>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 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 the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=99.97 E-value=8.5e-31 Score=225.36 Aligned_cols=198 Identities=31% Similarity=0.469 Sum_probs=165.0 Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757 Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 32 PPl~~eee~~l~~~l~-~Gd~~~~~~liernlrlvvyia~kf~ntG~~~edl~s~GtiGlikav~tf~P~k~iklatyas 110 (234) T TIGR02835 32 PPLTKEEEEALLEKLE-KGDEAAKSILIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFNPEKKIKLATYAS 110 (234) T ss_pred CCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 9887157999999987-547999999886222431121012202562110222221478887765227301103556776 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302) T Consensus 111 ~Cieneilmylrr~~~~---------------------------------------------------------~~evsf 133 (234) T TIGR02835 111 RCIENEILMYLRRNNKI---------------------------------------------------------RSEVSF 133 (234) T ss_pred HHHHHHHHHHHHHHCCC---------------------------------------------------------CCEEEE T ss_conf 76788899988751121---------------------------------------------------------000000 Q ss_pred HHHCCC-CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHC Q ss_conf 552023-2345320000012356870565566666667779999996219999999999982788--8889899999977 Q gi|254780611|r 187 NALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFE 263 (302) Q Consensus 187 d~~i~~-~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lg 263 (302) T Consensus 134 ~ePln~dW~Gnelllsd~lGt~~~~----~~~~~e~~v~~~ll~~al~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lG 209 (234) T TIGR02835 134 DEPLNVDWDGNELLLSDVLGTDSDI----VYKVLEEEVDRELLKKALKKLNDREKKIMELRFGLAGGTEKTQKEVADLLG 209 (234) T ss_pred CCCCCCCCCCCHHHHHHHHCCCHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH T ss_conf 2554656676211434441474268----899999999999999999987676787667630436772146788898862 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999999999999999999997 Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 210 isqsyisrlek~i~krl~ke~~~ 232 (234) T TIGR02835 210 ISQSYISRLEKRILKRLKKEINR 232 (234) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 46899999999999999999873

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02835