HHsearch alignment for GI: 254780511 and conserved domain: PRK12780

>PRK12780 fliR flagellar biosynthesis protein FliR; Reviewed.
Probab=100.00  E-value=0  Score=393.99  Aligned_cols=246  Identities=32%  Similarity=0.566  Sum_probs=233.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCHHHHHHHHHHHHHH
Q ss_conf             986836999999999999999999985527888628899999999999999521444560-0012206899999999999
Q gi|254780511|r    1 MTISPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDL-QNFVNRAYYSKLVMVELFL   79 (248)
Q Consensus         1 m~~~~~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~-~~~~~~~~~~~l~l~E~~i   79 (248)
T Consensus         1 ~~~~lp~~~l~~lLvf~Ri~~~~~~~P~f~~~~vP~~vR~~lal~la~~l~P~l~~~~~~~~~~~~~~~~~~~~~~E~~i   80 (250)
T PRK12780          1 MSLPLPDSVLGVFLIFCRIGGCLMVVPGYSSARIPVQVRLFIALSVTLALTPLLLPLFRPFLEGAAPAETLLWIGSEMLT   80 (250)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99887799999999999999999986652777784999999999999999987354457644544279999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999999999999999987542220268888753016999999999999999451899999999999755566
Q gi|254780511|r   80 GCVHGLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIG  159 (248)
Q Consensus        80 Gl~lG~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g  159 (248)
T Consensus        81 Gl~lG~~~~l~f~a~~~AG~ii~~q~Gl~~a~~~dP~~~~~~~~l~~f~~~~~~llFl~~~gH~~li~~l~~Sf~~~P~g  160 (250)
T PRK12780         81 GLLIGLLGRVFFFALETMATAVATAIGLGSIPGTPVEDTEPAPALVSLIVLAATALFFATDLHWELLRGLIASYDRIPPG  160 (250)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999999999987075143479878897759999999999999999786999999999976210799


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             55685799999999999999999999999999999999999999985332548999999999999999999999999999
Q gi|254780511|r  160 QELNFGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQF  239 (248)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~  239 (248)
T Consensus       161 ~~~~~~~~~~~~~~~~~~~F~lal~lAaPvi~~~ll~nv~lGil~R~~PQlNvf~vg~P~~i~~Gl~vL~l~~p~l~~~f  240 (250)
T PRK12780        161 EGFGGQAALVQLVDQLSEAFTLALRIASPFIIYSVIVNLAVGLANKLTPTIPVYFISTPFVLFGGLLLLYLLSDEMLTQF  240 (250)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             77563789999999999999999999999999999999999999980335558999956999999999999999999999


Q ss_pred             HHHHHHH
Q ss_conf             9999950
Q gi|254780511|r  240 SHSFLYG  246 (248)
Q Consensus       240 ~~~f~~~  246 (248)
T Consensus       241 ~~~f~~~  247 (250)
T PRK12780        241 SLAYAAW  247 (250)
T ss_pred             HHHHHHH
T ss_conf             9999999