>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=2.4e-39 Score=329.58 Aligned_cols=220 Identities=30% Similarity=0.482 Sum_probs=200.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEE Q ss_conf 11246899987555789998875223567778875443679999887438545731201028989999999997228704 Q gi|254780289|r 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519 (682) Q Consensus 440 e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~ 519 (682) T Consensus 8 GDk~A~dkLi~~N~~LV~siv~rF~nRGYe~eDlFQIGciGLvKAidkFD~~y~VKFSTYAVPmI~GEIkRFLRDD-G~i 86 (231) T TIGR02885 8 GDKEARDKLIEENLRLVSSIVKRFLNRGYEYEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDD-GII 86 (231) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHCCC-CCE T ss_conf 0489999998723346899999852068870000222115566655421767770155212220221222310268-855 Q ss_pred ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--EEEEEECCCCC Q ss_conf 6142058898999999999877608899978999870999899999998608987553635889986--04756238988 Q gi|254780289|r 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNA 597 (682) Q Consensus 520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~--~~~~~~~d~~~ 597 (682) T Consensus 87 kVSRSlK~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGdPi~LlD~i~d~~~ 166 (231) T TIGR02885 87 KVSRSLKELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGDPILLLDQIADKGS 166 (231) T ss_pred EEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCCHHHHHHHHCCCCC T ss_conf 75152789999998779999998389988899988758788786644202576101100114179464467665212577 Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 598 ~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) T Consensus 167 ~~-~~~~~ki----~Lke~i~~Ld~rer~ii~LRY----FKDkTQ~eVA~~LGISQVQVSRlEkk~L~~~k~ 229 (231) T TIGR02885 167 ED-SDLLEKI----ALKEAISKLDERERQIIMLRY----FKDKTQTEVAKMLGISQVQVSRLEKKVLKKMKE 229 (231) T ss_pred CH-HHHHHHH----HHHHHHHHCCCCCCEEEEEEC----CCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHH T ss_conf 13-6899989----999998612522678977410----140017999977185700122789999999874

HHsearch alignment for GI: 254780289 and conserved domain: TIGR02885