183 RYRSFQLaQEDRIRlqQALAQLEERTREVLEFVF 216
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
115-361 1.22e-20

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 89.72  E-value: 1.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 115 LTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGS--KGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYAT 192
Cdd:PRK07670    4 LTYEEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGlpKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYAS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 193 WWIRQAITRSLADQSrtiRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKIS--QDTISLETS 270
Cdd:PRK07670   84 FRIRGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGffANLLSIDEK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 271 VGEDDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILemrfGLLDGVSHTLEEVGAEFDVTRERIRQ 350
Cdd:PRK07670  161 THDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVI----SLFYKEELTLTEIGQVLNLSTSRISQ 236

                         250
                  ....*....|.
gi 1958115121 351 IEYKTLEKIQK 361
Cdd:PRK07670  237 IHSKALFKLKK 247
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 107-367 2.75e-20

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 89.36  E-value: 2.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 107 REIGKVPLLTTEEEIELAKR-KERGDKDAERKLIEANLRLVVSIAKKFAGS--KGLSLLDLIQEGNIGLFRAVEKFEYRK 183
Cdd:PRK06288    4 KMSGKIPKYAQQDETELWREyKKTGDPKIREYLILKYSPLVKYVAGRIAVGmpQNVEFDDLVSYGVFGLIDAIEKFDPER 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 184 GYKFSTYATWWIRQAI---TRSLADQSRTIRIPVHMVETINKFqhiqrqLIQDLGREPLPEEIASEMGETIDKVRYII-K 259
Cdd:PRK06288   84 EIKFKTYAVTRIRGAIfdeLRSIDWIPRSVRQKARQIERAIAM------LEARLGRTPSDEEIADELGISLEEYNSLLsK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 260 ISQ-DTISLET--SVGEDDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRF--GLldgvshTL 334
Cdd:PRK06288  158 LSGtSVVSLNDlwFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYyeDL------TL 231

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1958115121 335 EEVGAEFDVTRERIRQIEYKTLEKIQ-KHSLIKK 367
Cdd:PRK06288  232 KEIGKVLGVTESRISQLHTKAVLQLRaKLAEIKK 265
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 218-296 2.27e-19

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


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 81.50  E-value: 2.27e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958115121 218 ETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQDTISLETSVGeDDEDSTLEDFIEDVKNVTPDRAA 296
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVG-EEEDGELGDLLEDDDIESPEEAV 78
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
113-361 5.42e-17

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 79.13  E-value: 5.42e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 113 PLLTTEEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGSkGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYAT 192
Cdd:PRK08301   32 PPLSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENT-GINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 193 WWIRQAITRSLADQSRTiRIPVHMVETINkfqhiqrqlIQDLGREPLPEEIASEMGETIDKvryiikisqdtiSLETSVg 272
Cdd:PRK08301  111 RCIENEILMYLRRNNKV-KAEVSFDEPLN---------IDWDGNELLLSDVLGTDNDIIYK------------DIEDEV- 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 273 eddedstledfiedvknvtpDRaaalQLLKDYVHeiitQLTPREQKILEMRFGLLDGVSHTLEEVGAEFDVTRERIRQIE 352
Cdd:PRK08301  168 --------------------DR----KLLKKALK----KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLE 219


                  ....*....
gi 1958115121 353 YKTLEKIQK 361
Cdd:PRK08301  220 KRIIKRLKK 228
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 163-369 3.48e-15

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 74.11  E-value: 3.48e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 163 DLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAI---TRSLADQSRTIRIPVHMVEtinkfqHIQRQLIQDLGREPL 239
Cdd:PRK06986   40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldeLRSLDWVPRSVRRNAREVA------QAIRQLEQELGREPT 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 240 PEEIASEMGETIDKVRYI---IKISQdTISLETSVGEDDEDSTLedfIEDVKNVTPDRAAALQLLKDYVHEIITQLTPRE 316
Cdd:PRK06986  114 DTEVAEKLGLSLEEYREMlldTNISQ-LFSIDELRGEHGDSILV---TEDHQDEDPLQQLEDEELREALVEAIESLPERE 189

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958115121 317 QKILEM--RFGLldgvshTLEEVGAEFDVTRERIRQIeyktlekiqkHS-LIKKLK 369
Cdd:PRK06986  190 QLVLSLyyQEEL------NLKEIGAVLGVSESRVSQI----------HSqAIKRLR 229
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 115-360 3.67e-13

