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