HHsearch alignment for GI: 254780694 and conserved domain: TIGR02846

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 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 , . The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.87  E-value=0.042  Score=32.38  Aligned_cols=45  Identities=42%  Similarity=0.566  Sum_probs=38.3

Q ss_pred             CCCHHHHHHHHH---HHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             889779999999---9859--99799999949998899999999999807
Q gi|254780694|r  185 ELTGREVECLTW---ISEG--KTSDEIAVILGISRNTVNNYIASIMRKTA  229 (246)
Q Consensus       185 ~LT~RE~eVl~l---ia~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  229 (246)
T Consensus       175 ~L~~rE~~vi~~RyGL~~~~~~tQREIA~~LgISRSYVSRIEK~Al~Kl~  224 (228)
T TIGR02846       175 VLKGREREVIEMRYGLKDGREKTQREIAKILGISRSYVSRIEKKALKKLY  224 (228)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             74088899998743668889541789987708650045488899999998