HHsearch alignment for GI: 254780351 and conserved domain: pfam04545
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Probab=92.19 E-value=0.29 Score=27.99 Aligned_cols=43 Identities=16% Similarity=-0.028 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 9999999999993217968899999854771056799999997
Q gi|254780351|r 54 DVNAVQALLLFNIGDLELTAGELRSRGYYLGSNVSYNLKKLID 96 (171)
Q Consensus 54 ~l~~~q~~~L~~~~~~~~t~~eLa~~l~i~~~tvs~~i~~Le~ 96 (171)
T Consensus 4 ~L~~~~r~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~ 46 (50)
T pfam04545 4 SLPPREREVLVLRFGEGLTLEEIGERLGISRERVRQIEKRALR 46 (50)
T ss_pred HCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 6899999999987068824999999989799999999999999