HHsearch alignment for GI: 254780611 and conserved domain: PRK12531
>PRK12531 RNA polymerase sigma factor; Provisional.
Probab=99.80 E-value=2.5e-17 Score=135.33 Aligned_cols=184 Identities=18% Similarity=0.209 Sum_probs=134.5
Q ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf 99899999999999828599999999943077875655557999988899999988899898621853456899975778
Q gi|254780611|r 29 LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108 (302)
Q Consensus 29 Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~w 108 (302)
T Consensus 9 ~~~~~~~eLi~r~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDlvQe~Flk~~~~~~~~~~~~s-~f~tWl~~I 86 (194)
T PRK12531 9 FGRQEWLECMEKVK-SRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTI 86 (194)
T ss_pred CCCHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHH
T ss_conf 35166999999999-5889999999999999999999999399999999999999999998886676536-099999999
Q ss_pred HHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 99999985320246001102300358999999997887866244788824677888618983211000000122343355
Q gi|254780611|r 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188 (302)
Q Consensus 109 Ir~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~ 188 (302)
T Consensus 87 a~N~~~d~lRk~~~----------------------~~~-------------------~~~~----------------~~ 109 (194)
T PRK12531 87 IRNLCFDLLRKQKG----------------------KDL-------------------HIHA----------------DD 109 (194)
T ss_pred HHHHHHHHHHHHCC----------------------CCC-------------------CCCH----------------HH
T ss_conf 99999999997404----------------------343-------------------4321----------------11
Q ss_pred HCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHH
Q ss_conf 20232345320000012356870565566666667779999996219999999999982788888989999997789999
Q gi|254780611|r 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268 (302)
Q Consensus 189 ~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eR 268 (302)
T Consensus 110 ~~~-~~~~~~---~~-~-~~~~~e--------~~~~~~~~~~~l~~Lp~~~R~vi~L~~~e~--~s~~EIAe~l~is~~T 173 (194)
T PRK12531 110 IWP-SDYYPP---DL-V-DHYSPE--------QDMLKEQVMKFLDRLPKAQRDVLQAVYLEE--LPHQQVAEMFDIPLGT 173 (194)
T ss_pred CCC-CCCCCC---CC-C-CCCCHH--------HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHH
T ss_conf 142-224783---00-0-125879--------999999999999869999999999998869--9999999998929999
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999974
Q gi|254780611|r 269 VRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 269 VrQI~~~AL~kLR~~l~~~ 287 (302)
T Consensus 174 VKsrl~rA~k~LR~~Le~e 192 (194)
T PRK12531 174 VKSRLRLAVEKLRHSMDAE 192 (194)
T ss_pred HHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999998657