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