HHsearch alignment for GI: 254780611 and conserved domain: TIGR02960

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305 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 sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=97.38  E-value=0.0076  Score=38.56  Aligned_cols=74  Identities=14%  Similarity=0.242  Sum_probs=53.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             35687056556666666777999999621999999999998278888898999999778999999999999999999999
Q gi|254780611|r  206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ  285 (302)
Q Consensus       206 ~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~  285 (302)
T Consensus       118 p~aa~P~~~~~~~---EsvrLAF~AAlQ~LpPrQRAvL~LRdvlG--w~A~E~A~~L~~s~ASV----nSaLQRARAtL~  188 (329)
T TIGR02960       118 PAAADPEAAAVAR---ESVRLAFVAALQLLPPRQRAVLLLRDVLG--WKAAEVAELLGTSVASV----NSALQRARATLA  188 (329)
T ss_pred             CCCCCHHHHHHHH---HHHHHHHHHHHHCCCCHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHH----HHHHHHHHHHHH
T ss_conf             8888711233211---46899999998748814578999898835--55568998743832678----658888788665


Q ss_pred             HHH
Q ss_conf             740
Q gi|254780611|r  286 KQV  288 (302)
Q Consensus       286 ~~~  288 (302)
T Consensus       189 ~~~  191 (329)
T TIGR02960       189 ESE  191 (329)
T ss_pred             HCC
T ss_conf             317