HHsearch alignment for GI: 254780611 and conserved domain: PRK12540
>PRK12540 RNA polymerase sigma factor; Provisional.
Probab=99.31 E-value=3.1e-10 Score=87.90 Aligned_cols=160 Identities=12% Similarity=0.154 Sum_probs=107.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf 99999999943077875655557999988899999988899898621853456899975778999999853202460011
Q gi|254780611|r 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302)
Q Consensus 47 ~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302)
T Consensus 4 ~~~f~~~~l~~~P~L~~fa~~l~~n~~dAEDlvQEtflk~~~~~~~~~~~--~~~~tWL~~IarN~~~~~---------- 71 (181)
T PRK12540 4 TDSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAWLFTILRNLFRSD---------- 71 (181)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHH----------
T ss_conf 08899999998799999999993999999999999999999849875987--624899999999999999----------
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCC
Q ss_conf 02300358999999997887866244788824677888618983211000000122343355202323453200000123
Q gi|254780611|r 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206 (302)
Q Consensus 127 P~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~ 206 (302)
T Consensus 72 ------------~Rk~~r~~~----------~-----------------~~------~~~~~--------------~~-~ 91 (181)
T PRK12540 72 ------------YRKRRREVE----------D-----------------AD------GSYAK--------------TL-K 91 (181)
T ss_pred ------------HHHHCCCCC----------C-----------------CC------CCCCC--------------CC-C
T ss_conf ------------998357666----------4-----------------32------11000--------------14-6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 56870565566666667779999996219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 207 ~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
T Consensus 92 ~~~~~~----~~~----~~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIA~iL~is~gTVKsRL~RAr~kLr~~L~~ 161 (181)
T PRK12540 92 SQPGQN----AHL----EFEEFRAALEKLPQDQREALILVGASG--FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (181)
T ss_pred CCCCHH----HHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 899735----677----899999999819999989988799809--9999999998949999999999999999999874
Q ss_pred HH
Q ss_conf 40
Q gi|254780611|r 287 QV 288 (302)
Q Consensus 287 ~~ 288 (302)
T Consensus 162 ~g 163 (181)
T PRK12540 162 DG 163 (181)
T ss_pred CC
T ss_conf 65