HHsearch alignment for GI: 254780289 and conserved domain: PRK12524
>PRK12524 RNA polymerase sigma factor; Provisional.
Probab=98.85 E-value=8.4e-07 Score=72.64 Aligned_cols=169 Identities=16% Similarity=0.235 Sum_probs=124.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682)
Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682)
T Consensus 14 ~~Lv~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~l~d~~~AEDlvQe~Fl~~~~~~~~~~~~~~-~~~t---WL~~Ia 86 (196)
T PRK12524 14 EALLVLFANGDP---AAARALTLRLAPRALAVATRVLGNRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVST---WLYRVV 86 (196)
T ss_pred HHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHH---HHHHHH
T ss_conf 999999992889---999999999999999999999199999999999999999997466156520-7999---999999
Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682)
Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682)
T Consensus 87 ~N~~~d-----------------~~R~~~--------~--------------------------~~~~~~------~~~~ 109 (196)
T PRK12524 87 CNLCTD-----------------RLRRQR--------R--------------------------ASVDLD------DAPE 109 (196)
T ss_pred HHHHHH-----------------HHHHHH--------C--------------------------CCCCCC------CCCC
T ss_conf 999999-----------------999850--------5--------------------------677611------2433
Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682)
Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682)
T Consensus 110 ----~~-~~~~~~e~~~~~~~~~~~l~~al~~Lp~~~R~vi~L~~----~eg~s~~EIA~~lgis~~tVk~~l~Rark~L 180 (196)
T PRK12524 110 ----PA-DAAPGAEEALQEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMQIGVEAVESLTARGKRAL 180 (196)
T ss_pred ----CC-CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf ----24-56898879999899999999999859999999989999----8089999999998929999999999999999
Q ss_pred CC
Q ss_conf 29
Q gi|254780289|r 668 KH 669 (682)
Q Consensus 668 ~~ 669 (682)
T Consensus 181 r~ 182 (196)
T PRK12524 181 AA 182 (196)
T ss_pred HH
T ss_conf 99