HHsearch alignment for GI: 254780690 and conserved domain: COG1377
>COG1377 FlhB Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion].
Probab=97.81 E-value=0.0066 Score=43.48 Aligned_cols=314 Identities=16% Similarity=0.169 Sum_probs=182.9
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf 99876787768665878799999--8578751335999999999999999999999999999999997200012104979
Q gi|254780690|r 1 MSENDAPDNKTEAPSSKKIEDAL--NEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDIS 78 (354)
Q Consensus 1 MAe~d~~~eKTE~PT~kRL~dAR--ekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 78 (354)
T Consensus 4 ~~~~eKTE~pT~kKl~dArekG~v~kS~el~~a--~~ll~g~~~l~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~-~~~~ 80 (363)
T COG1377 4 MADDEKTEKPTPKKLRDAREKGQVPKSRELTSA--ASLLVGFLLLFFFGSYFARRLSGFLRAFLEFPESMDLDDE-SALE 80 (363)
T ss_pred CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH-HHHH
T ss_conf 434456778985669999974788630668999--9999999999999999999999999999826242123722-5999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H--HCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 899999999999999999999999988776878532-1--0137121377910169343033201266799999999999
Q gi|254780690|r 79 HIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQR-I--PVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKI 155 (354)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~-G--~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv 155 (354)
T Consensus 81 ~~~~~~~~~~~~llp~~~~~~v~gi~~~~~q~g~~fs~e~ikP~~~kinP-~~G~KRiFs~~~~vEl--lKsllKi~~v~ 157 (363)
T COG1377 81 LIKALLLEILKALLPFLLVLLVVGLLANILQVGFLFSTEALKPKFSKLNP-IKGLKRIFSLQTLVEL--LKSLLKIVLVG 157 (363)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCH-HHHHHHHHHHHHHHHH--HHHHHHHHHHH
T ss_conf 99999999999999999999999999999984763146346777211493-6778998458899999--99999999999
Q ss_pred HHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHH
Q ss_conf 99999999999832156897840897999999999999999999999999999766799999998406-99899999975
Q gi|254780690|r 156 ILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLK-MSKQEIKDEIK 234 (354)
Q Consensus 156 ~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lk-MskqEvK~E~K 234 (354)
T Consensus 158 -~v~~~~l~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~liia~~D~~~qr~~~~k~lkMtKqEVKdE~K~sEG 236 (363)
T COG1377 158 -LVAYFVLKNHLSELLSLAGQSPVAALSIFMELLGKLLLAVLLLLLIVAAFDYFYQRFQYIKKLKMTKQEVKDEYKQSEG 236 (363)
T ss_pred -HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf -9999999941999997704898999999999999999999999999999999999999999666868999999861569
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHH-------------------CCCCCEEEEC-CCCEEEEEEECCCCCCCCEEEEE
Q ss_conf 448998999999999999999889860-------------------7768699873-55307888976888888889980
Q gi|254780690|r 235 QSYGNPIIKNRQKSIARSRIRHKMMEA-------------------TSRATIIITN-PTHYALALRYIQTENDAPVLVAK 294 (354)
Q Consensus 235 ~~EGdP~iK~~~r~~~re~~~~~~~~~-------------------V~~A~vvitN-PTH~AVAL~Y~~~~~~aP~vvaK 294 (354)
T Consensus 237 dPeVKsr~Rq~~re~a~~rm~~~Vp~AdvVItNPTH~AVAlkY~~~~~~AP~VvAKG~d~~AlkIreiA~e~~Ipi~enp 316 (363)
T COG1377 237 DPEVKSRIRQMQREIARRRMMSDVPKADVVITNPTHYAVALKYDPEKMPAPVVVAKGVDLVALKIREIAKEHGIPIIENP 316 (363)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCH
T ss_conf 80566899999999999999851899888972766113454665555899989981786999999999998499564180
Q ss_pred CCCHHHHHHHHHH-HHCCCCEEECHHHHHHH
Q ss_conf 7658999999999-97399788688999999
Q gi|254780690|r 295 GQNLIAKKMRKIA-YEHNIPIFEEPSLARSL 324 (354)
Q Consensus 295 G~~~~A~~Ir~~A-~~~~Vpive~~~LAR~L 324 (354)
T Consensus 317 ---pLARaLY~~~~v~~~IP~e~y~aVaevL 344 (363)
T COG1377 317 ---PLARALYRQVEVGQQIPEELYKAVAEVL 344 (363)
T ss_pred ---HHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf ---7799999725766648999999999999