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 68.57  E-value: 3.67e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 115 LTTEEEIELAKR-KERGDKDAERKLIEANLRLVVSIAKKFagSKGLSLL-DLIQEGNIGLFRAVEKFEYRKGYKFSTYAT 192
Cdd:PRK08583   10 LTKEEVNKWIAEyQENQDEEAQEKLVKHYKNLVESLAYKY--SKGQSHHeDLVQVGMVGLLGAIRRYDPSFGRSFEAFAV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 193 WWIRQAITRSLADQSRTIRIPVHMVETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVRYIIKISQ--DTISLETS 270
Cdd:PRK08583   88 PTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHS 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 271 VGEDDEDSTLEdFIEDVKNVTP--DRAAALQLLKDyvheIITQLTPREQKILEMRFglLDGVSHtlEEVGAEFDVTRERI 348
Cdd:PRK08583  168 IEADSDGSTVT-LLDIVGQQEDgyELTEQRMILEK----ILPVLSDREKSIIQCTF--IENLSQ--KETGERLGISQMHV 238

                         250
                  ....*....|..
gi 1958115121 349 RQIEYKTLEKIQ 360
Cdd:PRK08583  239 SRLQRQAIKKLR 250
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 133-362 3.76e-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: 66.60  E-value: 3.76e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 133 DAERKLIEANLRLVVSIAKKFAGSKGLSLlDLIQEGNIGLFRAVEKFEYRKgyKFSTYATWWIRQAITRSLADQSRTIRi 212
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAE-DLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRRLRR- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 213 pvhmvetinkfqhiqrqliqdlgreplpeeiasemgetidkvryiikisqdtisletsvgEDDEDSTLEDFIEdvknvTP 292
Cdd:TIGR02937  77 ------------------------------------------------------------ELDLLEELLDSDP-----SP 91

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 293 DRAAALQLLKDYVHEIITQLTPREQKILEMRFglLDGVSHtlEEVGAEFDVTRERIRQIEYKTLEKIQKH 362
Cdd:TIGR02937  92 EEELEQEEEREALREALEKLPEREREVLVLRY--LEGLSY--KEIAEILGISVGTVKRRLKRARKKLREL 157
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 137-324 6.37e-13

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 68.26  E-value: 6.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 137 KLIEANLRLVVSIAKKFAGsKGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSRTIRIPVHM 216
Cdd:PRK07122   44 RIVTRCLPLADHIARRFDG-RGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRL 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 217 VETINKFQHIQRQLIQDLGREPLPEEIASEMGETIDKV--RYIIKISQDTISLETSVGEDDEDS-----TLEDFIEDVKN 289
Cdd:PRK07122  123 KELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVveGLVAGSAYNTLSIDSGGGSGDDDAraiadTLGDVDAGLDQ 202

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1958115121 290 VTpDRAAALQLLKdyvheiitQLTPREQKILEMRF 324
Cdd:PRK07122  203 IE-NREALRPLLA--------ALPERERTVLVLRF 228
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
100-132 1.89e-12

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 60.79  E-value: 1.89e-12
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958115121 100 DSIQMYLREIGKVPLLTTEEEIELAKRKERGDK 132
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDE 33
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
115-343 4.45e-10

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 58.77  E-value: 4.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 115 LTTEEEIELAKRkerGDKDAERKLIEANLRLVVSIAKKFAGSkGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWW 194
Cdd:PRK08295    9 LEDEELVELARS---GDKEALEYLIEKYKNFVRAKARSYFLI-GADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELC 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 195 I-RQAITrsladqsrtiripvhMVETINKFQHIqrqliqdlgrePLpeeiasemgetidkvryiikisQDTISLETSVGE 273
Cdd:PRK08295   85 ItRQIIT---------------AIKTANRQKHI-----------PL----------------------NSYVSLDKPIYD 116

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958115121 274 DDEDSTLEDFIEDVKNVTPDRAAALQLLKDYVHEIITQ-LTPREQKILEMrfgLLDGVSHtlEEVGAEFDV 343
Cdd:PRK08295  117 EESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEElLSELEKEVLEL---YLDGKSY--QEIAEELNR 182
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 311-361 7.01e-10

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: 53.97  E-value: 7.01e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958115121 311 QLTPREQKILEMRFGlldgVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQK 361
Cdd:pfam04545   4 SLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 11-130 7.11e-10

