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Conserved domains on  [gi|581500401|gb|EVP09062|]
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RNA polymerase sigma factor rpoD [Staphylococcus aureus M1094]

Protein Classification

RNA polymerase sigma factor RpoD/SigA( domain architecture ID 11483650)

RNA polymerase sigma factor RpoD/SigA is the primary sigma factor during exponential growth

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 9-368 0e+00

RNA polymerase sigma factor RpoD; Validated


:

Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 720.62  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401   9 KKQTIDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNP---- 84
Cdd:PRK09210   1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEeeee 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  85 ---SDLSAPPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLI 161
Cdd:PRK09210  81 eldNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 162 QEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGE 241
Cdd:PRK09210 161 QEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAE 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 242 EMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 321
Cdd:PRK09210 241 EMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 320

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*..
gi 581500401 322 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:PRK09210 321 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 9-368 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 720.62  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401   9 KKQTIDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNP---- 84
Cdd:PRK09210   1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEeeee 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  85 ---SDLSAPPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLI 161
Cdd:PRK09210  81 eldNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 162 QEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGE 241
Cdd:PRK09210 161 QEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAE 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 242 EMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 321
Cdd:PRK09210 241 EMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 320

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*..
gi 581500401 322 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:PRK09210 321 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 101-368 3.48e-173

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: 482.25  E-value: 3.48e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 101 MYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKG 180
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 181 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEP 260
Cdd:COG0568   81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 261 VSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTR 340
Cdd:COG0568  161 VSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSR 240

                        250       260
                 ....*....|....*....|....*...
gi 581500401 341 ERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:COG0568  241 ERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 131-368 1.67e-165

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: 461.77  E-value: 1.67e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  131 AKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  211 HMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDH 290
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401  291 AAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 214-291 6.54e-30

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: 109.62  E-value: 6.54e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401  214 ETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHA 291
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 297-355 5.62e-14

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: 65.59  E-value: 5.62e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 581500401 297 KEQLEDVLDTLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 9-368 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 720.62  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401   9 KKQTIDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNP---- 84
Cdd:PRK09210   1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEeeee 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  85 ---SDLSAPPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLI 161
Cdd:PRK09210  81 eldNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 162 QEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGE 241
Cdd:PRK09210 161 QEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAE 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 242 EMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 321
Cdd:PRK09210 241 EMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 320

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*..
gi 581500401 322 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:PRK09210 321 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 3-368 0e+00

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 523.02  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401   3 DNTVKIKKQTIDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEK- 81
Cdd:PRK05901  98 DELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKe 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  82 -------------------LNPSDLSAPPGvKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQG--------------- 127
Cdd:PRK05901 178 leklsddddfvwdeddseaLRQARKDAKLT-ATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGlyaeellaegekldp 256

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 128 ------------DEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAI 195
Cdd:PRK05901 257 elrrdlqwigrdGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAI 336

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 196 TRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHL 275
Cdd:PRK05901 337 TRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQF 416

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 276 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK05901 417 GDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496

                        410
                 ....*....|...
gi 581500401 356 HPSRSKRLKDFMD 368
Cdd:PRK05901 497 HPSRSQVLRDFLD 509
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 101-368 3.48e-173

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: 482.25  E-value: 3.48e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 101 MYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKG 180
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 181 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEP 260
Cdd:COG0568   81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 261 VSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTR 340
Cdd:COG0568  161 VSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSR 240

                        250       260
                 ....*....|....*....|....*...
gi 581500401 341 ERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:COG0568  241 ERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 131-368 1.67e-165

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: 461.77  E-value: 1.67e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  131 AKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  211 HMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDH 290
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401  291 AAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 131-368 6.14e-159

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 459.65  E-value: 6.14e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 131 AKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
Cdd:PRK05658 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 460

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 211 HMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDH 290
Cdd:PRK05658 461 HMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDA 540

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401 291 AAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:PRK05658 541 AIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 56-367 4.05e-137

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 395.31  E-value: 4.05e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  56 DDFFDQLNDNDISLVNEKDSSDTDEK---LNPSDLSaPPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRI-------- 124
Cdd:PRK07406  20 TDDLDSDEDEESSSENADELSEKEAKakaLARIKIG-PKKVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIadllelee 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 125 -------EQGDEV-------------------------AKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172
Cdd:PRK07406  99 lreqfesELGREPsdkewaelvdmplpkfrrrlmlgrrAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAA 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 173 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVRE 252
Cdd:PRK07406 179 EKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRF 258

