HHsearch alignment for GI: 254781218 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=96.65  E-value=0.0045  Score=38.79  Aligned_cols=136  Identities=21%  Similarity=0.175  Sum_probs=84.4

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             77766654333100015668999999999999999985998899999848999999988779988899999999998289
Q gi|254781218|r    6 FLETSLKSLQEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI   85 (205)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v   85 (205)
T Consensus        13 ~li~~i~~R~~Tl~~V~~~Iv~~Q~~Ff~~--g~~~l~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~Gi~~lk~fFs~   90 (160)
T pfam04552        13 WLIRSLEQRAETLLKVAREIVRRQEDFLEK--GPEALRPLTLREVAEALGMHESTVSRATTNKYLATPRGLFELKYFFSS   90 (160)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEHHHHHHC
T ss_conf             999999999999999999999997999847--853575761999998809981069999961397679951659998501


Q ss_pred             CHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH----CCCCHHHHHHHHC-----CCHHHHHHHHCCCCCCCHH
Q ss_conf             999961453221000023213455467779999999997----2983899999977-----9999999974148899989
Q gi|254781218|r   86 SFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKD----KGMSQIEFGKLLG-----MPNSTLSNYEQGRTIPEIK  156 (205)
Q Consensus        86 s~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~----~glsq~elA~~lg-----is~~tis~~E~g~~~Ps~~  156 (205)
T Consensus        91 ~~~--------~~~~~------~~S~~~ik~~I~~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYR~~L~Ip~s~  156 (160)
T pfam04552        91 AVS--------TSGGG------EASATAIRALIKKLIAAEDPKKPLSDDKIVELLKEQGIDIARRTVAKYREALNIPSSS  156 (160)
T ss_pred             CCC--------CCCCC------CHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHCCCCCHH
T ss_conf             367--------88863------0229999999999998247899999999999999779952146199999883999665


Q ss_pred             H
Q ss_conf             9
Q gi|254781218|r  157 P  157 (205)
Q Consensus       157 ~  157 (205)
T Consensus       157 ~  157 (160)
T pfam04552       157 Q  157 (160)
T ss_pred             H
T ss_conf             3