HHsearch alignment for GI: 254780722 and conserved domain: COG1955

>COG1955 FlaJ Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion].
Probab=99.00  E-value=1.5e-07  Score=65.62  Aligned_cols=119  Identities=13%  Similarity=0.180  Sum_probs=107.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHH
Q ss_conf             69999999999999999999999995-69998999999999248428999999999863038888999997753487347
Q gi|254780722|r    3 HLIKKRTAKFLDDFPNALDIIVRSVR-AGLPVSDAVAVIVGQSSDPVRSEFRRVIETQHLGLSLSESISRMVRYMPLQEV   81 (187)
Q Consensus         3 ~~~~~R~~~~~~~l~~~l~~l~~~l~-aG~sl~~Al~~~a~~~~~~l~~e~~~i~~~~~~G~~~~~al~~~~~~~~~~~~   81 (187)
T Consensus       290 ~~~E~kI~~rDe~F~~FIRSLgss~sa~G~~l~~aLe~l~~~nfG~L~~~I~~LYkRL~~gids~~aW~~F~aeTGS~LI  369 (527)
T COG1955         290 RKEERKINRRDEAFPSFIRSLGSSLSAVGNTLVEALEALDRHNFGILTEDIRRLYKRLAMGIDSNKAWRLFSAETGSYLI  369 (527)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
T ss_conf             58877775377667999998612342202459999998634224003177999999987168988899885047466999


Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999998742574689999999999999999999999
Q gi|254780722|r   82 SFFSTVISVQSQLGGNLSEALANLSRILRDRKNMKAKVQA  121 (187)
Q Consensus        82 ~~~~~~l~~~~~~gg~~~~~L~~la~~~~~~~~~~~~~~~  121 (187)
T Consensus       370 ~~~S~if~d~i~lGGdp~~~GeiIS~n~~~iv~LR~kR~q  409 (527)
T COG1955         370 SKFSEIFTDAIDLGGDPDVVGEIISENFLEIVLLRKKREQ  409 (527)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999971898789999987727999999999987