HHsearch alignment for GI: 254780611 and conserved domain: PRK12542

>PRK12542 RNA polymerase sigma factor; Provisional.
Probab=99.67  E-value=9.5e-15  Score=118.11  Aligned_cols=171  Identities=21%  Similarity=0.216  Sum_probs=121.7

Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             99982859999999994307787565555799998889999998889989862185345689997577899999985320
Q gi|254780611|r   40 RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR  119 (302)
Q Consensus        40 ~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~  119 (302)
T Consensus         2 rv~-~GD~~afe~Ly~~y~~~ly~~a~~~~~d~~~AEDivQe~Flk~~~~~~~~~~~~~~~~~~wL~rIa~N~~id~~Rk   80 (185)
T PRK12542          2 KVT-NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRK   80 (185)
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             641-3489999999999999999999999499999999999999999998887166552679999999999999999997


Q ss_pred             CCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC
Q ss_conf             24600110230035899999999788786624478882467788861898321100000012234335520232345320
Q gi|254780611|r  120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ  199 (302)
Q Consensus       120 ~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~  199 (302)
T Consensus        81 ~k----------------------~~~--------~--~~~~~--------------~~-----~~----~~~-------   98 (185)
T PRK12542         81 NK----------------------RHE--------T--FLEEY--------------ER-----ES----IEA-------   98 (185)
T ss_pred             HC----------------------CCC--------C--CHHHH--------------HC-----CC----CCC-------
T ss_conf             32----------------------434--------4--20132--------------10-----23----356-------


Q ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             00001235687056556666666777999999621999999999998278888898999999778999999999999999
Q gi|254780611|r  200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK  279 (302)
Q Consensus       200 ~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~k  279 (302)
T Consensus        99 -----~--~~~~e~----~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g--ls~~EIA~~L~is~~tVk~rl~RArk~  165 (185)
T PRK12542         99 -----V--DENIEE----WEKRKMSEVQIDTLLKELNESNRQVFKYKVFYN--LTYQEISSVMGITEANVRKQFERARKR  165 (185)
T ss_pred             -----C--CCCHHH----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             -----7--877437----999998999999999829998889976799839--999999999892999999999999999


Q ss_pred             HHHHHHH
Q ss_conf             9999997
Q gi|254780611|r  280 VQESIQK  286 (302)
Q Consensus       280 LR~~l~~  286 (302)
T Consensus       166 Lr~~Lgg  172 (185)
T PRK12542        166 VQNMIGG  172 (185)
T ss_pred             HHHHHCC
T ss_conf             9998767