HHsearch alignment for GI: 254780611 and conserved domain: pfam04539
>pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Probab=98.02 E-value=3.1e-06 Score=61.18 Aligned_cols=72 Identities=18% Similarity=0.179 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCH
Q ss_conf 99997887866244788824677888618983211000000122343355202323453200000123568705
Q gi|254780611|r 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212 (302)
Q Consensus 139 ~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~ 212 (302)
T Consensus 3 i~ki~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~~SLd~p~~~~--~~~~l~d~i~D~~~~~P 74 (78)
T pfam04539 3 LNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEE--EDGELGDLLEDDDAESP 74 (78)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCC--CCCCHHHHCCCCCCCCH
T ss_conf 7999999999999988899999999996949999999998758986610676889--98628662059999881