>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 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 , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; 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=384.40 Aligned_cols=231 Identities=23% Similarity=0.358 Sum_probs=202.8 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99999982859999999994307787565555799998889999998889989862185345689997577899999985 Q gi|254780611|r 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302) Q Consensus 37 l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302) T Consensus 1 Li~~a~-~GDk~A~dkLi~~N~~LV~siv~rF~nRGYe~eDlFQIGciGLvKAidkFD~~y~VKFSTYAVPmI~GEIkRF 79 (231) T TIGR02885 1 LIKLAK-EGDKEARDKLIEENLRLVSSIVKRFLNRGYEYEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRF 79 (231) T ss_pred CCHHHH-HHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHH T ss_conf 904567-4048999999872334689999985206887000022211556665542176777015521222022122231 Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345 Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302) Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302) T Consensus 80 LRDDG-~ikVSRSl--K~la~---k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGd 153 (231) T TIGR02885 80 LRDDG-IIKVSRSL--KELAR---KIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGD 153 (231) T ss_pred HCCCC-CEEEEHHH--HHHHH---HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCC T ss_conf 02688-55751527--89999---99877999999838998889998875878878664420257610110011417946 Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999 Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302) Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302) T Consensus 154 Pi~LlD~i~d~~~~~-~~~~~-------ki~Lke~i~~Ld~rer~ii~LRYFKD--kTQ~eVA~~LGISQVQVSRlEkk~ 223 (231) T TIGR02885 154 PILLLDQIADKGSED-SDLLE-------KIALKEAISKLDERERQIIMLRYFKD--KTQTEVAKMLGISQVQVSRLEKKV 223 (231) T ss_pred HHHHHHHHCCCCCCH-HHHHH-------HHHHHHHHHHCCCCCCEEEEEECCCC--CHHHHHHHHCCCCCCHHHHHHHHH T ss_conf 446766521257713-68999-------89999998612522678977410140--017999977185700122789999 Q ss_pred HHHHHHHH Q ss_conf 99999999 Q gi|254780611|r 277 FKKVQESI 284 (302) Q Consensus 277 L~kLR~~l 284 (302) T Consensus 224 L~~~k~~l 231 (231) T TIGR02885 224 LKKMKEKL 231 (231) T ss_pred HHHHHHHC T ss_conf 99987409

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02885