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