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