HHsearch alignment for GI: 254780611 and conserved domain: COG1191
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription].
Probab=100.00 E-value=0 Score=350.50 Aligned_cols=241 Identities=24% Similarity=0.378 Sum_probs=204.8
Q ss_pred CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH
Q ss_conf 999998999999999998285999999999430778756555579999-8889999998889989862185345689997
Q gi|254780611|r 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATY 104 (302)
Q Consensus 26 ~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~-~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTY 104 (302)
T Consensus 3 ~~~~~~~e~~~~~~~~~-~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~ty 80 (247)
T COG1191 3 PQPLSKEEEEKLLEYYA-EGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTY 80 (247)
T ss_pred CCCCCHHHHHHHHHHHH-HCCHHHH-HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH
T ss_conf 76224689999999998-4589999-999997899999999998059985438999789999999997493128614888
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--C
Q ss_conf 57789999998532024600110230035899999999788786624478882467788861898321100000012--2
Q gi|254780611|r 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--G 182 (302)
Q Consensus 105 A~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~ 182 (302)
T Consensus 81 A~~~I~Gei~d~LR~~~-~v~vp-----R~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~ 154 (247)
T COG1191 81 AVRRIRGEILDYLRKND-SVKVP-----RSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQ 154 (247)
T ss_pred HHHHHHHHHHHHHHHCC-CCCCC-----HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf 99999999999998478-74676-----8998887788999999999847998689999896989999999998730124
Q ss_pred CCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 34335520232345320000012356870565566666667779999996219999999999982788888989999997
Q gi|254780611|r 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262 (302)
Q Consensus 183 ~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~l 262 (302)
T Consensus 155 ~~sld~~~~~~~d~~-------~~~~~~~~~---~~~~~~~~~~~l~~~i~~L~EREk~Vl~l~y~ee--lt~kEI~~~L 222 (247)
T COG1191 155 LLSLDEDVLKDDDDD-------VDDQIENPD---DGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE--LTQKEIAEVL 222 (247)
T ss_pred CCCCCCCCCCCCCCC-------HHHCCCCCH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHH
T ss_conf 541100001356520-------220235603---5778899999999998766899999999999701--5799999994
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 789999999999999999999997
Q gi|254780611|r 263 EVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 263 giS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
T Consensus 223 gISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 223 GISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 914989999999999999998604