HHsearch alignment for GI: 254780289 and conserved domain: TIGR02948

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor; InterPro: IPR014294 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 sigmaW, which is restricted to certain lineages of the order Bacillales..
Probab=98.39  E-value=3.2e-06  Score=68.02  Aligned_cols=161  Identities=19%  Similarity=0.318  Sum_probs=131.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             99999987653321124689998755578999887522356777887544367999988743854573120102898999
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
T Consensus         5 ~Kk~ik~v~~GD~~Af---AdlVdlYKDKiY~l~YRMlGN~HEA~D~AQEAF~RAY~~IDtyd~~~--KFST---WLyRI   76 (187)
T TIGR02948         5 IKKRIKEVKKGDENAF---ADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYVNIDTYDIER--KFST---WLYRI   76 (187)
T ss_pred             HHHHHHHHHHCHHHHH---HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCC--CHHH---HHHHH
T ss_conf             6889999860217888---99999964247777776506743055688888888654114316664--3147---89999


Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877608899978999870999899999998608987553635889986
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS  586 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  586 (682)
T Consensus        77 A---------------TNl--~IDrlR-----------------------------------KrKPD~yLd~~V~G~dGL  104 (187)
T TIGR02948        77 A---------------TNL--TIDRLR-----------------------------------KRKPDFYLDDEVAGTDGL  104 (187)
T ss_pred             H---------------HHH--HHHHHH-----------------------------------CCCCCCCCCCCCCCCCCC
T ss_conf             9---------------877--886541-----------------------------------348886436755786774


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC
Q ss_conf             047562389889989999999999999999732998899999998187986746889998996678
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT  652 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~  652 (682)
T Consensus       105 T~~sQlaa-~~~~~~d~V~~lE~~~~iQ~~I~~LP~KYR~~ivLKY----~edLSL~EIS~IL~lP  165 (187)
T TIGR02948       105 TMESQLAA-DEASPEDEVVSLELRDTIQEEIEALPEKYRSVIVLKY----MEDLSLKEISEILDLP  165 (187)
T ss_pred             HHHHCCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCHHHCEEHHHHH----HHHHHHHHHHHHHCCC
T ss_conf             00100110-1246214655535678999999743433512224544----4442188899985789