HHsearch alignment for GI: 254780611 and conserved domain: PRK12526
>PRK12526 RNA polymerase sigma factor; Provisional.
Probab=99.73 E-value=2.3e-15 Score=122.25 Aligned_cols=186 Identities=13% Similarity=0.157 Sum_probs=130.1
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 19 ~~p~~~~~~Lv~~A~-~GD~~AF~~Ly~~y~~~l~~~~~r~l~d~~~AEDvvQetFlkvw~~~~~~~~~~~-~f~tWL~~ 96 (206)
T PRK12526 19 QVPTELSQWLILVAI-SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYT 96 (206)
T ss_pred CCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHH
T ss_conf 673689999999999-6589999999999999999999999199999999999999999983876586425-29999999
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 97 IarN~~~d~lRk~----------------------~~~~~~------------------~~~-~d~----------~~~~ 125 (206)
T PRK12526 97 VMRNAAFDMLRKI----------------------KAKKEQ------------------NLG-DDI----------WPIE 125 (206)
T ss_pred HHHHHHHHHHHHH----------------------HCCCCC------------------CCC-CHH----------CHHH
T ss_conf 9999999999865----------------------312222------------------321-000----------0044
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 126 --------------~~~~~-~~~~~~~~~~~----~~~~~l~~~l~~LP~~~R~vi~L~~~eg--ls~~EIA~~l~is~~ 184 (206)
T PRK12526 126 --------------QALAE-SQSESEEFSDH----LMDKQILSYIEKLPEAQQTVVKGVYFQE--LSQEQLAQQLNVPLG 184 (206)
T ss_pred --------------HCCCC-CCCCHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH
T ss_conf --------------30145-78835789989----9999999999868999888989999859--999999999893999
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999974
Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 268 RVrQI~~~AL~kLR~~l~~~ 287 (302)
T Consensus 185 TVksrl~rAlk~LR~~L~e~ 204 (206)
T PRK12526 185 TVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred HHHHHHHHHHHHHHHHHHCC
T ss_conf 99999999999999987303