HHsearch alignment for GI: 254780289 and conserved domain: PRK07406
>PRK07406 RNA polymerase sigma factor RpoD; Validated.
Probab=100.00 E-value=0 Score=706.36 Aligned_cols=246 Identities=54% Similarity=0.874 Sum_probs=237.6
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 139 l~~~~~~g----~~Ar~~LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RFSTYA~WWIRqaI~ 214 (385)
T PRK07406 139 FRRRLMLG----RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAIT 214 (385)
T ss_pred HHHHHHHH----HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHHH
T ss_conf 99999879----99999999998999999998656899898899998589999999981965488221102999999999
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 215 RaI~~~sr~IRlP~h~~e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~~~vSLD~pvg~~~ds~l~ 294 (385)
T PRK07406 215 RAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLG 294 (385)
T ss_pred HHHHHCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHH
T ss_conf 99997386120208999999999999999998708998699999993999999999998548986545888876533188
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 295 D~i~~-d~~~pe~~~~~~~lr~~L~~~L~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~ 373 (385)
T PRK07406 295 DFIEA-DGETPEDDVSKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 373 (385)
T ss_pred HHHHC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf 89863-59999999999999999999986499999999999758999996469999989795999999999999999677
Q ss_pred HHHHHHHHHHH
Q ss_conf 67778756651
Q gi|254780289|r 670 PSRSKKLRSFL 680 (682)
Q Consensus 670 ~~~~~~l~~~~ 680 (682)
T Consensus 374 p~r~~~L~~yl 384 (385)
T PRK07406 374 PNRNSVLKEYI 384 (385)
T ss_pred CHHHHHHHHHH
T ss_conf 17789999974