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