HHsearch alignment for GI: 254780289 and conserved domain: PRK12541
>PRK12541 RNA polymerase sigma factor; Provisional.
Probab=98.44 E-value=2.6e-05 Score=60.87 Aligned_cols=155 Identities=15% Similarity=0.156 Sum_probs=102.7
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 4 r~afe~ly~~~~~~l~~~~~~~~~d~~~AeDl~QetFlk~~~~~~~~~---~~~~~~---WL~~Ia~N~~~-d~------ 70 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK---GEEIRP---WLFTIAYNAFI-DW------ 70 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC---CCCHHH---HHHHHHHHHHH-HH------
T ss_conf 999999999999999999999939999999999999999998361316---675689---99999999999-99------
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 71 ----------~Rk~~--------~~~~-------------------------~~~~-------~~~----~--~~~~~~~ 94 (161)
T PRK12541 71 ----------YRKEK--------KYKT-------------------------TTVE-------EFH----L--PNVPSTE 94 (161)
T ss_pred ----------HHHHH--------CCCC-------------------------CCHH-------HHC----C--CCCCCCH
T ss_conf ----------99860--------4465-------------------------5255-------540----4--6899962
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682)
Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682)
T Consensus 95 ~~~~~~~~~~~~~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RArk~Lr~ 158 (161)
T PRK12541 95 HEYFVKHEIASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 7789999999999999819999999999899----749999999999893999999999999999987