HHsearch alignment for GI: 254780611 and conserved domain: TIGR02980

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 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 group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=100.00  E-value=0  Score=422.92  Aligned_cols=224  Identities=28%  Similarity=0.380  Sum_probs=203.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf             59999999994307787565555799998-88999999888998986218534568999757789999998532024600
Q gi|254780611|r   46 DLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV  124 (302)
Q Consensus        46 d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~-~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I  124 (302)
T Consensus         1 ~~~~R~~Lv~~nlpLv~~~A~RF~~RGe~~~EDL~QVG~iGL~kAidrFD~~~g~~F~tyAVPtI~GEIkR~fRD~~W~v   80 (229)
T TIGR02980         1 DKEAREKLVELNLPLVESIARRFRSRGEPHLEDLVQVGTIGLVKAIDRFDPSYGVKFSTYAVPTIMGEIKRFFRDDTWAV   80 (229)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCEEEEEEEEEECCCCEE
T ss_conf             96788999996127999999985137887431157888888887775301111698664104602332313342487326


Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCHHHHCC-CCCCCCCCHH
Q ss_conf             1102300358999999997887866244788824677888618983211000000122--343355202-3234532000
Q gi|254780611|r  125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALIN-SSDKNSSQWQ  201 (302)
Q Consensus       125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~--~~SLd~~i~-~~d~~~~~~~  201 (302)
T Consensus        81 rVPRrl-----kEl~~~~~~a~eeL~~~lgR~Pt~~EiAe~L~~s~EEv~~aleA~~~Y~~~Sld~~~~a~~dg~~~~L~  155 (229)
T TIGR02980        81 RVPRRL-----KELRLKINKATEELTQRLGRSPTVAEIAEELGVSEEEVVEALEAGNSYSALSLDATIEADDDGDPIALL  155 (229)
T ss_pred             ECCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             605138-----988999999999999982889887899988588999999999865417861120004558888424566


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             00123568705655666666677799999962199999999999827888889899999977899999999999999999
Q gi|254780611|r  202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ  281 (302)
Q Consensus       202 d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR  281 (302)
T Consensus       156 D~lG~~D~~~e~~--------~~~~aLk~~l~~LpeRER~il~lRFf~~--~TQ~eiA~~lGiSQMhVSRl~~~~L~~LR  225 (229)
T TIGR02980       156 DTLGDEDDALETV--------EDRLALKPLLAALPERERRILLLRFFED--KTQSEIAERLGISQMHVSRLLRRALKRLR  225 (229)
T ss_pred             HHHCCCCCHHHHH--------HHHHHHHHHHHHCCHHHCEEEEEEEECC--CCHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             4440224326789--------9999999998507902707610001069--77899997818436788999999999999


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780611|r  282 ESI  284 (302)
Q Consensus       282 ~~l  284 (302)
T Consensus       226 ~~l  228 (229)
T TIGR02980       226 EQL  228 (229)
T ss_pred             HHC
T ss_conf             860