HHsearch alignment for GI: 254780289 and conserved domain: PRK09636
>PRK09636 RNA polymerase sigma factor SigJ; Provisional.
Probab=97.94 E-value=0.0011 Score=48.17 Aligned_cols=153 Identities=14% Similarity=0.190 Sum_probs=99.6
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHH
Q ss_conf 98755578999887522356777887544367999988743854573120102898999999999722870461420588
Q gi|254780289|r 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527 (682)
Q Consensus 448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~ 527 (682)
T Consensus 5 ~fe~~R~~L~~~AyRmlGs~~DAEDvvQEt~lr~~~~-~~~------~~~~~~aWL~rI~~n~~ld-------------- 63 (289)
T PRK09636 5 EFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNA-DRA------EIRDPRAFLTRVVTRLCLD-------------- 63 (289)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC-CCC------CCCCHHHHHHHHHHHHHHH--------------
T ss_conf 8998799999999998099978999999999998506-842------2347899999999999999--------------
Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH-HHHHH
Q ss_conf 98999999999877608899978999870999899999998608987553635889986047562389889989-99999
Q gi|254780289|r 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL-DSAIQ 606 (682)
Q Consensus 528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~-~~~~~ 606 (682)
T Consensus 64 ---~LR~ar~rre~~~g-------------~----------------wlpep~~------------~-~~~~p~~~~~~~ 98 (289)
T PRK09636 64 ---RLRSARHRRETYVG-------------P----------------WLPEPVV------------E-DSDDPLEAVVAA 98 (289)
T ss_pred ---HHHHHHCCCCCCCC-------------C----------------CCCCCCC------------C-CCCCCHHHHHHH
T ss_conf ---99854016554678-------------7----------------7887667------------8-889935678877
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf 9999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682)
Q Consensus 607 ~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682)
T Consensus 99 e~~~~al~~~L~~L~p~qRav~vLrdv~----g~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~ 158 (289)
T PRK09636 99 EDLSLALMLALERLSPLERAAFLLHDVF----GVPFDEIASTLGRSEAACRQLASRARKHVRAA 158 (289)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHH----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf 8899999999973999896254049860----99999999998179999999999999987344