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Conserved domains on  [gi|491477850|ref|WP_005335591|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacillati]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11495650)

sigma-70 family RNA polymerase sigma factor is a general transcription factor that reversibly binds RNA polymerase and mediates transcription.

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  28117604

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 79-138 1.10e-09

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: 53.85  E-value: 1.10e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMMEEE 138
Cdd:COG1595  119 EALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEE 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-135 5.41e-09

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: 51.58  E-value: 5.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491477850   20 KVIKRAAMKYNRDISRRLKHEVPFSEISDLELNkagvydkyssdytafNVLGMEVQVSDDQLSKALKCLPERKRNIILLS 99
Cdd:TIGR02937  58 RIARNLILDYLRRKRRLRRELDLLEELLDSDPS---------------PEEELEQEEEREALREALEKLPEREREVLVLR 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 491477850  100 YFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMM 135
Cdd:TIGR02937 123 YLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 79-138 1.10e-09

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: 53.85  E-value: 1.10e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMMEEE 138
Cdd:COG1595  119 EALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEE 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-135 5.41e-09

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: 51.58  E-value: 5.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491477850   20 KVIKRAAMKYNRDISRRLKHEVPFSEISDLELNkagvydkyssdytafNVLGMEVQVSDDQLSKALKCLPERKRNIILLS 99
Cdd:TIGR02937  58 RIARNLILDYLRRKRRLRRELDLLEELLDSDPS---------------PEEELEQEEEREALREALEKLPEREREVLVLR 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 491477850  100 YFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMM 135
Cdd:TIGR02937 123 YLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 84-133 2.10e-07

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: 44.73  E-value: 2.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 491477850   84 ALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRK 133
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 79-122 1.37e-06

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: 42.86  E-value: 1.37e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNV----VRTTVYR 122
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGIsrstVRQRLHR 49
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 69-136 2.14e-05

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 41.99  E-value: 2.14e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491477850  69 VLGMEVQvsdDQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNV----VRTTVYRHRtstlEELRKMME 136
Cdd:PRK09641 121 VVSLELQ---ETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLpvgtVKTRIHRGR----EALRKQLR 185
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 79-138 1.10e-09

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: 53.85  E-value: 1.10e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMMEEE 138
Cdd:COG1595  119 EALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEE 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-135 5.41e-09

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: 51.58  E-value: 5.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491477850   20 KVIKRAAMKYNRDISRRLKHEVPFSEISDLELNkagvydkyssdytafNVLGMEVQVSDDQLSKALKCLPERKRNIILLS 99
Cdd:TIGR02937  58 RIARNLILDYLRRKRRLRRELDLLEELLDSDPS---------------PEEELEQEEEREALREALEKLPEREREVLVLR 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 491477850  100 YFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMM 135
Cdd:TIGR02937 123 YLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 79-137 6.17e-09

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: 52.13  E-value: 6.17e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMMEE 137
Cdd:COG1191  178 EALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 84-133 2.10e-07

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: 44.73  E-value: 2.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 491477850   84 ALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRK 133
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 79-122 1.37e-06

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: 42.86  E-value: 1.37e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNV----VRTTVYR 122
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGIsrstVRQRLHR 49
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 79-123 7.87e-06

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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 40.52  E-value: 7.87e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 491477850   79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRH 123
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSR 46
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 69-136 2.14e-05

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 41.99  E-value: 2.14e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491477850  69 VLGMEVQvsdDQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNV----VRTTVYRHRtstlEELRKMME 136
Cdd:PRK09641 121 VVSLELQ---ETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLpvgtVKTRIHRGR----EALRKQLR 185
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 81-132 4.25e-05

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 41.60  E-value: 4.25e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 491477850  81 LSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELR 132
Cdd:PRK06288 206 IVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 79-135 2.12e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 39.45  E-value: 2.12e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMM 135
Cdd:PRK12538 163 DLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 71-115 3.48e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 38.48  E-value: 3.48e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 491477850  71 GMEVQVSDDQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNV 115
Cdd:PRK05602 112 GLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDI 156
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 85-136 6.32e-04

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 38.22  E-value: 6.32e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 491477850  85 LKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMME 136
Cdd:PRK07122 213 LAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 80-136 6.48e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 37.64  E-value: 6.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491477850  80 QLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNV----VRTTVYRHRTStleeLRKMME 136
Cdd:PRK11924 118 RIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVpvgtVKSRLRRARQL----LRECLE 174
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 79-138 1.08e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 37.36  E-value: 1.08e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491477850  79 DQLSKALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMMEEE 138
Cdd:PRK12513 131 RRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEE 190
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 75-137 2.51e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 36.19  E-value: 2.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491477850  75 QVSDDQLS----KALKCLPERKRNIILLSYFMDMSDAEIGELMNVVRTTVYRHRTSTLEELRKMMEE 137
Cdd:PRK12519 125 QASLAERSqrvqTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQD 191
 
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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