>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 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 , . Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription.

Probab=100.00 E-value=0 Score=347.98 Aligned_cols=220 Identities=23% Similarity=0.358 Sum_probs=191.8 Q ss_pred HHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 999430778756555579---99988899999988899898621853456899975778999999853202460011023 Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302) Q Consensus 53 Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302) T Consensus 1 l~~~Y~pLVk~~a~rl~~~~P~~v~~~DL~q~G~~GL~dA~~ryd~~~g~~F~TyA~~RIRGAmlDELR~~DW---~P-- 75 (227) T TIGR02479 1 LIKKYLPLVKRIAGRLVVQLPSSVELDDLIQAGMIGLLDAIERYDPSKGVKFETYAVQRIRGAMLDELRKLDW---VP-- 75 (227) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCHHHHHHHHHHCCC---CC-- T ss_conf 9001268999988664310488234875898889999999983188888944100011130205788753066---78-- Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCHHHHCCCCCCC--CCCHHCCCC Q ss_conf 0035899999999788786624478882467788861898321100000012--234335520232345--320000012 Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKN--SSQWQDWLV 205 (302) Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~~~SLd~~i~~~d~~--~~~~~d~l~ 205 (302) T Consensus 76 ---Rs~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~ 152 (227) T TIGR02479 76 ---RSLRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIE 152 (227) T ss_pred ---HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEEC T ss_conf ---36899986899999999998698988889999839999899999999889987648999841463223453231001 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 35687056556666666777999999621999999999998278888898999999778999999999999999999999 Q gi|254780611|r 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 206 ~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 153 ~~~~~~P~~~---~~~~~L~~~l~~ai~~L~eRE~LVl~LYY~eE--LnLKEIg~VL~lsESRvSQiHs~A~~~Lr~~L~ 227 (227) T TIGR02479 153 DDKSEDPEEE---LEREELREALAEAIEKLSEREKLVLSLYYYEE--LNLKEIGEVLGLSESRVSQIHSQALKKLRAKLS 227 (227) T ss_pred CCCCCCHHHH---HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 4357681358---99999999999997406855788888864127--668899988378705799999999999987539

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02479