HHsearch alignment for GI: 254780289 and conserved domain: PRK06986

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated.
Probab=100.00  E-value=0  Score=417.42  Aligned_cols=221  Identities=27%  Similarity=0.453  Sum_probs=198.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHC
Q ss_conf             2112468999875557899988752235---6777887544367999988743854573120102898999999999722
Q gi|254780289|r  439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ  515 (682)
Q Consensus       439 ~e~~~AK~~l~~anlr~v~~~~~~~~~~---~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~  515 (682)
T Consensus         4 ~~g~~Ar~~Lv~~nl~LV~~iA~r~~~r~~~~v~~~DLiQeG~iGLi~AvekFDp~~G~rFsTYA~~~Ir~aI~~~~r~~   83 (234)
T PRK06986          4 AQGKMSQDSLVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEASRRYDGEQGASFETYAGQRIRGAMLDELRSG   83 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             76899999999981999999999997338999988999999999999999981886699969999999999999999854


Q ss_pred             CCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             870461420588989999999998776088999789998709998999999986--089875536358899860475623
Q gi|254780289|r  516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIE  593 (682)
Q Consensus       516 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~~~~~~~~~~~~  593 (682)
T Consensus        84 ~~---~~r~~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~~~~~~-~-~~~~-~  157 (234)
T PRK06986         84 DW---VPRSVRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDLGESGE-L-LTDE-D  157 (234)
T ss_pred             CC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC-C-CCCC-C
T ss_conf             56---649999999999999999999878799899999895949999999999850577868776776643-1-1122-2


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             8988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       594 d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
T Consensus       158 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y----~~~~tl~eIa~~lgiS~eRVrQie~~AL~kLR~  229 (234)
T PRK06986        158 QSEHEDPLQQLEDEELREALVEAIEKLPEREQLVLSLYY----DEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA  229 (234)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             457899999999999999999999809999999999873----899899999999797899999999999999999