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