HHsearch alignment for GI: 254780611 and conserved domain: pfam04552

>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=90.33  E-value=0.5  Score=26.37  Aligned_cols=25  Identities=28%  Similarity=0.407  Sum_probs=19.9

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCCCC
Q ss_conf             4788824677888618983211000
Q gi|254780611|r  152 NNLKPEQVVAIAKKLNVSESEVISM  176 (302)
Q Consensus       152 ~~~~~~~~~eiA~~Lgis~~~v~~l  176 (302)
T Consensus        45 ~~l~PLtlk~iA~~l~lh~STVSRa   69 (160)
T pfam04552        45 EALRPLTLREVAEALGMHESTVSRA   69 (160)
T ss_pred             CCCCCCCHHHHHHHCCCCCCHHHHH
T ss_conf             3575761999998809981069999