HHsearch alignment for GI: 254780611 and conserved domain: PRK12523

>PRK12523 RNA polymerase sigma factor; Reviewed.
Probab=99.24  E-value=1.4e-09  Score=83.53  Aligned_cols=165  Identities=13%  Similarity=0.113  Sum_probs=111.2

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r   44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL  123 (302)
Q Consensus        44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~  123 (302)
T Consensus         6 ~p~~~~~~~Ly~~~~~~L~~~~~r~~~~~e~AEDivQd~Flrl~~~-~~~~~~--~~~~a~Lf~iarNl~~D~~Rr~---   79 (172)
T PRK12523          6 SPHSELVGALYRDHRGWLLAWLRRNLACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRA---   79 (172)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCC--CCHHHHHHHHHHHHHHHHHHHH---
T ss_conf             9739999999999999999999999498868999999999999827-765673--4599999999999999999989---


Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf             01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r  124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW  203 (302)
Q Consensus       124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~  203 (302)
T Consensus        80 -------------------~~~~~~----------~~~~~~-------------------------~~------------   93 (172)
T PRK12523         80 -------------------ALEQAY----------LAELAL-------------------------VP------------   93 (172)
T ss_pred             -------------------HHHHHH----------HHHHHC-------------------------CC------------
T ss_conf             -------------------988500----------888862-------------------------66------------


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             12356870565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r  204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES  283 (302)
Q Consensus       204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~  283 (302)
T Consensus        94 -~~~~~~~e~~~~~~----e~~~~l~~al~~Lp~~~R~v~~L~~~eG--ls~~EIA~~LgiS~~tVk~~l~rAl~~~~~~  166 (172)
T PRK12523         94 -EAEQPSPEEQHLIL----EDLKAIDRLLGKLSSKARAAFLYNRLDG--MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA  166 (172)
T ss_pred             -CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             -54689979999999----9999999998649999999999999939--9999999998939999999999999999998


Q ss_pred             HHHH
Q ss_conf             9974
Q gi|254780611|r  284 IQKQ  287 (302)
Q Consensus       284 l~~~  287 (302)
T Consensus       167 l~~~  170 (172)
T PRK12523        167 LYGE  170 (172)
T ss_pred             HHCC
T ss_conf             6079