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 253 ILKIAQEPVSLETPIGEEDDSHLGDFIEdQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332
Cdd:PRK07406 259 IAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEI 337

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 581500401 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
Cdd:PRK07406 338 GQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 97-366 1.02e-136

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 392.17  E-value: 1.02e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  97 DPVRMYLKEIGRVNLLSAQEEIELAKRIEQG---------------------------DEVAKSRLAEANLRLVVSIAKR 149
Cdd:PRK07921  26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGlyaehlletrkrlsearkrdlaavvrdGEAARRHLLEANLRLVVSLAKR 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 150 YVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQD 229
Cdd:PRK07921 106 YTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQ 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 230 LGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTD 309
Cdd:PRK07921 186 LGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDE 265

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 581500401 310 REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDF 366
Cdd:PRK07921 266 REQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 97-355 6.31e-128

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: 368.88  E-value: 6.31e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401   97 DPVRMYLKEIGRVNLLSAQEEIELA-----------------------------------------KRIEQGdEVAKSRL 135
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELArqvqqmmvleelreeleeqlgrepskeewaaaaglseaelrQRLRQG-QRAKEKM 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  136 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215
Cdd:TIGR02997  80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDqEAQSPSDHAAYEL 295
Cdd:TIGR02997 160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVERES 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  296 LKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:TIGR02997 239 LRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 97-356 2.92e-102

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: 303.18  E-value: 2.92e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401   97 DPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFD 176
Cdd:TIGR02394  13 DVTQLYLREIGFKPLLTAEEEIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFD 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  177 FNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKI 256
Cdd:TIGR02394  93 PERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLAL 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  257 AQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVF 336
Cdd:TIGR02394 173 NERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEV 252

                         250       260
                  ....*....|....*....|
gi 581500401  337 GVTRERIRQIEAKALRKLRH 356
Cdd:TIGR02394 253 GLTRERVRQIQVEALKKLRR 272
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 39-355 1.24e-98

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 295.33  E-value: 1.24e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  39 EEIAEKLQNFDIDSDQMDDFfdqlnDNDISLVNEKDSSDTDEklnPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQEEI 118
Cdd:PRK05657   3 LKVHDLNEDADFDENGVEVF-----DEKALVEEEPSDNDLAE---EELLSQGATQRVLDATQLYLNEIGYSPLLTAEEEV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRA 198
Cdd:PRK05657  75 YFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 199 IADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDF 278
Cdd:PRK05657 155 IMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDI 234

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 581500401 279 IEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK05657 235 LADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 97-355 1.08e-89

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 272.87  E-value: 1.08e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  97 DPVRMYLKEIGRVNLLSAQEEI-----------------------------------------ELAKRIEQGDEvAKSRL 135
Cdd:PRK05949  18 DMVRTYLHEIGRVPLLTHEQEIvygkqvqqmmslleakealakklgrepslpewaeavnlsetELKQTLKQGKR-AKQKM 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 136 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215
Cdd:PRK05949  97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDqEAQSPSDHAAYEL 295
Cdd:PRK05949 177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLED-EGPSPDQYITQEL 255

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 296 LKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK05949 256 LRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 97-355 2.50e-89

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 271.63  E-value: 2.50e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  97 DPVRMYLKEIGRVNLLSAQEEIELAKRIEQ----------------------------------------GDEVAKSRLA 136
Cdd:PRK07405   8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRlvalqeireelaeelgreptdaewakaaklseeelrsaiaEGEAAKRKMV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 137 EANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETI 216
Cdd:PRK07405  88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 217 NKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDqEAQSPSDHAAYELL 296
Cdd:PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLED-TGASPEDFATQSSL 246

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 581500401 297 KEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK07405 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 61-368 4.87e-89

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 274.05  E-value: 4.87e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  61 QLNDNDISLVNEKDSSDTDEKL-----NPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE---------- 125
Cdd:PRK07598  19 QALDPDILEDDPDDSLDDVQELeiaaaDEAVETAARNRRSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQrymklivlan 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 126 ---QGDEV---------------------------------------------------------------------AKS 133
Cdd:PRK07598  99 aakEGDEVikpylrlievrerltselghrpslerwaktadisladlkptlaegkrrwaeiakltveeleqiqkqglrAKE 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 134 RLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 213
Cdd:PRK07598 179 HMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHIT 258

