HHsearch alignment for GI: 254780611 and conserved domain: PRK12543
>PRK12543 RNA polymerase sigma factor; Provisional.
Probab=99.73 E-value=1.5e-15 Score=123.53 Aligned_cols=176 Identities=17% Similarity=0.189 Sum_probs=125.5
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf 99999999998285999999999430778756555579999888999999888998986218534568999757789999
Q gi|254780611|r 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112 (302)
Q Consensus 33 ee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~ 112 (302)
T Consensus 5 d~~~Li~~~~-~Gd~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeD~vQe~Flk~~~~~~~~~~~~--~~~~WL~~ia~n~ 81 (190)
T PRK12543 5 DYKHLIQLTL-SGNKEAYSELYDVTIQEVYKTVHFLIEDKTDVDDVVQEVYIQLYESLRKYDSEK--PFRPWLIGLVIKQ 81 (190)
T ss_pred CHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHH
T ss_conf 8999999999-566999999999999999999999909999999999999999999998718888--6899999999999
Q ss_pred HHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCC
Q ss_conf 99853202460011023003589999999978878662447888246778886189832110000001223433552023
Q gi|254780611|r 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192 (302)
Q Consensus 113 I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~ 192 (302)
T Consensus 82 ~~~~~r~~~----------------------~~~~~~-------------------------------~~~~~~~----- 103 (190)
T PRK12543 82 IHSYRRKRW----------------------MRLRIF-------------------------------KKAEEQR----- 103 (190)
T ss_pred HHHHHHHHH----------------------HHCCCC-------------------------------CCHHHHC-----
T ss_conf 999999875----------------------003412-------------------------------2001001-----
Q ss_pred CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 23453200000123568705655666666677799999962199999999999827888889899999977899999999
Q gi|254780611|r 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 193 ~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI 272 (302)
T Consensus 104 ------------~~~~~~~~~~~~~~----~~~~~l~~~l~~Lp~~~R~vi~L~~~~g--~s~~EIA~~l~is~~tVk~r 165 (190)
T PRK12543 104 ------------KPVQIDFSNDLLSK----ISNQKLIELIHKLPYKLKQVIILRYLHD--YSQEEVAQILHIPIGTVKSR 165 (190)
T ss_pred ------------CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHH
T ss_conf ------------55568826899999----9999999999849999999999999859--99999999989399999999
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999974
Q gi|254780611|r 273 EARAFKKVQESIQKQ 287 (302)
Q Consensus 273 ~~~AL~kLR~~l~~~ 287 (302)
T Consensus 166 l~rA~k~LR~kle~~ 180 (190)
T PRK12543 166 IHAALKKLRQKEQIE 180 (190)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999999