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