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 214 ETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEdQEAQSPSDHAAY 293
Cdd:PRK07598 259 EKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMR 337

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 581500401 294 ELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368
Cdd:PRK07598 338 ESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 102-355 9.23e-51

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 171.13  E-value: 9.23e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKG 180
Cdd:PRK06596  19 YIQAVNKIPMLTAEEEYMLAKRLrEHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVG 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 181 FKFSTYATWWIRQAITRAIadqARTIRIpVHMVETIN--KL---IRVQRQLLQDLGRDPApEEIGEEMDLPAEKVREI-L 254
Cdd:PRK06596  99 VRLVSFAVHWIKAEIHEYI---LRNWRI-VKVATTKAqrKLffnLRKAKKRLGWLNPEEV-EMVAEELGVSEEEVREMeS 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 255 KIAQEPVSLETPIGEEDDSH------LGDFIEDQEAQSpSDHAAYELLKEQLEDVLDTLTDREENVLRLRFgLDDGRTrT 328
Cdd:PRK06596 174 RLSGQDASLDAPIDDDDEESgapqdyLEDKSSDPADVL-EEDNWEDQRRALLADALEGLDERSRDIIEARW-LDDDKS-T 250

                        250       260
                 ....*....|....*....|....*..
gi 581500401 329 LEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK06596 251 LQELAAEYGVSAERVRQIEKNAMKKLK 277
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 116-355 3.90e-50

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: 167.69  E-value: 3.90e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 116 EEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFL-DLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQA 194
Cdd:COG1191    1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 195 ITRAIADQArtiRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQ--EPVSLETPIGEEDd 272
Cdd:COG1191   81 ILDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGD- 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 273 shlgDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALR 352
Cdd:COG1191  157 ----DLLDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEE----LTLKEIAEVLGVSESRVSRLHKKALA 228


                 ...
gi 581500401 353 KLR 355
Cdd:COG1191  229 RLR 231
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 102-355 2.24e-48

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: 164.38  E-value: 2.24e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKG 180
Cdd:TIGR02392   6 YIRAVNRIPMLTPEEEYQLAKRLrEHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERG 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  181 FKFSTYATWWIRQAITRAIadqARTIRIpVHMVETIN--KLIRVQRQLLQDLGRDPAPEE---IGEEMDLPAEKVREI-L 254
Cdd:TIGR02392  86 VRLVSFAVHWIKAEIHEYI---LRNWRL-VKVATTKAqrKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMeS 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  255 KIAQEPVSLETPIGEEDDS------HLGDFIEDQEAQSpSDHAAYELLKEQLEDVLDTLTDREENVLRLRFgLDDGRTrT 328
Cdd:TIGR02392 162 RLSGQDMSLNASIDDDEDDggapiaYLVDKRSDPEDTL-EEEQWEELQRQALANALGSLDARSRRIIEARW-LDDDKL-T 238

                         250       260
                  ....*....|....*....|....*..
gi 581500401  329 LEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:TIGR02392 239 LQELAAEYGVSAERIRQIEKNAMKKLK 265
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 111-355 6.10e-38

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 137.47  E-value: 6.10e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 111 LLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATW 189
Cdd:PRK07500  20 YLEREEEHALAYRWkDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATW 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 190 WIRQAItraiadQARTIRiPVHMVET----------INkLIRVQRQLLQD---LGRDPAPEEIGEEMDLPAEKVREI-LK 255
Cdd:PRK07500 100 WIRASI------QDYILR-NWSIVRGgtssaqkalfFN-LRRLRARLAQAdeeLTKQEIHREIATALGVSLSDVEMMdAR 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 256 IAQEPVSLETPIGEEDDSHLG--DFIEDQEAQSP---SDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGrtRTLE 330
Cdd:PRK07500 172 LSGPDASLNAPQSEEDEGRSErmDFLVDDSPLPDeqvESSIDGERRRRWLTQALQTLNERELRIIRERRLREDG--ATLE 249

                        250       260
                 ....*....|....*....|....*
gi 581500401 331 EVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK07500 250 ALGEELGISKERVRQIEARALEKLR 274
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
105-355 3.33e-35

