HHsearch alignment for GI: 254780289 and conserved domain: PRK12542
>PRK12542 RNA polymerase sigma factor; Provisional.
Probab=98.67 E-value=3.4e-06 Score=67.90 Aligned_cols=162 Identities=19% Similarity=0.155 Sum_probs=113.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682)
Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682)
T Consensus 8 ~~afe~Ly~~y~~~ly~~a~~~~~d~~~AEDivQe~Flk~~~~~~~~~~~~~~~~~~---wL~rIa~N~~id-------- 76 (185)
T PRK12542 8 YEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKR---YILRVAKNKAID-------- 76 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH---HHHHHHHHHHHH--------
T ss_conf 999999999999999999999949999999999999999999888716655267999---999999999999--------
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682)
Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682)
T Consensus 77 ---------~~Rk~k--------~~~~~--------------------------~~~~~--~~~------~-~~~~~~~e 104 (185)
T PRK12542 77 ---------SYRKNK--------RHETF--------------------------LEEYE--RES------I-EAVDENIE 104 (185)
T ss_pred ---------HHHHHC--------CCCCC--------------------------HHHHH--CCC------C-CCCCCCHH
T ss_conf ---------999732--------43442--------------------------01321--023------3-56787743
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf 999999999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682)
Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682)
T Consensus 105 ~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~gls~~EIA~~L~is~~tVk~rl~RArk~Lr~~ 169 (185)
T PRK12542 105 EWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 7999998999999999829998889976799----8399999999998929999999999999999998