HHsearch alignment for GI: 254780611 and conserved domain: PRK12524
>PRK12524 RNA polymerase sigma factor; Provisional.
Probab=99.72 E-value=2.4e-15 Score=122.06 Aligned_cols=179 Identities=17% Similarity=0.231 Sum_probs=127.9
Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
T Consensus 10 ~~sD~---~Lv~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~l~d~~~AEDlvQe~Fl~~~~~~~~~~~~~~-~~~tWL~~ 84 (196)
T PRK12524 10 DVSDE---ALLVLFA-NGDPAAARALTLRLAPRALAVATRVLGNRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVSTWLYR 84 (196)
T ss_pred CCCHH---HHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHH
T ss_conf 89999---9999999-2889999999999999999999999199999999999999999997466156520-79999999
Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335
Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302)
Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302)
T Consensus 85 Ia~N~~~d~----------------------~R~~~~~---------~----------------------------~~~~ 105 (196)
T PRK12524 85 VVCNLCTDR----------------------LRRQRRA---------S----------------------------VDLD 105 (196)
T ss_pred HHHHHHHHH----------------------HHHHHCC---------C----------------------------CCCC
T ss_conf 999999999----------------------9985056---------7----------------------------7611
Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999
Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302)
Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302)
T Consensus 106 ~------~--~----~~~~~~~~~e~~~~----~~~~~~~l~~al~~Lp~~~R~vi~L~~~eg--~s~~EIA~~lgis~~ 167 (196)
T PRK12524 106 D------A--P----EPADAAPGAEEALQ----EGDRMRALDAALAALPERQRQAVVLRHIEG--LSNPEIAEVMQIGVE 167 (196)
T ss_pred C------C--C----CCCCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH
T ss_conf 2------4--3----32456898879999----899999999999859999999989999808--999999999892999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999999740
Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~ 288 (302)
T Consensus 168 tVk~~l~Rark~Lr~~L~~~r 188 (196)
T PRK12524 168 AVESLTARGKRALAALLAGQR 188 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999987179