HHsearch alignment for GI: 254780289 and conserved domain: PRK12529
>PRK12529 RNA polymerase sigma factor; Provisional.
Probab=97.77 E-value=0.0046 Score=43.16 Aligned_cols=155 Identities=10% Similarity=0.080 Sum_probs=95.2
Q ss_pred HHHHHHHHHHHHH-HHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf 6899987555789-998875223567-77887544367999988743854573120102898999999999722870461
Q gi|254780289|r 444 AKKEMVEANLRLV-ISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682)
Q Consensus 444 AK~~l~~anlr~v-~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682)
T Consensus 14 a~~~Ly~~h~~~L~~~l~~Rl~~~~~~~AeDl~QDvFlrl~~~~~~~~~~~i~~p---~a~L~rIA-~Nl~id~------ 83 (178)
T PRK12529 14 KVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQP---RAYLARIA-NCVLVSW------ 83 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHH---HHHHHHHH-HHHHHHH------
T ss_conf 9999999999999999999828998354699999999999973444564323348---99999999-9999999------
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 84 ----------~Rr~~~~~~-------~le~~-----------------~-------------------~-~~~~~~pspE 109 (178)
T PRK12529 84 ----------RRRQSLELA-------WLEAL-----------------A-------------------T-LPEPLHPSPE 109 (178)
T ss_pred ----------HHHHHHHHH-------HHHHH-----------------H-------------------C-CCCCCCCCHH
T ss_conf ----------998888987-------89988-----------------6-------------------4-7866689989
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682)
Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682)
T Consensus 110 ~~~~~~e~l~~l~~al~~Lp~r~R~vF~L~r----~eGls~~EIAe~LgiS~~tV~~~l~rAl~~ 170 (178)
T PRK12529 110 QQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 9999999999999998569978889987998----829999999999895999999999999999