HHsearch alignment for GI: 254780687 and conserved domain: COG1868

>COG1868 FliM Flagellar motor switch protein [Cell motility and secretion].
Probab=100.00  E-value=0  Score=455.19  Aligned_cols=304  Identities=18%  Similarity=0.315  Sum_probs=291.5

Q ss_pred             CCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCCEEEEE
Q ss_conf             55587845778888853012236679999999999999999999998629807998647256679989711688639999
Q gi|254780687|r    6 IHKNTSPLHPILLARLTGKLGDKKTIEKISSSLGYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQ   85 (318)
Q Consensus         6 ~~~~~~p~d~~~~~r~~g~~~~~~~~~~~~~~~~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p~~~~i   85 (318)
T Consensus        28 ~~~~v~~ydf~~~~r~------s~e~lrtl~~I~e~far~l~~~ls~~lr~~v~v~~~sV~~~~y~efi~sl~~pt~lni  101 (332)
T COG1868          28 DERKVKPYDFKRPDRF------SKEQLRTLEIIHERFARLLTTSLSNLLRRSVDVEVGSVDQMTYEEFIRSLPNPTILNL  101 (332)
T ss_pred             CCCCEEEECCCCCCCH------HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEHHHHHHHCCCCEEEEE
T ss_conf             2133343036773203------6888778999999999998999998738834899955777769999974898727988


Q ss_pred             EECCCCCCEEEEEECHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHH
Q ss_conf             97367783399998878999999887278887666666565798999999999999999999985100273200000244
Q gi|254780687|r   86 ASLSSWSSNFFIGCSNNLVITLLENLLGASHETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYD  165 (318)
Q Consensus        86 ~~~~pl~g~~ll~id~~l~~~lid~~lGG~g~~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~~  165 (318)
T Consensus       102 ~~~~p~~g~~~~~~d~~~vf~~vd~LfGG~G~~~~~~~~R~lT~iE~~v~~~il~~i~~~l~eaw~~v~~~ep~~~~~e~  181 (332)
T COG1868         102 FSMKPLKGTALLEFDPSLVFIMVDRLFGGDGRFPAKPEGRELTDIEQRVITKLLERILEALKEAWNAVIELEPEIVRSET  181 (332)
T ss_pred             EECCCCCCEEEEEECHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             84166786289998867899999996099998888767898759999999999999999999875145503301344125


Q ss_pred             HHCHHHHCCCCCCCEEEEEEEEEEECCEEEEEEEEEEHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHHHCEEEEEE
Q ss_conf             311000012478718999998866678137999985047752567754320-2442237989999999997408007999
Q gi|254780687|r  166 IDYLKKNTNRLSNEFVTTINMNMTIENVASSFVLIIPQETLLKTTLISLSS-QNKSENQSEDLIDPFARKTYQLNVNIDT  244 (318)
Q Consensus       166 ~~~~~~~~~~~p~e~vi~i~~~v~~~~~~g~~~l~lP~~~l~~~~~~~~~~-~~~~~~~~~~~~~~l~~~l~~~~v~i~a  244 (318)
T Consensus       182 --~p~~~~iv~pne~vv~i~~~i~ig~~~g~~niciP~~~le~i~~kl~~~~~~~~~~~~~~w~~~L~~~v~~v~V~l~A  259 (332)
T COG1868         182 --NPQFAQIVSPNEIVVLITLEVEIGNLSGMFNICIPYSMLEPIREKLSSRMQENTREKDPEWRKELRQQVQRVEVELEA  259 (332)
T ss_pred             --CHHHHCCCCCCCEEEEEEEEEEECCCCEEEEEEEEHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCEEEEE
T ss_conf             --766650468886299999999977860399999428888989998754432114445747899999997118668999


Q ss_pred             EEEEEEECHHHHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEEEEEECCCCHHHHHHHHHHC
Q ss_conf             9812343098994579997898257899738999999999999998788978999984258146788887514
Q gi|254780687|r  245 RINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRINFDQKSLKNFLHK  317 (318)
Q Consensus       245 ~Lg~~~l~l~dil~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AVrI~~~i~~~~~~l~~~~~~  317 (318)
T Consensus       260 ~l~~~~ltl~~il~L~vGDVI~l~~~~~d~v~v~v~g~~~f~c~~G~~g~~~aVkI~~~i~~~~~~~~~~~~~  332 (332)
T COG1868         260 RLGEISLTLREILRLEVGDVIPLEKPADDRVTVSVGGKPKFLCQYGKSGGQYAVKILELINSEEESLDELLPK  332 (332)
T ss_pred             EEECCEEEHHHHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEECCCCCCEEEEEEEEECCCCHHHHHHHCCC
T ss_conf             9604354699985898886797788777607999999898998116518778999831047602343432059