HHsearch alignment for GI: 254780351 and conserved domain: pfam03965

>pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
Probab=97.91  E-value=0.00072  Score=44.77  Aligned_cols=100  Identities=16%  Similarity=0.150  Sum_probs=67.2

Q ss_pred             CCHHHHHHHHHHHC-CCCCHHHHHHHHCC----CCCHHHHHHHHHHHCCCEEEEECCCCCCEEEEE--ECHHH------H
Q ss_conf             99999999999321-79688999998547----710567999999977887886361007105644--57889------9
Q gi|254780351|r   55 VNAVQALLLFNIGD-LELTAGELRSRGYY----LGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRIS--LTQSG------K  121 (171)
Q Consensus        55 l~~~q~~~L~~~~~-~~~t~~eLa~~l~i----~~~tvs~~i~~Le~~G~i~r~~~~~D~R~~~i~--LT~~G------~  121 (171)
T Consensus         1 Ls~~E~~IM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~~~---gr~~~Y~p~v~~~~~~~~~~~   77 (115)
T pfam03965         1 IGDAEWEVMRILWALGPATVKEVVEELPEPRDWAYSTVKTLLTRLVKKGLLSREKD---GRAYIYSPLVSREEAVASAVK   77 (115)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEEEC---CCCEEEEECCCHHHHHHHHHH
T ss_conf             98899999999980799779999998514568857289999999997786268733---994798746889999999999


Q ss_pred             HHHHHHHH-HHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             99999999-9999999998534999899999999999
Q gi|254780351|r  122 EIAETISQ-LYQRHIESIDKVGGLSVDDFIAMNKLLQ  157 (171)
Q Consensus       122 ~~~~~~~~-~~~~~~~~l~~~~~ls~ee~~~l~~~L~  157 (171)
T Consensus        78 ~~~~~~f~gs~~~lv~~l~~~~~ls~~el~~L~~~i~  114 (115)
T pfam03965        78 QLLDRLFGGSVGALVANFVEREKLSPDDIEELRELLE  114 (115)
T ss_pred             HHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             9999997989999999998669999999999999870