HHsearch alignment for GI: 254780694 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=97.71 E-value=8.5e-05 Score=49.66 Aligned_cols=46 Identities=39% Similarity=0.416 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
T Consensus 3 ~~L~~~~r~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~~LR 49 (50)
T pfam04545 3 ASLPPREREVLVLRFGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49 (50)
T ss_pred HHCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 66899999999987068824999999989799999999999999862