HHsearch alignment for GI: 254780611 and conserved domain: PRK11924
>PRK11924 RNA polymerase sigma factor; Provisional.
Probab=99.73 E-value=9.8e-16 Score=124.69 Aligned_cols=178 Identities=17% Similarity=0.194 Sum_probs=130.3
Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998
Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302)
Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302)
T Consensus 2 ~l~~~a~-~Gd~~Af~~ly~~y~~~l~~~~~~~~~d~~~AeDi~Qe~fi~l~~~~~~~~~~~--~~~~wL~~iarn~~~d 78 (180)
T PRK11924 2 QLPAVAA-SGDKEAFSELFLPHAPDLLRYARRQLGNRALAEDAVQEAFLRAWRKADLFNGKG--SARTWLLTIARNKCYD 78 (180)
T ss_pred HHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHHHHHHHHHHH
T ss_conf 8889999-559999999999999999999999929999999999999999988632235434--7999999999999999
Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC
Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234
Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302)
Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302)
T Consensus 79 ~~rk~~~~~~--------------------------~---~~---------------------------~~~~~~----- 97 (180)
T PRK11924 79 MLRRRRRERK--------------------------E---AA---------------------------EDEDLA----- 97 (180)
T ss_pred HHHHHHHHCC--------------------------C---CC---------------------------CHHHCC-----
T ss_conf 9999720102--------------------------2---33---------------------------110013-----
Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999
Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
T Consensus 98 -------~~~~~~~~~e~~~----~~~~~~~~l~~~l~~L~~~~r~il~l~~~~g--~s~~eIA~~lgis~~tv~~~l~R 164 (180)
T PRK11924 98 -------PLSAEFETPEAAL----LAKDDLARIDRCLDALPEKQREVFLLRYVEG--LSYQEIADQLGVPLGTVKSRLRR 164 (180)
T ss_pred -------CCCCCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf -------3344669858999----9999999999999859999999999999968--59999999989499999999999
Q ss_pred HHHHHHHHHHHHHCC
Q ss_conf 999999999974012
Q gi|254780611|r 276 AFKKVQESIQKQVEL 290 (302)
Q Consensus 276 AL~kLR~~l~~~~~~ 290 (302)
T Consensus 165 a~~~Lr~~Le~~~~~ 179 (180)
T PRK11924 165 ARQKLRECLEAQWSA 179 (180)
T ss_pred HHHHHHHHHHHHHCC
T ss_conf 999999999986546