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