HHsearch alignment for GI: 254780289 and conserved domain: PRK12544
>PRK12544 RNA polymerase sigma factor; Provisional.
Probab=98.82 E-value=8.4e-07 Score=72.67 Aligned_cols=170 Identities=16% Similarity=0.153 Sum_probs=114.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH---HHCCCEEECCC
Q ss_conf 998755578999887522356777887544367999988743854573120102898999999999---72287046142
Q gi|254780289|r 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI---ADQSCTIRIPV 523 (682)
Q Consensus 447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~---~~~~~~~r~~~ 523 (682)
T Consensus 23 ~l~e~y~~~L~r~A~r~l~d~~~AEDlvQEtFlka~~~l~~F~g~s--~f~t---WL~~Ia~N~~iD~lRk~~r~~~~~- 96 (207)
T PRK12544 23 VFLEDLRAQMLKFAKLQLRDNHLAEDAVQEALFSAYQNADSFAGRA--AFKT---WVFAILKNKIIDLLRQKKRHVSAS- 96 (207)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH---HHHHHHHHHHHHHHHHHCCCCCCC-
T ss_conf 9999999999999999949999999999999999998177438888--6098---999999999999999851656521-
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682)
Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682)
T Consensus 97 ------------------~~~~~~~~~~-----------------------~~~-~~~d-~~g~~~~~e~p~~~~~pee~ 133 (207)
T PRK12544 97 ------------------QLEDGDEGEA-----------------------LIE-ALFD-ESGHWQKDERPQKWDQPEEG 133 (207)
T ss_pred ------------------CCCCCCCHHH-----------------------HHH-HHHC-CCCCCCCCCCCCCCCCHHHH
T ss_conf ------------------0134541013-----------------------466-6511-12343333465333898999
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682)
Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682)
T Consensus 134 l~~~e~~~~l~~aL~~Lp~~~R~vl~Lr~----~eglS~~EIAe~Lgis~~tVks~L~RAR~~Lr~ 195 (207)
T PRK12544 134 VEQEQFWRIFDACLDALPAKYARVFMMRE----FIELETPEICHNEDLTVSNLNVMLYRSRLRLRE 195 (207)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999839999999999999----819999999999797999999999999999999