HHsearch alignment for GI: 254780289 and conserved domain: PRK12513
>PRK12513 RNA polymerase sigma factor; Provisional.
Probab=99.04 E-value=9.4e-08 Score=80.16 Aligned_cols=172 Identities=15% Similarity=0.205 Sum_probs=126.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682)
Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682)
T Consensus 14 ~eL~~~~~~GD~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDl~Qevfl~~~~~~~~~~~~--~~~~~wL~~ia~n~ 88 (194)
T PRK12513 14 EALMLRYRAGDAA---AFEALYARHRTGLYRFLLRLARDPALADDIFQETWLRVIRARSQWQPR--ARFRTWLYQIARNR 88 (194)
T ss_pred HHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHH
T ss_conf 9999999946299---999999999999999999996999999999989999999887616975--45999999999999
Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682)
Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682)
T Consensus 89 ~~~~~R~~~~--------------------~-------~~~------------------------~~~~~--------~- 108 (194)
T PRK12513 89 LIDHWRKHGA--------------------R-------QAP------------------------SLDAD--------E- 108 (194)
T ss_pred HHHHHHHHHC--------------------C-------CCC------------------------CCCHH--------H-
T ss_conf 9999998744--------------------3-------775------------------------31103--------6-
Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682)
Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682)
T Consensus 109 ~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~Lp~~~r~il~L~~----~~g~s~~EIA~~l~is~~tVk~~l~rA~~~L 183 (194)
T PRK12513 109 LAHALA-DDGAGPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLSLEEIAQLTGVPLETVKSRLRYALQKL 183 (194)
T ss_pred HHHCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 650367-78899999999999999999999729989999999999----8499999999998949999999999999999
Q ss_pred CC
Q ss_conf 29
Q gi|254780289|r 668 KH 669 (682)
Q Consensus 668 ~~ 669 (682)
T Consensus 184 r~ 185 (194)
T PRK12513 184 RE 185 (194)
T ss_pred HH
T ss_conf 99