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