HHsearch alignment for GI: 254780289 and conserved domain: PRK12515
>PRK12515 RNA polymerase sigma factor; Provisional.
Probab=98.88 E-value=4.7e-07 Score=74.68 Aligned_cols=169 Identities=18% Similarity=0.261 Sum_probs=124.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf 99999987653321124689998755578999887522356777887544367999988743854573120102898999
Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682)
Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682)
T Consensus 9 D~~Lv~~~~~gd~---~Af~~L~~ry~~~l~~~~~~~~~~~~~AeDivQe~Fl~~~~~~~~~~~~~~--~~~---WL~~I 80 (189)
T PRK12515 9 DEMLLARIAQGDR---TAMHTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQ--VST---WLLSI 80 (189)
T ss_pred HHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCH--HHH---HHHHH
T ss_conf 9999999993779---999999999999999999999299999999999999999986510253022--999---99999
Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99999972287046142058898999999999877608899978999870999899999998608987553635889986
Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682)
Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682)
T Consensus 81 arn~~~-----------------~~~r~~~--------~--------------------------~~~------~~~~~~ 103 (189)
T PRK12515 81 ARFKAL-----------------SALRQRK--------D--------------------------EEI------DDEAAA 103 (189)
T ss_pred HHHHHH-----------------HHHHHCC--------C--------------------------CCC------CHHHHH
T ss_conf 999999-----------------9998513--------3--------------------------666------545676
Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682)
Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682)
T Consensus 104 ~----~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~R~vi~l~~----~e~~s~~EIA~~lgis~~tV~~~l~RAr~~ 174 (189)
T PRK12515 104 A----IED-GSDTPEVALQKKDTSAILRACIAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARKK 174 (189)
T ss_pred H----CCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 3----367-7899889998999999999998759999999999999----849999999999892999999999999999
Q ss_pred HCC
Q ss_conf 329
Q gi|254780289|r 667 LKH 669 (682)
Q Consensus 667 l~~ 669 (682)
T Consensus 175 Lr~ 177 (189)
T PRK12515 175 LAE 177 (189)
T ss_pred HHH
T ss_conf 999