HHsearch alignment for GI: 254780611 and conserved domain: PRK12536
>PRK12536 RNA polymerase sigma factor; Provisional.
Probab=99.62 E-value=1.5e-13 Score=110.07 Aligned_cols=173 Identities=16% Similarity=0.175 Sum_probs=119.5
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf 99999999999828599999999943077875655557999-98889999998889989862185345689997577899
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g-~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302)
T Consensus 3 ~~l~~Ll~~~~-~GD~~Af~~l~~~y~~~l~~~~~~~l~~~~~~AEDl~Qe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~ 79 (178)
T PRK12536 3 SRLKALLLRGL-AGDAAAYRQFLTELARHLRAFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRPDQ--PLTAWVQAIAR 79 (178)
T ss_pred HHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHH
T ss_conf 88999999998-1569999999999999999999999099876899999999999999787669999--68999999999
Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC
Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520
Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302)
Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302)
T Consensus 80 n~~~d~~R~~~----------------------r~~------~~~----------------------------~~~~~~~ 103 (178)
T PRK12536 80 YKLADFLRRRA----------------------RRE------ALH----------------------------DPLDDEA 103 (178)
T ss_pred HHHHHHHHHHH----------------------CCC------CCC----------------------------CCCHHHH
T ss_conf 99999999874----------------------645------445----------------------------7511232
Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999
Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302)
T Consensus 104 -----------~~~~~~~~~~~----------~~~~~l~~~l~~Lp~~~R~~~~l~~~eg--~s~~EIA~~lgis~~tVk 160 (178)
T PRK12536 104 -----------ELFATSDDEAA----------EARRDLGKLLEQLPDRQRLPIVHVKLEG--LSVEETAQLTGLSESAVK 160 (178)
T ss_pred -----------HCCCCCCCCHH----------HHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH
T ss_conf -----------02478863589----------9999999999869998999999998859--999999999892999999
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999997
Q gi|254780611|r 271 QIEARAFKKVQESIQK 286 (302)
Q Consensus 271 QI~~~AL~kLR~~l~~ 286 (302)
T Consensus 161 ~rl~Ra~k~Lr~~L~g 176 (178)
T PRK12536 161 VGIHRGLKALAAKIRG 176 (178)
T ss_pred HHHHHHHHHHHHHHCC
T ss_conf 9999999999998079