HHsearch alignment for GI: 254780289 and conserved domain: PRK12536
>PRK12536 RNA polymerase sigma factor; Provisional.
Probab=98.69 E-value=2.7e-06 Score=68.71 Aligned_cols=170 Identities=16% Similarity=0.209 Sum_probs=114.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf 68899999987653321124689998755578999887522356-77788754436799998874385457312010289
Q gi|254780289|r 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682)
Q Consensus 424 i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~-~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682)
T Consensus 2 ~~~l~~Ll~~~~~GD~~---Af~~l~~~y~~~l~~~~~~~l~~~~~~AEDl~Qe~fl~~~~~~~~~~~~~--~~~~---- 72 (178)
T PRK12536 2 ESRLKALLLRGLAGDAA---AYRQFLTELARHLRAFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRPDQ--PLTA---- 72 (178)
T ss_pred HHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH----
T ss_conf 48899999999815699---99999999999999999999099876899999999999999787669999--6899----
Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682)
Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682)
T Consensus 73 WL~-~Ia~n~---------------~~d~~R~~~--------r~~~~~---------------------------~~~~~ 101 (178)
T PRK12536 73 WVQ-AIARYK---------------LADFLRRRA--------RREALH---------------------------DPLDD 101 (178)
T ss_pred HHH-HHHHHH---------------HHHHHHHHH--------CCCCCC---------------------------CCCHH
T ss_conf 999-999999---------------999999874--------645445---------------------------75112
Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682)
Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682)
T Consensus 102 ~~-----~~~~~~~-~~~------~~~~~~l~~~l~~Lp~~~R~~~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~R 165 (178)
T PRK12536 102 EA-----ELFATSD-DEA------AEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVEETAQLTGLSESAVKVGIHR 165 (178)
T ss_pred HH-----HCCCCCC-CCH------HHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 32-----0247886-358------99999999999869998999999998----85999999999989299999999999
Q ss_pred HHHHHCC
Q ss_conf 9998329
Q gi|254780289|r 663 AIRKLKH 669 (682)
Q Consensus 663 a~~~l~~ 669 (682)
T Consensus 166 a~k~Lr~ 172 (178)
T PRK12536 166 GLKALAA 172 (178)
T ss_pred HHHHHHH
T ss_conf 9999999