HHsearch alignment for GI: 254780611 and conserved domain: PRK12534
>PRK12534 RNA polymerase sigma factor; Provisional.
Probab=99.79 E-value=6.6e-17 Score=132.53 Aligned_cols=186 Identities=16% Similarity=0.204 Sum_probs=138.0
Q ss_pred HCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf 07999998999999999998285999999999430778756555579999888999999888998986218534568999
Q gi|254780611|r 24 RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103 (302)
Q Consensus 24 ~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsT 103 (302)
T Consensus 2 ~~~p~~~~de~~~Li~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~~~~~AeDv~Qe~Fl~vw~~~~~~~~~~~-~~~t 79 (187)
T PRK12534 2 SAIPGHDDDETGRLLTATA-GGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLT 79 (187)
T ss_pred CCCCCCCCHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCC-CHHH
T ss_conf 9999999628999999999-3689999999999999999999998699999999999999999987533687522-1899
Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 75778999999853202460011023003589999999978878662447888246778886189832110000001223
Q gi|254780611|r 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183 (302)
Q Consensus 104 YA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~ 183 (302)
T Consensus 80 Wl~~IarN~~~d~lR~~~~~------------------------------~~---------------------------~ 102 (187)
T PRK12534 80 WLAMIARNKAIDHLRANAPQ------------------------------RR---------------------------N 102 (187)
T ss_pred HHHHHHHHHHHHHHHHCCCC------------------------------CC---------------------------C
T ss_conf 99999999999999962441------------------------------35---------------------------7
Q ss_pred CCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf 43355202323453200000123568705655666666677799999962199999999999827888889899999977
Q gi|254780611|r 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302)
Q Consensus 184 ~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302)
T Consensus 103 ~~~~~------~~~------~~~~~~~~~----e~~~~~~~~~~l~~al~~L~~~~r~vi~l~~~eg--~s~~EIA~~l~ 164 (187)
T PRK12534 103 VALDD------AGE------LRAADASPL----ERTERASTRRRIDHCLAELEPPRSELIRTAFFEG--ITYEELAARTD 164 (187)
T ss_pred CCCCC------CCC------CCCCCCCHH----HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHC
T ss_conf 77341------100------135689827----7899999999999999868998999999999849--99999999989
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999999999997
Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
T Consensus 165 i~~gTVksrl~ra~~~Lr~~Lek 187 (187)
T PRK12534 165 TPIGTVKSWIRRGLAKLKACLER 187 (187)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 19999999999999999998667