HHsearch alignment for GI: 254780611 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=100.00  E-value=0  Score=329.61  Aligned_cols=243  Identities=23%  Similarity=0.327  Sum_probs=216.6

Q ss_pred             CCCHHHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf             99989999999999982-85999999999430778756555579999888999999888998986218534568999757
Q gi|254780611|r   28 MLEKQEEYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM  106 (302)
Q Consensus        28 ~Lt~eee~~l~~~~~~~-gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~  106 (302)
T Consensus         9 n~~~e~v~~wI~e~Q~nP~n~eaQeklV~hY~~Lv~SiAykYSKg~~~HEDlvQVGM~GLlgAirRyD~s~g~~FE~Fai   88 (256)
T TIGR02941         9 NLTKEDVIQWIKEFQKNPKNEEAQEKLVKHYQDLVESIAYKYSKGSAIHEDLVQVGMVGLLGAIRRYDYSYGKAFEAFAI   88 (256)
T ss_pred             CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             57887899999996369983257899999998999988754048788333045676899999986511000456566236


Q ss_pred             HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCC
Q ss_conf             7899999985320246001102300358999999997887866244788824677888618983211000000--12234
Q gi|254780611|r  107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDE  184 (302)
Q Consensus       107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~  184 (302)
T Consensus        89 PTiiGEIKrylRDKTWsvHVPR-----RIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~sY~al  163 (256)
T TIGR02941        89 PTIIGEIKRYLRDKTWSVHVPR-----RIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQSYKAL  163 (256)
T ss_pred             CCHHHHHHHHHCCCCCCCCCCC-----CHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCEE
T ss_conf             6100101121115643001574-----11003772014556644442148706546412177488898776147774333


Q ss_pred             CHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf             335520232-3453200000123568705655666666677799999962199999999999827888889899999977
Q gi|254780611|r  185 SLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE  263 (302)
Q Consensus       185 SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg  263 (302)
T Consensus       164 SvD~~iEadsDGStVa~ld~vG~~edgYd~t-----E---~Rm~LekIlpiLserE~~ii~c~f~en--lsQKeTGErlG  233 (256)
T TIGR02941       164 SVDDKIEADSDGSTVALLDLVGEVEDGYDQT-----E---KRMVLEKILPILSEREKEIIECTFIEN--LSQKETGERLG  233 (256)
T ss_pred             ECCCCCCCCCCCCCCHHHHHHCCCCCCHHHH-----H---HHHHHHHHHHHCCHHHHHHHHHHHHCC--CCCCHHHHHCC
T ss_conf             2253000368885111111216766654578-----8---888888741000544567666553147--87300232224


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999999999999999999
Q gi|254780611|r  264 VSRERVRQIEARAFKKVQESIQ  285 (302)
Q Consensus       264 iS~eRVrQI~~~AL~kLR~~l~  285 (302)
T Consensus       234 iSQMHVSRl~R~ai~KL~eAa~  255 (256)
T TIGR02941       234 ISQMHVSRLQRRAIKKLKEAAF  255 (256)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC
T ss_conf             0355677888999999999722