HHsearch alignment for GI: 254780611 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=98.41 E-value=1.7e-07 Score=69.57 Aligned_cols=152 Identities=14% Similarity=0.252 Sum_probs=94.6
Q ss_pred HHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH
Q ss_conf 99943077875655557-99998889999998889989862185345689997577899999985320246001102300
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~-~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302)
T Consensus 11 f~~~r~~~L~r~A~lLt~GD~~~AEDLvQ~Al~~~y~rW~Ri-~~~~~-~~a----YvR~vl~n~~~s~w---------- 74 (165)
T TIGR02983 11 FVAARYPRLLRTAYLLTAGDPHEAEDLVQEALVRTYVRWDRI-RDADA-PDA----YVRRVLVNLAISRW---------- 74 (165)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC-CCCCC-CHH----HHHHHHHHHHHHHH----------
T ss_conf 999999999999999827887569999999999998862215-88254-057----89999999999999----------
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC
Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870
Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302)
Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302)
T Consensus 75 --------RrR~~~~e~~~~~~Pd~---------------------------------------------------~ga~ 95 (165)
T TIGR02983 75 --------RRRRVRLELPTEELPDA---------------------------------------------------AGAP 95 (165)
T ss_pred --------HHHHHHHHCCCCCCCCC---------------------------------------------------CCCC
T ss_conf --------98876442146686488---------------------------------------------------8898
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 565566666667779999996219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
T Consensus 96 d~-~----~~~~~r~~l~~AL~~LP~rQR~vvVLRY~eD--lSe~~~A~~LG~SvGTVKS~~sRal~~LR~~~~~ 163 (165)
T TIGR02983 96 DP-A----ADVALRAALARALRRLPARQRAVVVLRYYED--LSEAEVAEVLGISVGTVKSRLSRALARLRELLEE 163 (165)
T ss_pred CC-C----CCHHHHHHHHHHHHHCCHHCCEEEEEECCCC--CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 75-3----1122699999999735641236723204578--9868999881999322899899999998873257