HHsearch alignment for GI: 254780289 and conserved domain: PRK05949
>PRK05949 RNA polymerase sigma factor; Validated.
Probab=100.00 E-value=0 Score=650.02 Aligned_cols=245 Identities=43% Similarity=0.793 Sum_probs=235.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHH
Q ss_conf 99987653321124689998755578999887522356777887544367999988743854573120102898999999
Q gi|254780289|r 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509 (682)
Q Consensus 430 i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~ 509 (682)
T Consensus 82 l~~~~~~g----~~A~~~LI~sNLRLVvsIAkrY~~~Gl~~~DLIQEGniGLirAvekFDp~rG~RFSTYA~wWIRq~I~ 157 (327)
T PRK05949 82 LKQALKQG----KRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAIT 157 (327)
T ss_pred HHHHHHHH----HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHH
T ss_conf 99998758----99999999981999999998643699898999998589999999980965597134200999989999
Q ss_pred HHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
Q ss_conf 99972287046142058898999999999877608899978999870999899999998608987553635889986047
Q gi|254780289|r 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589 (682)
Q Consensus 510 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~ 589 (682)
T Consensus 158 r~i~~~~r~IRlP~~~~~~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~~~~SLD~~v~d~~~~~l~ 237 (327)
T PRK05949 158 RAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMARQPISLDVRVGDNQDTELS 237 (327)
T ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHH
T ss_conf 99998288744637899999999999999999818899889999894999999999998418872236746999740266
Q ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 56238988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682)
Q Consensus 590 ~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682)
T Consensus 238 dll~d~~-~~pe~~~~~~~lr~~l~~~L~~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~ 316 (327)
T PRK05949 238 ELLEDEG-VSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred HHHCCCC-CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 6733688-999999999999999999985699999999999718999698579999999895999999999999999862
Q ss_pred HHHHHHHHHHHC
Q ss_conf 677787566517
Q gi|254780289|r 670 PSRSKKLRSFLD 681 (682)
Q Consensus 670 ~~~~~~l~~~~~ 681 (682)
T Consensus 317 --~~~~l~~y~~ 326 (327)
T PRK05949 317 --RRANVKEYIA 326 (327)
T ss_pred --CHHHHHHHHC
T ss_conf --5788899865