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 60.58  E-value: 7.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121  11 KALDDLVAKVRPRGFVTETELLQVFP-------QVENyiydyelTLERLQRNSIRIIEDSGGFLDVDANVKKAGQLT--- 80
Cdd:PRK05658   11 SQLKKLIKRGKERGYLTYAELNDHLPedivdseQIED-------IIAMLNDMGIQVVEEAPDADDLLLAENEADAQTded 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958115121  81 ----SILGSDKDRLKFDISElsaDSIQMYLREIGKVPLLTTEEEIELAKRKERG 130
Cdd:PRK05658   84 aeeeAAAALSSVESEIGRTD---DPVRMYLREMGTVELLTREGEIEIAKRIEAG 134
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 138-360 1.44e-09

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 58.09  E-value: 1.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 138 LIEANLRLVVSIAKKFAGS--KGLSLLDLIQEGNIGLFRAVEKFEYRKGYKFSTYATWWIRQAITRSLADQSrtiRIPVH 215
Cdd:PRK05911   28 LIEFYLPLVKNVAHRLISGmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---WVPRS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 216 MVETINKFQHIQRQLIQDLGREPLPEEIA-------SEMGETIDKVRYIIKISqdtISLETSVGEDDEDS-TLEDFIEDV 287
Cdd:PRK05911  105 VHQKANKLADAMDSLRQSLGKEPTDGELCeylnisqQELSGWFSSARPALILS---LNEEFPCQSDDEAGlALEERIADE 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958115121 288 KNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRFglLDGVshTLEEVGAEFDVTRERIRQIEYKTLEKIQ 360
Cdd:PRK05911  182 RAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY--YEEL--VLKEIGKILGVSESRVSQIHSKALLKLR 250
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 302-360 2.29e-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: 52.88  E-value: 2.29e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958115121 302 KDYVHEIITQLTPREQKILEMRFGlldgVSHTLEEVGAEFDVTRERIRQIEYKTLEKIQ 360
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
135-360 4.98e-04

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 41.00  E-value: 4.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 135 ERKLIEANLRLVVSIAKKFA--GSKGLSLLDLIQEGNIGLFRAVEKFEYRKGyKFSTYATWWIRQAIT---RSLADQSRT 209
Cdd:PRK12427   17 EGKYLNAYLPLVKKVVRQLAfqADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 210 IRIPVHmvetinKFQHIQRQLIQDLGREPLPEEIASEMGETIDKVryiikisQDTISLETSVGEDDEDSTLEDfieDVKN 289
Cdd:PRK12427   96 LRQKTH------KTNDAIREIAKRLGHEPNFEEISAELNLTAEEY-------QEYLLLENAGTLESLDELLAL---EAHN 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958115121 290 VTPD-RAAALQLL-KDYVHEIITQLTPREQKILEMRFglldgvSH--TLEEVGAEFDVTRERIRQIEYKTLEKIQ 360
Cdd:PRK12427  160 DILQsRDLEENIIiEDNLKQALSQLDEREQLILHLYY------QHemSLKEIALVLDLTEARICQLNKKIAQKIK 228
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 118-362 1.94e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 38.82  E-value: 1.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 118 EEEIELAKRKERGDKDAERKLIEANLRLVVSIAKKFAGSKGLSLlDLIQEGNIGLFRAVEKFEYRKgyKFSTYATwwirq 197
Cdd:COG1595     2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAE-DLVQETFLRLWRKLDSFRGRG--SFRAWLY----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 198 AITRSLAdqsrtiripvhmvetINKFQHIQRqliqdlgREPLPEEIASEMGETidkvryiikisqdtisletsvgedded 277
Cdd:COG1595    74 RIARNLA---------------IDHLRKRRR-------RRELLDELAEELPDE--------------------------- 104

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958115121 278 stledfiedvkNVTPDRAAALQLLKDYVHEIITQLTPREQKILEMRFglLDGVSHtlEEVGAEFDVTRERIRQIEYKTLE 357
Cdd:COG1595   105 -----------AADPEEALEAEELLEALLAALERLPPRQREVLVLRY--LEGLSY--AEIAEILGISEGTVKSRLSRARK 169


                  ....*
gi 1958115121 358 KIQKH 362
Cdd:COG1595   170 KLREA 174
 
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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