HHsearch alignment for GI: 254780693 and conserved domain: TIGR02479

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 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 , . Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription.
Probab=94.96  E-value=0.065  Score=32.79  Aligned_cols=47  Identities=38%  Similarity=0.394  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             44998999999999-879997899999499988999999999998079
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
T Consensus       177 ~~L~eRE~LVl~LYY~eELnLKEIg~VL~lsESRvSQiHs~A~~~Lr~  224 (227)
T TIGR02479       177 EKLSEREKLVLSLYYYEELNLKEIGEVLGLSESRVSQIHSQALKKLRA  224 (227)
T ss_pred             HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             406855788888864127668899988378705799999999999987