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 129.30  E-value: 3.33e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 105 EIGRVN-----LLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNK 179
Cdd:PRK08215   7 EICGVNtsklpVLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQ 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 180 GFKFSTYATWWIRQAITRAIADQaRTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQE 259
Cdd:PRK08215  87 NVKFSTYAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQD 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 260 PVSLETPIGEE--DDSHLGDFIEDQEAQspsDHAAYELLkeQLEDVLDTLTDREENVLRLRFGldDGRTRTleEVGKVFG 337
Cdd:PRK08215 166 PVSLFEPIYHDggDPIYVMDQISDEKNK---DENWLEEI--ALKEAMKKLNDREKLILNLRFF--QGKTQM--EVAEEIG 236

                        250
                 ....*....|....*...
gi 581500401 338 VTRERIRQIEAKALRKLR 355
Cdd:PRK08215 237 ISQAQVSRLEKAALKHMR 254
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 159-355 7.93e-35

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: 127.39  E-value: 7.93e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  159 DLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAI---TRAIADQARTIRIPVHMVEtinkliRVQRQLLQDLGRDPA 235
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKARKLE------RAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  236 PEEIGEEMDLPAEKVREILK--IAQEPVSLETPIGEEDDS-HLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREE 312
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 581500401  313 NVLRLRF--GLddgrtrTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:TIGR02479 182 LVLSLYYyeEL------NLKEIGEVLGLTESRVSQIHSQALKKLR 220
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
112-356 1.24e-33

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 124.67  E-value: 1.24e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 112 LSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYAtwwi 191
Cdd:PRK05803  31 LSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA---- 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 192 rqaitraiadqARTIRIPVHMvetinkLIRVQRQLLQDlgrdpapeeigeemdlpaekvreilkiaqepVSLETPIGEED 271
Cdd:PRK05803 107 -----------ARCIENEILM------HLRNLKKTKKE-------------------------------VSLQDPIGVDK 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 272 DSH---LGDFIEDqEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 348
Cdd:PRK05803 139 EGNeisLIDILGS-EEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEK 217


                 ....*...
gi 581500401 349 KALRKLRH 356
Cdd:PRK05803 218 RALKKLFK 225
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 118-355 1.21e-31

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: 119.43  E-value: 1.21e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  118 IELAKrieQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITR 197
Cdd:TIGR02885   2 IKLAQ---NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  198 AIADQArTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLgd 277
Cdd:TIGR02885  79 FLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPI-- 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401  278 FIEDQEAQSPSDHAAYeLLKEQLEDVLDTLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:TIGR02885 156 YLLDQIADKGSEDSDW-LEKIALKEAISKLDERERQIIMLRYFKD----KTQTEVANMLGISQVQVSRLEKKVLKKMK 228
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
112-355 3.13e-31

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 118.54  E-value: 3.13e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 112 LSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWI 191
Cdd:PRK05572  14 LKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMI 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 192 RQAITRAIADQArTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEED 271
Cdd:PRK05572  94 IGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHEND 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 272 DS--HLGDFIEDQEAQSPSDHAAyelLKEQLEDvldtLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAK 349
Cdd:PRK05572 173 GDpiTLLDQIADQSEEDWFDKIA---LKEAIRE----LDERERLIVYLRYFKD----KTQSEVAKRLGISQVQVSRLEKK 241


                 ....*.
gi 581500401 350 ALRKLR 355
Cdd:PRK05572 242 ILKQMK 247
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 214-291 6.54e-30

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: 109.62  E-value: 6.54e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401  214 ETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHA 291
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 125-355 2.41e-28

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 111.32  E-value: 2.41e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 125 EQGDEVAKSRLAEANLRLVVSIAKRyVGRGML----FLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAI---TR 197
Cdd:PRK06288  26 KTGDPKIREYLILKYSPLVKYVAGR-IAVGMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdeLR 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 198 AIADQARTIRIPVHMVEtinkliRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILK--IAQEPVSLET--PIGEEDDS 273
Cdd:PRK06288 105 SIDWIPRSVRQKARQIE------RAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDlwFGGDEGDE 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 274 -HLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRF--GLddgrtrTLEEVGKVFGVTRERIRQIEAKA 350
Cdd:PRK06288 179 vSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYyeDL------TLKEIGKVLGVTESRISQLHTKA 252


                 ....*
gi 581500401 351 LRKLR 355
Cdd:PRK06288 253 VLQLR 257
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
159-356 8.73e-27

