HHsearch alignment for GI: 254780611 and conserved domain: PRK06986
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated.
Probab=100.00 E-value=0 Score=382.92 Aligned_cols=227 Identities=21% Similarity=0.292 Sum_probs=182.8
Q ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9982859999999994307787565555799---9988899999988899898621853456899975778999999853
Q gi|254780611|r 41 YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117 (302)
Q Consensus 41 ~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~---g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i 117 (302)
T Consensus 2 ~~~-~g~~Ar~~Lv~~nl~LV~~iA~r~~~r~~~~v~~~DLiQeG~iGLi~AvekFDp~~G~rFsTYA~~~Ir~aI~~~~ 80 (234)
T PRK06986 2 YTA-QGKMSQDSLVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEASRRYDGEQGASFETYAGQRIRGAMLDEL 80 (234)
T ss_pred CCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 617-6899999999981999999999997338999988999999999999999981886699969999999999999999
Q ss_pred HCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC--CCCCCHHHHCCCCCC
Q ss_conf 202460011023003589999999978878662447888246778886189832110000001--223433552023234
Q gi|254780611|r 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDK 195 (302)
Q Consensus 118 ~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~--~~~~SLd~~i~~~d~ 195 (302)
T Consensus 81 r~~~~---~~r~-----~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~~~~~~- 151 (234)
T PRK06986 81 RSGDW---VPRS-----VRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDLGESGE- 151 (234)
T ss_pred HHCCC---CCHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC-
T ss_conf 85456---6499-----99999999999999999878799899999895949999999999850577868776776643-
Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999
Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
T Consensus 152 ---~~~~~~~~~~~~----~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y~--~~~tl~eIa~~lgiS~eRVrQie~~ 222 (234)
T PRK06986 152 ---LLTDEDQSEHED----PLQQLEDEELREALVEAIEKLPEREQLVLSLYYD--EELNLKEIGAVLGVSESRVSQIHSQ 222 (234)
T ss_pred ---CCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf ---111222457899----9999999999999999998099999999998738--9989999999979789999999999
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999997
Q gi|254780611|r 276 AFKKVQESIQK 286 (302)
Q Consensus 276 AL~kLR~~l~~ 286 (302)
T Consensus 223 AL~kLR~~L~e 233 (234)
T PRK06986 223 AIKRLRARLGE 233 (234)
T ss_pred HHHHHHHHHHC
T ss_conf 99999998753