>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=97.38 E-value=0.00037 Score=45.49 Aligned_cols=123 Identities=20% Similarity=0.254 Sum_probs=78.7 Q ss_pred HHHCCC-HHHHH------------HHHHHHHHHHHHHHHC------CCCHHHHHHHHCCCHHH-HHHHHCCCCCCCHHHH Q ss_conf 100015-66899------------9999999999999985------99889999984899999-9988779988899999 Q gi|254781218|r 17 YTLIIT-PEIRQ------------YWKDVGTRIKDIRKAN------NKTQKEMAIGANQLESA-VNLFENGMCSTSIRYA 76 (205) Q Consensus 17 ~~~~~~-~~~~~------------~~~~iG~rik~lR~~~------gltQ~elA~~~gis~~~-is~~E~G~~~psi~~l 76 (205) T Consensus 67 YAVPmI~GEIkRFLRDDG~ikVSRSlK~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~t 146 (231) T TIGR02885 67 YAVPMIMGEIKRFLRDDGIIKVSRSLKELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDT 146 (231) T ss_pred CCCCHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCE T ss_conf 12220221222310268855751527899999987799999983899888999887587887866442025761011001 Q ss_pred HHHHHHHCCCHHHHHCCCCCCCCCCCC--CCHHHHHHHHHHHHHHH----------HHHHCCCCHHHHHHHHCCCHHHHH Q ss_conf 999998289999961453221000023--21345546777999999----------999729838999999779999999 Q gi|254781218|r 77 LYLRNEYEISFDWIYDGEVIDRRYEDV--TNKKRLDPYAIGARLKS----------IRKDKGMSQIEFGKLLGMPNSTLS 144 (205) Q Consensus 77 ~~la~~~~vs~d~Ll~ge~~~~~~~~~--~~~~~~d~~~iG~rLk~----------lR~~~glsq~elA~~lgis~~tis 144 (205) T Consensus 147 v---h~dDGdPi~LlD-----~i-~d~~~~~~~~~~ki~Lke~i~~Ld~rer~ii~LRYFKDkTQ~eVA~~LGISQVQVS 217 (231) T TIGR02885 147 V---HEDDGDPILLLD-----QI-ADKGSEDSDLLEKIALKEAISKLDERERQIIMLRYFKDKTQTEVAKMLGISQVQVS 217 (231) T ss_pred E---ECCCCCHHHHHH-----HH-CCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHCCCCCCHHH T ss_conf 1---417946446766-----52-12577136899989999998612522678977410140017999977185700122 Q ss_pred HHHC Q ss_conf 9741 Q gi|254781218|r 145 NYEQ 148 (205) Q Consensus 145 ~~E~ 148 (205) T Consensus 218 RlEk 221 (231) T TIGR02885 218 RLEK 221 (231) T ss_pred HHHH T ss_conf 7899

HHsearch alignment for GI: 254781218 and conserved domain: TIGR02885