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