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 106.67  E-value: 8.73e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 159 DLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITraiaDQARTI-RIPVHMVETINKLIRVQRQLLQDLGRDPAPE 237
Cdd:PRK07670  54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 238 EIGEEMDLPAEKVREILK--IAQEPVSL-ETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENV 314
Cdd:PRK07670 130 EVAAELGMTEEEVEATMNegFFANLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 581500401 315 LRLrFGLDDgrtRTLEEVGKVFGVTRERIRQIEAKALRKLRH 356
Cdd:PRK07670 210 ISL-FYKEE---LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 134-338 1.20e-25

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 103.85  E-value: 1.20e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 134 RLAEANLRLVVSIAKRYVGR-GMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212
Cdd:PRK07408  29 QLVELNLGLVRKEAHRWSNQcSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREIlKIAQ---EPVSLETPIGEEDDSH--LGDFIEDQEAQSp 287
Cdd:PRK07408 109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-KLALqnrTPLSLDAPVNQDEDGStsLGDLLPDPRYRS- 186

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 581500401 288 sdhaaYELLKE---QLEDVLDTLTDREENVLRLRFgLDDgrtRTLEEVGKVFGV 338
Cdd:PRK07408 187 -----FQLAQEdriRLQQALAQLEERTREVLEFVF-LHD---LTQKEAAERLGI 231
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 135-205 2.39e-24

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: 94.58  E-value: 2.39e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 581500401  135 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQART 205
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 132-355 9.80e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 96.00  E-value: 9.80e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 132 KSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 211
Cdd:PRK07122  42 RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRR 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 212 MVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKI--AQEPVSLETPIG--EEDDSHLGDFIEDQEAQsp 287
Cdd:PRK07122 122 LKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGsgDDDARAIADTLGDVDAG-- 199

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401 288 SDHAAYellKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVgkvfGVTRERIRQIEAKALRKLR 355
Cdd:PRK07122 200 LDQIEN---REALRPLLAALPERERTVLVLRFFESMTQTQIAERV----GISQMHVSRLLAKTLARLR 260
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
112-355 2.02e-21

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 91.46  E-value: 2.02e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 112 LSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWI 191
Cdd:PRK08301  34 LSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCI 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 192 RQAITRAIADQARTiRIPVHMVETINKLIRVQRQLLQDLgrdpapeeIGEEMDlpaekvrEILKiaqepvsletpigeed 271
Cdd:PRK08301 114 ENEILMYLRRNNKV-KAEVSFDEPLNIDWDGNELLLSDV--------LGTDND-------IIYK---------------- 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 272 dshlgdFIEDqeaqspsdhaayELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL 351
Cdd:PRK08301 162 ------DIED------------EVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRII 223


                 ....
gi 581500401 352 RKLR 355
Cdd:PRK08301 224 KRLK 227
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 131-355 3.32e-21

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 91.06  E-value: 3.32e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 131 AKSRLAEANLRLVVSIAKRYVGR--GMLFL-DLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQ---AR 204
Cdd:PRK06986   9 DQDELVEQYAPLVKRIALRLKARlpASVDLdDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdwvPR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 205 TIRIPVHMVETinklirVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQ--EPVSLETPIGEEDDSHLGdfIEDQ 282
Cdd:PRK06986  89 SVRRNAREVAQ------AIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNisQLFSIDELRGEHGDSILV--TEDH 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 581500401 283 EAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRL--RFGLDdgrtrtLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK06986 161 QDEDPLQQLEDEELREALVEAIESLPEREQLVLSLyyQEELN------LKEIGAVLGVSESRVSQIHSQAIKRLR 229
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 131-355 4.84e-18

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: 80.08  E-value: 4.84e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  131 AKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKgfKFSTYATWWIRQAITRAIADQARtiripv 210
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRR------ 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  211 hmvetinkLIRVQRQLLQDLGRDPAPEEigeemdlpaekvreilkiaqepvsletpigeeddshlgdfiedqeaqspsdH 290
Cdd:TIGR02937  74 --------LRRELDLLEELLDSDPSPEE---------------------------------------------------E 94

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 581500401  291 AAYELLKEQLEDVLDTLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:TIGR02937  95 LEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 24-137 2.10e-17

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 83.69  E-value: 2.10e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401  24 KQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSD------------TDEKLNPSDLSAPP 91
Cdd:PRK05658  14 KKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADdlllaeneadaqTDEDAEEEAAAALS 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 581500401  92 GVKIN-----DPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAE 137
Cdd:PRK05658  94 SVESEigrtdDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCE 144
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 125-355 4.09e-17

