HHsearch alignment for GI: 254780289 and conserved domain: TIGR02941
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=99.94 E-value=1.5e-25 Score=220.74 Aligned_cols=240 Identities=22% Similarity=0.422 Sum_probs=207.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682)
Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682)
T Consensus 10 ~~~e~v~~wI~e~Q~nP-~n~eaQeklV~hY~~Lv~SiAykYSKg~~~HEDlvQVGM~GLlgAirRyD~s~g~~FE~Fai 88 (256)
T TIGR02941 10 LTKEDVIQWIKEFQKNP-KNEEAQEKLVKHYQDLVESIAYKYSKGSAIHEDLVQVGMVGLLGAIRRYDYSYGKAFEAFAI 88 (256)
T ss_pred CCHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 78878999999963699-83257899999998999988754048788333045676899999986511000456566236
Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCCC
Q ss_conf 9899999999972287046142058898999999999877608899978999870999899999998608--98755363
Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP 579 (682)
Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~~~ 579 (682)
T Consensus 89 PTiiGEIKrylRDKTWsvHVPRRIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~sY~alSvD~~ 168 (256)
T TIGR02941 89 PTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQSYKALSVDDK 168 (256)
T ss_pred CCHHHHHHHHHCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCEEECCCC
T ss_conf 61001011211156430015741100377201455664444214870654641217748889877614777433322530
Q ss_pred CCCCCC-CE--EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 588998-60--475623898899899999999999999997329988999999981879867468899989966789999
Q gi|254780289|r 580 IGDEDT-SH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656 (682)
Q Consensus 580 ~~~~~~-~~--~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~ 656 (682)
T Consensus 169 iEadsDGStVa~ld~vG~~-----edgYd~tE~Rm~LekIlpiLserE~~ii~c~f----~enlsQKeTGErlGiSQMHV 239 (256)
T TIGR02941 169 IEADSDGSTVALLDLVGEV-----EDGYDQTEKRMVLEKILPILSEREKEIIECTF----IENLSQKETGERLGISQMHV 239 (256)
T ss_pred CCCCCCCCCCHHHHHHCCC-----CCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCCCHHHHHCCHHHHHH
T ss_conf 0036888511111121676-----66545788888888741000544567666553----14787300232224035567
Q ss_pred HHHHHHHHHHHCCHH
Q ss_conf 999999999832967
Q gi|254780289|r 657 RQIEAKAIRKLKHPS 671 (682)
Q Consensus 657 rqi~~~a~~~l~~~~ 671 (682)
T Consensus 240 SRl~R~ai~KL~eAa 254 (256)
T TIGR02941 240 SRLQRRAIKKLKEAA 254 (256)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 788899999999972