>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=4.5e-36 Score=303.68 Aligned_cols=215 Identities=30% Similarity=0.514 Sum_probs=201.0 Q ss_pred HHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCH Q ss_conf 9875557899988752235---6777887544367999988743854573120102898999999999722870461420 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~---~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~ 524 (682) T Consensus 1 l~~~Y~pLVk~~a~rl~~~~P~~v~~~DL~q~G~~GL~dA~~ryd~~~g~~F~TyA~~RIRGAmlDELR~~DW---~PRs 77 (227) T TIGR02479 1 LIKKYLPLVKRIAGRLVVQLPSSVELDDLIQAGMIGLLDAIERYDPSKGVKFETYAVQRIRGAMLDELRKLDW---VPRS 77 (227) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCHHHHHHHHHHCCC---CCHH T ss_conf 9001268999988664310488234875898889999999983188888944100011130205788753066---7836 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCCCCCCCCCCC----EEEEEECCCCCC Q ss_conf 58898999999999877608899978999870999899999998--608987553635889986----047562389889 Q gi|254780289|r 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS----HLGDFIEDKNAV 598 (682) Q Consensus 525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~~~~~~~~~~----~~~~~~~d~~~~ 598 (682) T Consensus 78 ~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (227) T TIGR02479 78 LRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIEDDKSE 157 (227) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCC T ss_conf 89998689999999999869898888999983999989999999988998764899984146322345323100143576 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 98999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 599 ~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) T Consensus 158 ~P~~~~~~~~L~~~l~~ai~~L~eRE~LVl~LYY----~eELnLKEIg~VL~lsESRvSQiHs~A~~~Lr~ 224 (227) T TIGR02479 158 DPEEELEREELREALAEAIEKLSEREKLVLSLYY----YEELNLKEIGEVLGLSESRVSQIHSQALKKLRA 224 (227) T ss_pred CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 8135899999999999997406855788888864----127668899988378705799999999999987

HHsearch alignment for GI: 254780289 and conserved domain: TIGR02479