HHsearch alignment for GI: 254781049 and conserved domain: cd06294

>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=91.87  E-value=1  Score=24.39  Aligned_cols=104  Identities=14%  Similarity=0.141  Sum_probs=68.7

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             999999658996248842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
T Consensus       144 f~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~tai~-------~~nD~~A~g~~~al~~~g~~iP~disvv  216 (270)
T cd06294         144 YKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIV-------ATDDLLALGVLKVLNELGLKVPEDLSII  216 (270)
T ss_pred             HHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             999999869997733331377667889999999984699984899-------8774999999999998399999984999


Q ss_pred             CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             9858999999997699589-9499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
T Consensus       217 gfDd~---~~~~~~~P~LTtv~q~~~~~G~~A~~~L  249 (270)
T cd06294         217 GFNNS---ILSELAHPPLTSVDINPRELGYEAAELL  249 (270)
T ss_pred             EECCH---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             98972---8998428981799739999999999999