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