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