HHsearch alignment for GI: 254781218 and conserved domain: cd04780

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=91.60  E-value=0.15  Score=29.36  Aligned_cols=69  Identities=10%  Similarity=0.267  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9889999984899999998877-998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN-GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~-G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
T Consensus         1 M~IgelA~~tGvs~~TIRyYe~~GLL~p~~R~~~g----~--------------r~Y~----~~~v~r--L-~~Ir~l~~   55 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPN----Q--------------AEYS----EAHVER--L-RLIRALQQ   55 (95)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCC----C--------------EECC----HHHHHH--H-HHHHHHHH
T ss_conf             97899999989789999999997899987769998----7--------------1549----999999--9-99999999


Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             729838999999779
Q gi|254781218|r  124 DKGMSQIEFGKLLGM  138 (205)
Q Consensus       124 ~~glsq~elA~~lgi  138 (205)
T Consensus        56 ~lG~sL~eIr~lL~~   70 (95)
T cd04780          56 EGGLPISQIKEVLDA   70 (95)
T ss_pred             HCCCCHHHHHHHHHC
T ss_conf             369999999999843