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