HHsearch alignment for GI: 254780611 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=98.99 E-value=6.9e-10 Score=85.62 Aligned_cols=50 Identities=42% Similarity=0.678 Sum_probs=47.0
Q ss_pred HHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9621999999999998278888898999999778999999999999999999
Q gi|254780611|r 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 231 ~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
T Consensus 1 Al~~L~~~~r~ii~l~y~~~--~t~~EIA~~lgis~~~V~~~~~ral~~LR~ 50 (50)
T pfam04545 1 ALASLPPREREVLVLRFGEG--LTLEEIGERLGISRERVRQIEKRALRKLRK 50 (50)
T ss_pred CHHHCCHHHHHHHHHHCCCC--CHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf 97668999999999870688--249999999897999999999999998629