HHsearch alignment for GI: 254780611 and conserved domain: PRK12514

>PRK12514 RNA polymerase sigma factor; Provisional.
Probab=99.73  E-value=1.4e-15  Score=123.65  Aligned_cols=178  Identities=14%  Similarity=0.169  Sum_probs=127.9

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             98999999999998285999999999430778756555579999888999999888998986218534568999757789
Q gi|254780611|r   30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI  109 (302)
Q Consensus        30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wI  109 (302)
T Consensus         2 ~p~d~~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~a~~~~~d~~~AeDi~Qe~fl~~~~~~~~~~~~~-~~~~~wL~~ia   79 (179)
T PRK12514          2 QPDDIEKLIVRVS-LGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIA   79 (179)
T ss_pred             CCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHH
T ss_conf             9710999999999-658999999999999999999999909999999999999999998875157665-53999999999


Q ss_pred             HHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             99999853202460011023003589999999978878662447888246778886189832110000001223433552
Q gi|254780611|r  110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL  189 (302)
Q Consensus       110 r~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~  189 (302)
T Consensus        80 rN~~id~~----------------------R~~~----------~~~---------------------------~~~~~~  100 (179)
T PRK12514         80 RNHAIDRL----------------------RARK----------AVA---------------------------VDIDEA  100 (179)
T ss_pred             HHHHHHHH----------------------HHCC----------CCC---------------------------CCHHHH
T ss_conf             99999999----------------------8637----------777---------------------------874567


Q ss_pred             CCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf             02323453200000123568705655666666677799999962199999999999827888889899999977899999
Q gi|254780611|r  190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV  269 (302)
Q Consensus       190 i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV  269 (302)
T Consensus       101 ~-----------~-~~~~~~~~e~~~~~~~----~~~~l~~~l~~Lp~~~r~~~~l~~~eg--~s~~EIA~~l~is~~tV  162 (179)
T PRK12514        101 H-----------D-LADPSPGPEAEVIAGD----EGQRIDACLEELEKDRAAAVRRAYLEG--LSYKELAERHDVPLNTM  162 (179)
T ss_pred             H-----------H-HCCCCCCHHHHHHHHH----HHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHH
T ss_conf             6-----------5-1246898699999889----999999999875599999999996069--98999999889099999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999997
Q gi|254780611|r  270 RQIEARAFKKVQESIQK  286 (302)
Q Consensus       270 rQI~~~AL~kLR~~l~~  286 (302)
T Consensus       163 k~~l~rA~~~Lr~~L~k  179 (179)
T PRK12514        163 RTWLRRSLLKLRECLSR  179 (179)
T ss_pred             HHHHHHHHHHHHHHHCC
T ss_conf             99999999999998576