HHsearch alignment for GI: 254780611 and conserved domain: PRK12519
>PRK12519 RNA polymerase sigma factor; Provisional.
Probab=99.78 E-value=5.5e-17 Score=133.07 Aligned_cols=185 Identities=16% Similarity=0.233 Sum_probs=134.6
Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
T Consensus 10 ~m~~~tD~eLi~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDlvQe~fl~~~~~~~-~~~~~~-~~~~wL~~ 86 (194)
T PRK12519 10 SLSSRSDAELFSALK-AGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRG-SLSSYLLT 86 (194)
T ss_pred CCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH-CCCCCC-CHHHHHHH
T ss_conf 999960999999999-385999999999999999999999939999999999999999998633-166624-29999999
Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335
Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302)
Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302)
T Consensus 87 ia~n~~~d~~R~~~~~~----------------------~~----------~~~~~------------------------ 110 (194)
T PRK12519 87 LTRSRAIDRLRSRRSRQ----------------------RL----------LERWQ------------------------ 110 (194)
T ss_pred HHHHHHHHHHHHHHCCC----------------------CH----------HHHHH------------------------
T ss_conf 99999999999863201----------------------22----------44444------------------------
Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999
Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302)
Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302)
T Consensus 111 ~~~~~--~----------~~~~~~~~----~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~~eg--~s~~EIA~~lgis~~ 172 (194)
T PRK12519 111 QELLG--E----------ASEDTPLE----QASLAERSQRVQTALAQLPESQRQVLELAYYEG--LSQSEIAKRLGIPLG 172 (194)
T ss_pred HHHCC--C----------CCCCCHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH
T ss_conf 54114--6----------77898588----998999999999999819988756889999819--999999999894999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999999999999997401
Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~~ 289 (302)
T Consensus 173 tVk~rl~rA~~~Lr~~L~e~le 194 (194)
T PRK12519 173 TVKARARQGLLKLRELLQDLLE 194 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999898739