HHsearch alignment for GI: 254780611 and conserved domain: PRK12535
>PRK12535 RNA polymerase sigma factor; Provisional.
Probab=99.56 E-value=2.5e-12 Score=101.88 Aligned_cols=178 Identities=16% Similarity=0.144 Sum_probs=118.6
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302)
T Consensus 11 a~~~~Lv~~a~-~GD~~Af~~L~~r~~~~v~r~~~~l~~~-~~AeDl~QEtflk~~~~l~~f~~~--~~f~tWL~~Ia~n 86 (195)
T PRK12535 11 AHVTELALAAG-RGDRAALTEFIRATQDDVWRLLAHLGGH-DIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARR 86 (195)
T ss_pred HHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHH
T ss_conf 88999999998-2209999999999999999999893799-779999999999999988770788--8799999999999
Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202
Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302)
Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302)
T Consensus 87 ~~~d----------------------~~R~~~~----------~~~~----------~~-------------~~~~---- 107 (195)
T PRK12535 87 VWVD----------------------NIRHDMA----------RPRK----------SA-------------VEYE---- 107 (195)
T ss_pred HHHH----------------------HHHHHHC----------CCCC----------CC-------------CCCC----
T ss_conf 9999----------------------9998851----------6665----------53-------------3322----
Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999
Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
T Consensus 108 ---~~-------~~~d~-~~~~~~~~-------~~~l~~~l~~Lp~~~R~~l~L~~~~g--~s~~EIA~ilgi~~gTVKs 167 (195)
T PRK12535 108 ---DT-------GATDA-TNAGIWSE-------WIDVRTLIDALPPERREALILTQVLG--YTYEEAAKIADVRVGTIRS 167 (195)
T ss_pred ---CC-------CCCCC-CCCHHHHH-------HHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH
T ss_conf ---35-------66777-64035777-------99999999849998879999999829--9899999998939999999
Q ss_pred HHHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999999999997401224
Q gi|254780611|r 272 IEARAFKKVQESIQKQVELSS 292 (302)
Q Consensus 272 I~~~AL~kLR~~l~~~~~~~~ 292 (302)
T Consensus 168 Rl~RAr~~Lr~~L~~~~~~~~ 188 (195)
T PRK12535 168 RVARARADLVAATATGDSSAE 188 (195)
T ss_pred HHHHHHHHHHHHHHCCCCCCC
T ss_conf 999999999999756897655