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 80.12  E-value: 4.09e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 125 EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQAR 204
Cdd:PRK08583  24 ENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTW 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 205 TIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQ--EPVSLETPIGEEDDSH---LGDFI 279
Cdd:PRK08583 104 SVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSIEADSDGStvtLLDIV 183

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581500401 280 EDQEaqspsdhAAYELLKEQ--LEDVLDTLTDREENVLRLRFglddGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK08583 184 GQQE-------DGYELTEQRmiLEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLR 250
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 135-355 6.41e-17

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 79.66  E-value: 6.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 135 LAEANLRLVVSIAKRYVGrGM----LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAItraIADQARTIRIPV 210
Cdd:PRK05911  28 LIEFYLPLVKNVAHRLIS-GMpshvKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPR 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 211 HMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEP--VSLETPIGEEDDSHLG----DFIEDQEA 284
Cdd:PRK05911 104 SVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPAliLSLNEEFPCQSDDEAGlaleERIADERA 183

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 581500401 285 QSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK05911 184 ETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLR 250
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 303-356 2.34e-14

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 66.68  E-value: 2.34e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 581500401  303 VLDTLTDREENVLRLRFGlddgRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 356
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
97-129 4.61e-14

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 65.41  E-value: 4.61e-14
                          10        20        30
                  ....*....|....*....|....*....|...
gi 581500401   97 DPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDE 129
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDE 33
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 297-355 5.62e-14

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: 65.59  E-value: 5.62e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 581500401 297 KEQLEDVLDTLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r1_1 pfam03979
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ...
 24-89 3.23e-13

Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding


Pssm-ID: 461117 [Multi-domain]  Cd Length: 69  Bit Score: 64.13  E-value: 3.23e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 581500401   24 KQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSA 89
Cdd:pfam03979   4 KELIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEEAPDADELLLSDEADDAE 69
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
109-255 2.67e-08

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 53.76  E-value: 2.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 109 VNLLSAQEEIELAKrieQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYAT 188
Cdd:PRK08295   6 YDELEDEELVELAR---SGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAE 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 581500401 189 WWI-RQAITrAIADQARTIRIPVHMVETINKLI---RVQRQLLQDL--GRDPAPEEI---GEEMDLPAEKVREILK 255
Cdd:PRK08295  83 LCItRQIIT-AIKTANRQKHIPLNSYVSLDKPIydeESDRTLLDVIseAKVTDPEELiisKEELEDIEEKIEELLS 157
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 115-355 1.26e-06

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 48.07  E-value: 1.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 115 QEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEgnmGLIKAVEKFD-FNKGFKFSTyatwWIRQ 193
Cdd:COG1595    2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQE---TFLRLWRKLDsFRGRGSFRA----WLYR 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 194 AITRAIADQARtiripvhmvetinKLIRVQRQLlqdlgrdpapeeigeemdlpaekvreilkiaqepvsletpigEEDDS 273
Cdd:COG1595   75 IARNLAIDHLR-------------KRRRRRELL------------------------------------------DELAE 99

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 274 HLGDfiedqEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALRK 353
Cdd:COG1595  100 ELPD-----EAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEG----LSYAEIAEILGISEGTVKSRLSRARKK 170


                 ..
gi 581500401 354 LR 355
Cdd:COG1595  171 LR 172
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
159-355 2.63e-06

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 47.93  E-value: 2.63e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 159 DLIQEGNMGLIKAVEKFDFNKGfKFSTYATWWIRQAIT---RAIADQARTIRIPVHmveTINKLIRvqrQLLQDLGRDPA 235
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH---KTNDAIR---EIAKRLGHEPN 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581500401 236 PEEIGEEMDLPAEKVREILKI--AQEPVSLETPIGEE--DDSHLGDFIEDQeaqspsdhaayELLKEQLEDVLDTLTDRE 311
Cdd:PRK12427 120 FEEISAELNLTAEEYQEYLLLenAGTLESLDELLALEahNDILQSRDLEEN-----------IIIEDNLKQALSQLDERE 188

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 581500401 312 ENVLRLRFGLDdgrtRTLEEVGKVFGVTRERIRQIEAKALRKLR 355
Cdd:PRK12427 189 QLILHLYYQHE----MSLKEIALVLDLTEARICQLNKKIAQKIK 228
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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