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