HHsearch alignment for GI: 254780289 and conserved domain: PRK11924
>PRK11924 RNA polymerase sigma factor; Provisional.
Probab=98.91 E-value=2.8e-07 Score=76.46 Aligned_cols=170 Identities=17% Similarity=0.207 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH
Q ss_conf 99998765332112468999875557899988752235677788754436799998874385457312010289899999
Q gi|254780289|r 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508 (682)
Q Consensus 429 ~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i 508 (682)
T Consensus 2 ~l~~~a~~Gd~---~Af~~ly~~y~~~l~~~~~~~~~d~~~AeDi~Qe~fi~l~~~~~~~~~~~~~~--~----wL~~ia 72 (180)
T PRK11924 2 QLPAVAASGDK---EAFSELFLPHAPDLLRYARRQLGNRALAEDAVQEAFLRAWRKADLFNGKGSAR--T----WLLTIA 72 (180)
T ss_pred HHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHH--H----HHHHHH
T ss_conf 88899995599---99999999999999999999929999999999999999988632235434799--9----999999
Q ss_pred HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEE
Q ss_conf 99997228704614205889899999999987760889997899987099989999999860898755363588998604
Q gi|254780289|r 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588 (682)
Q Consensus 509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~ 588 (682)
T Consensus 73 rn~~~d~~r----------------k~~~~-------------------------------~~~~~~~~~~--------- 96 (180)
T PRK11924 73 RNKCYDMLR----------------RRRRE-------------------------------RKEAAEDEDL--------- 96 (180)
T ss_pred HHHHHHHHH----------------HHHHH-------------------------------CCCCCCHHHC---------
T ss_conf 999999999----------------97201-------------------------------0223311001---------
Q ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 75623898899899999999999999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682)
Q Consensus 589 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682)
T Consensus 97 ~~~--~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 170 (180)
T PRK11924 97 APL--SAEFETPEAALLAKDDLARIDRCLDALPEKQREVFLLRY----VEGLSYQEIADQLGVPLGTVKSRLRRARQKLR 170 (180)
T ss_pred CCC--CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 333--446698589999999999999999859999999999999----96859999999989499999999999999999
Q ss_pred C
Q ss_conf 9
Q gi|254780289|r 669 H 669 (682)
Q Consensus 669 ~ 669 (682)
T Consensus 171 ~ 171 (180)
T PRK11924 171 E 171 (180)
T ss_pred H
T ss_conf 9