>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=99.32 E-value=2.1e-11 Score=95.74 Aligned_cols=179 Identities=18% Similarity=0.277 Sum_probs=131.6 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302) T Consensus 6 Kk~ik~v~-~GD~~AfAdlVdlYKDKiY~l~YRMlGN~HEA~D~AQEAF~RAY~~IDtyd~~~--KFSTWLy-------- 74 (187) T TIGR02948 6 KKRIKEVK-KGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYVNIDTYDIER--KFSTWLY-------- 74 (187) T ss_pred HHHHHHHH-HCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHH-------- T ss_conf 88999986-021788899999964247777776506743055688888888654114316664--3147899-------- Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323 Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302) Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302) T Consensus 75 ----------RIATNl~----IDrlRK----------rKP----------------------------D~yLd~~V~G~d 102 (187) T TIGR02948 75 ----------RIATNLT----IDRLRK----------RKP----------------------------DFYLDDEVAGTD 102 (187) T ss_pred ----------HHHHHHH----HHHHHC----------CCC----------------------------CCCCCCCCCCCC T ss_conf ----------9998778----865413----------488----------------------------864367557867 Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 103 G--LT~~sQlaa~~~~~~d~V~~l----E~~~~iQ~~I~~LP~KYR~~ivLKY~ed--LSL~EIS~IL~lPVgTVK---- 170 (187) T TIGR02948 103 G--LTMESQLAADEASPEDEVVSL----ELRDTIQEEIEALPEKYRSVIVLKYMED--LSLKEISEILDLPVGTVK---- 170 (187) T ss_pred C--CHHHHCCCCCCCCCHHHHHHH----HHHHHHHHHHHHCCHHHCEEHHHHHHHH--HHHHHHHHHHCCCCCCEE---- T ss_conf 7--400100110124621465553----5678999999743433512224544444--218889998578943100---- Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999740 Q gi|254780611|r 275 RAFKKVQESIQKQV 288 (302) Q Consensus 275 ~AL~kLR~~l~~~~ 288 (302) T Consensus 171 TRiHRGREALRk~l 184 (187) T TIGR02948 171 TRIHRGREALRKQL 184 (187) T ss_pred CCCCCCHHHHHHHH T ss_conf 24302458999873

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02948