HHsearch alignment for GI: 254780693 and conserved domain: TIGR02983
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 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 , . This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=97.14 E-value=0.00046 Score=48.16 Aligned_cols=45 Identities=33% Similarity=0.476 Sum_probs=36.8
Q ss_pred CCCHHHHHH--HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf 499899999--9999879997899999499988999999999998079
Q gi|254780693|r 173 NLTERETSC--LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235)
Q Consensus 173 ~LT~RE~ev--L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235)
T Consensus 113 ~LP~rQR~vvVLRY-~eDlSe~~~A~~LG~SvGTVKS~~sRal~~LR~ 159 (165)
T TIGR02983 113 RLPARQRAVVVLRY-YEDLSEAEVAEVLGISVGTVKSRLSRALARLRE 159 (165)
T ss_pred HCCHHCCEEEEEEC-CCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 35641236723204-578986899988199932289989999999887