HHsearch alignment for GI: 254780511 and conserved domain: COG1684

>COG1684 FliR Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion].
Probab=100.00  E-value=0  Score=373.33  Aligned_cols=241  Identities=30%  Similarity=0.507  Sum_probs=231.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             83699999999999999999998552788862889999999999999952144456000122068999999999999999
Q gi|254780511|r    4 SPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFLGCVH   83 (248)
Q Consensus         4 ~~~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~iGl~l   83 (248)
T Consensus         7 ~~~~~v~~~~l~f~Rv~afl~~~P~~s~~~IP~~vrl~lal~ls~~v~p~l~~-~p~--~~~~~~~~ll~~~EiliG~~~   83 (258)
T COG1684           7 QLEEWVLAFFLPFVRVLAFLMTMPFFSERSIPARVRLGLALALSFAVLPLLPA-VPA--PLFSLEFLLLALSEILIGLAL   83 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC-CCC--CCCCHHHHHHHHHHHHHHHHH
T ss_conf             76899999999999999999982010556553789999999999999945767-885--434488999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             99999999999999999999875422202688887530169999999999999994518999999999997555665568
Q gi|254780511|r   84 GLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIGQELN  163 (248)
Q Consensus        84 G~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g~~~~  163 (248)
T Consensus        84 G~~~~l~f~a~~~aG~~i~~qmGls~a~~~Dp~~~~~~~~l~~~l~~~all~fl~~dgh~~li~~l~~Sf~~~Pv~~~~~  163 (258)
T COG1684          84 GFFAQLLFAALQFAGEIISMQMGLSFATMVDPSSGEQSPLLGQFLNFLALLLFLSLDGHLLLILGLVDSFKALPVGGFFL  163 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHEEECCCCCC
T ss_conf             99999999999999999999872242024688788763399999999999999990775999999998732200466667


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57999999999999999999999999999999999999999853325489999999999999999999999999999999
Q gi|254780511|r  164 FGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSF  243 (248)
Q Consensus       164 ~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f  243 (248)
T Consensus       164 ~~~~~~~l~~~l~~~F~~~l~iAlPii~~lLlvnlalGlv~R~~PQinvf~ig~Pl~i~~Gl~lL~~~lp~i~~~~~~~~  243 (258)
T COG1684         164 NDNAFLLLAKALSAIFLIGLRLALPIIALLLLVNLALGLLNRLAPQLNVFFIGFPLKIAVGLLLLYLILPLIAPVFKHLF  243 (258)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             74099999999999999999999899999999999999998425420068755319999999999999999999999999


Q ss_pred             HHHC
Q ss_conf             9504
Q gi|254780511|r  244 LYGF  247 (248)
Q Consensus       244 ~~~f  247 (248)
T Consensus       244 ~~~~  247 (258)
T COG1684         244 SELF  247 (258)
T ss_pred             HHHH
T ss_conf             9999