HHsearch alignment for GI: 254780289 and conserved domain: COG1191
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription].
Probab=100.00 E-value=2.9e-36 Score=305.21 Aligned_cols=235 Identities=29% Similarity=0.485 Sum_probs=210.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf 12688999999876533211246899987555789998875223567-77887544367999988743854573120102
Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682)
Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682)
T Consensus 6 ~~~~e~~~~~~~~~~g~---~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA 81 (247)
T COG1191 6 LSKEEEEKLLEYYAEGD---EEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYA 81 (247)
T ss_pred CCHHHHHHHHHHHHHCC---HHHH-HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf 24689999999998458---9999-9999978999999999980599854389997899999999974931286148889
Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCC
Q ss_conf 89899999999972287046142058898999999999877608899978999870999899999998608--9875536
Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLET 578 (682)
Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~~ 578 (682)
T Consensus 82 ~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~ 160 (247)
T COG1191 82 VRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDE 160 (247)
T ss_pred HHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 9999999999998478-746768998887788999999999847998689999896989999999998730124541100
Q ss_pred CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 35889986047562389889989999999999999999732998899999998187986746889998996678999999
Q gi|254780289|r 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658 (682)
Q Consensus 579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq 658 (682)
T Consensus 161 ~~~~~~d~~-----~~~~~~~~~~~~~~~~~~~~l~~~i~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSq 231 (247)
T COG1191 161 DVLKDDDDD-----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSR 231 (247)
T ss_pred CCCCCCCCC-----HHHCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHH
T ss_conf 001356520-----2202356035778899999999998766899999999999----7015799999994914989999
Q ss_pred HHHHHHHHHCCH
Q ss_conf 999999983296
Q gi|254780289|r 659 IEAKAIRKLKHP 670 (682)
Q Consensus 659 i~~~a~~~l~~~ 670 (682)
T Consensus 232 l~kkai~kLr~~ 243 (247)
T COG1191 232 LHKKAIKKLRKE 243 (247)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999998