HHsearch alignment for GI: 254780611 and conserved domain: PRK09636

>PRK09636 RNA polymerase sigma factor SigJ; Provisional.
Probab=98.78  E-value=6.1e-07  Score=65.90  Aligned_cols=153  Identities=18%  Similarity=0.182  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHH
Q ss_conf             99430778756555579999888999999888998986218534568999757789999998532024600110230035
Q gi|254780611|r   54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK  133 (302)
Q Consensus        54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r  133 (302)
T Consensus         6 fe~~R~~L~~~AyRmlGs~~DAEDvvQEt~lr~~~~----~~~~~~~~~aWL~rI~~n~~ld~-----------------   64 (289)
T PRK09636          6 FEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNA----DRAEIRDPRAFLTRVVTRLCLDR-----------------   64 (289)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHH-----------------
T ss_conf             998799999999998099978999999999998506----84223478999999999999999-----------------


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHH
Q ss_conf             89999999978878662447888246778886189832110000001223433552023234532000001235687056
Q gi|254780611|r  134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ  213 (302)
Q Consensus       134 ~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~  213 (302)
T Consensus        65 -----LR~ar~rre~~~g~--------------------------------wlpep--------------~~~~~~~p~~   93 (289)
T PRK09636         65 -----LRSARHRRETYVGP--------------------------------WLPEP--------------VVEDSDDPLE   93 (289)
T ss_pred             -----HHHHHCCCCCCCCC--------------------------------CCCCC--------------CCCCCCCCHH
T ss_conf             -----98540165546787--------------------------------78876--------------6788899356


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             5566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r  214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES  283 (302)
Q Consensus       214 ~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~  283 (302)
T Consensus        94 ~~~~---~e~~~~al~~~L~~L~p~qRav~vLrdv~g--~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~  158 (289)
T PRK09636         94 AVVA---AEDLSLALMLALERLSPLERAAFLLHDVFG--VPFDEIASTLGRSEAACRQLASRARKHVRAA  158 (289)
T ss_pred             HHHH---HHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf             7887---788999999999739998962540498609--9999999998179999999999999987344