HHsearch alignment for GI: 254780289 and conserved domain: PRK12538
>PRK12538 RNA polymerase sigma factor; Provisional.
Probab=98.79 E-value=2.4e-06 Score=69.08 Aligned_cols=171 Identities=13% Similarity=0.238 Sum_probs=128.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH
Q ss_conf 88999999876533211246899987555789998875223567778875443679999887438545731201028989
Q gi|254780289|r 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504 (682)
Q Consensus 425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i 504 (682)
T Consensus 48 d~D~eLv~R~~~GD~---~AF~~Ly~ry~~~l~~~a~r~l~d~~dAEDvvQEvFlk~w~~~~~f~~g~-s~f~---tWL~ 120 (233)
T PRK12538 48 DEDEELLDRLATDDE---AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGR-AKFS---TWLY 120 (233)
T ss_pred CCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHH---HHHH
T ss_conf 978999999996029---99999999999999999999959999999999999999999884477786-7399---9999
Q ss_pred HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 99999999722870461420588989999999998776088999789998709998999999986089875536358899
Q gi|254780289|r 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584 (682)
Q Consensus 505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~ 584 (682)
T Consensus 121 ~IA~N~~id-~-----------------~R---k-----~r~-------------------------~~~--d~-~~e-- 144 (233)
T PRK12538 121 RVVSNRCID-L-----------------RR---K-----PRT-------------------------ENV--DA-VPE-- 144 (233)
T ss_pred HHHHHHHHH-H-----------------HH---H-----HCC-------------------------CCC--CC-CCC--
T ss_conf 999999999-9-----------------97---4-----145-------------------------652--23-444--
Q ss_pred CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 86047562389889989999999999999999732998899999998187986746889998996678999999999999
Q gi|254780289|r 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664 (682)
Q Consensus 585 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~ 664 (682)
T Consensus 145 -------~~d-~~~~~~~~l~~~e~~~~L~~aL~~Lp~~~R~vl~L~~----~egls~~EIA~~Lgis~~TVKsrL~RAr 212 (233)
T PRK12538 145 -------VAD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGR 212 (233)
T ss_pred -------CCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf -------456-8988878999999999999999759999999999999----8499999999998929999999999999
Q ss_pred HHHCCH
Q ss_conf 983296
Q gi|254780289|r 665 RKLKHP 670 (682)
Q Consensus 665 ~~l~~~ 670 (682)
T Consensus 213 ~~LR~~ 218 (233)
T PRK12538 213 QQLRDL 218 (233)
T ss_pred HHHHHH
T ss_conf 999999