HHsearch alignment for GI: 254780694 and conserved domain: TIGR02859

>TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218 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 RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.41  E-value=0.063  Score=31.23  Aligned_cols=45  Identities=27%  Similarity=0.333  Sum_probs=43.3

Q ss_conf             889779999999985999799999949998899999999999807
Q Consensus       185 ~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  229 (246)
T Consensus       150 ~ls~le~~vl~~yl~G~~yqei~~~l~r~~ksidnalqrvkrkle  194 (198)
T ss_conf             999999999999845740788998864566789999999999997