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Conserved domains on  [gi|488287241|ref|WP_002358449|]
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MULTISPECIES: RNA polymerase sigma factor [Bacteria]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

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]; ...
 14-127 1.31e-11

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: 58.47  E-value: 1.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241  14 FDAYCKKVLRNE-ITSIRKRNTNIKYNEEPLTDSTEGKYSqthfDEQDVyflfgmEILISDQKLSTAIDHLSEIRRKVIL 92
Cdd:COG1595   68 FRAWLYRIARNLaIDHLRKRRRRRELLDELAEELPDEAAD----PEEAL------EAEELLEALLAALERLPPRQREVLV 137

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 488287241  93 LYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:COG1595  138 LRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-127 1.31e-11

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: 58.47  E-value: 1.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241  14 FDAYCKKVLRNE-ITSIRKRNTNIKYNEEPLTDSTEGKYSqthfDEQDVyflfgmEILISDQKLSTAIDHLSEIRRKVIL 92
Cdd:COG1595   68 FRAWLYRIARNLaIDHLRKRRRRRELLDELAEELPDEAAD----PEEAL------EAEELLEALLAALERLPPRQREVLV 137

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 488287241  93 LYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:COG1595  138 LRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 3-130 5.17e-10

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: 53.89  E-value: 5.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241    3 QNYNEKSIQHQFDAYCKKVLRNEITSIRKRNTNIKYNEEPLTDSTEgkySQTHFDEQdvyflfgMEILISDQKLSTAIDH 82
Cdd:TIGR02937  41 EALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD---SDPSPEEE-------LEQEEEREALREALEK 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 488287241   83 LSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLKTEY 130
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
40-127 7.98e-08

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 49.27  E-value: 7.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241  40 EEPLTDSTEGK-YSQTHFDEQDVyfLFGMEILISDQ--KLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIW 116
Cdd:PRK07670 158 DEKTHDQDDGEnVSVTIRDDKTP--TPEEKLLKEELieELAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRIS 235

                         90
                 ....*....|.
gi 488287241 117 YQRKKAVEQLK 127
Cdd:PRK07670 236 QIHSKALFKLK 246
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 74-127 2.07e-05

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: 39.40  E-value: 2.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488287241  74 QKLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 79-127 3.05e-05

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: 38.95  E-value: 3.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488287241   79 AIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-127 1.31e-11

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: 58.47  E-value: 1.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241  14 FDAYCKKVLRNE-ITSIRKRNTNIKYNEEPLTDSTEGKYSqthfDEQDVyflfgmEILISDQKLSTAIDHLSEIRRKVIL 92
Cdd:COG1595   68 FRAWLYRIARNLaIDHLRKRRRRRELLDELAEELPDEAAD----PEEAL------EAEELLEALLAALERLPPRQREVLV 137

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 488287241  93 LYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:COG1595  138 LRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 3-130 5.17e-10

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: 53.89  E-value: 5.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241    3 QNYNEKSIQHQFDAYCKKVLRNEITSIRKRNTNIKYNEEPLTDSTEgkySQTHFDEQdvyflfgMEILISDQKLSTAIDH 82
Cdd:TIGR02937  41 EALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD---SDPSPEEE-------LEQEEEREALREALEK 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 488287241   83 LSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLKTEY 130
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
40-127 7.98e-08

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 49.27  E-value: 7.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241  40 EEPLTDSTEGK-YSQTHFDEQDVyfLFGMEILISDQ--KLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIW 116
Cdd:PRK07670 158 DEKTHDQDDGEnVSVTIRDDKTP--TPEEKLLKEELieELAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRIS 235

                         90
                 ....*....|.
gi 488287241 117 YQRKKAVEQLK 127
Cdd:PRK07670 236 QIHSKALFKLK 246
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 74-127 2.75e-07

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: 47.51  E-value: 2.75e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488287241  74 QKLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:COG1191  178 EALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLR 231
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 74-128 3.42e-07

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 47.37  E-value: 3.42e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488287241  74 QKLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLKT 128
Cdd:PRK06288 204 RVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRA 258
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 75-129 6.43e-07

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: 46.50  E-value: 6.43e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 488287241   75 KLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLKTE 129
Cdd:TIGR02479 168 ALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 74-127 2.07e-05

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: 39.40  E-value: 2.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488287241  74 QKLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 79-127 3.05e-05

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: 38.95  E-value: 3.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488287241   79 AIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 76-127 1.16e-04

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 40.37  E-value: 1.16e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488287241  76 LSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLK 127
Cdd:PRK05911 199 LAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 74-133 4.96e-04

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 38.29  E-value: 4.96e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488287241  74 QKLSTAIDHLSEIRRKVILLYYFAGFNNTEIGKILNMSTSGIWYQRKKAVEQLKTEYDLW 133
Cdd:PRK06986 176 EALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGEW 235
 
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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