HHsearch alignment for GI: 254780611 and conserved domain: PRK12541

>PRK12541 RNA polymerase sigma factor; Provisional.
Probab=99.46  E-value=1.1e-11  Score=97.63  Aligned_cols=160  Identities=11%  Similarity=0.142  Sum_probs=108.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf             85999999999430778756555579999888999999888998986218534568999757789999998532024600
Q gi|254780611|r   45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV  124 (302)
Q Consensus        45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I  124 (302)
T Consensus         2 ~~r~afe~ly~~~~~~l~~~~~~~~~d~~~AeDl~QetFlk~~~~~~~~~---~~~~~~WL~~Ia~N~~~d~~-------   71 (161)
T PRK12541          2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK---GEEIRPWLFTIAYNAFIDWY-------   71 (161)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC---CCCHHHHHHHHHHHHHHHHH-------
T ss_conf             63999999999999999999999939999999999999999998361316---67568999999999999999-------


Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC
Q ss_conf             11023003589999999978878662447888246778886189832110000001223433552023234532000001
Q gi|254780611|r  125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL  204 (302)
Q Consensus       125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l  204 (302)
T Consensus        72 ---------------Rk~~~~--------~~-~---------------------------~~~~--------------~~   86 (161)
T PRK12541         72 ---------------RKEKKY--------KT-T---------------------------TVEE--------------FH   86 (161)
T ss_pred             ---------------HHHHCC--------CC-C---------------------------CHHH--------------HC
T ss_conf             ---------------986044--------65-5---------------------------2555--------------40


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             23568705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r  205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI  284 (302)
Q Consensus       205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l  284 (302)
T Consensus        87 ~~~~~~~~~~~~~~~----~~~~~~~~l~~Lp~~~R~v~~L~~~~g--~s~~EIA~~lgis~~tVk~~l~RArk~Lr~l~  160 (161)
T PRK12541         87 LPNVPSTEHEYFVKH----EIASWLDSLSSLPLERRNVLLLRDYYG--FSYKEIAEMTGLSLAKVKIELHRGRKETKSIK  160 (161)
T ss_pred             CCCCCCCHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             468999627789999----999999999819999999999899749--99999999989399999999999999998762


Q ss_pred             H
Q ss_conf             9
Q gi|254780611|r  285 Q  285 (302)
Q Consensus       285 ~  285 (302)
T Consensus       161 E  161 (161)
T PRK12541        161 E  161 (161)
T ss_pred             C
T ss_conf             9