HHsearch alignment for GI: 254780444 and conserved domain: cd04762
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=92.32 E-value=0.18 Score=29.66 Aligned_cols=41 Identities=22% Similarity=0.245 Sum_probs=28.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CCHHHHHHHH
Q ss_conf 9988999982899879889975157887557------7989999987
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRNRW------PSTESIFKIL 62 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~------p~~~~l~kia 62 (223)
T Consensus 1 lt~~e~A~~lgVs~~TlrrW~~~G~i~~~rt~~GhRry~~~dl~~ll 47 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLL 47 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCEEECCCCCEEECHHHHHHHH
T ss_conf 98899999979899999999987994315889987761899999985