HHsearch alignment for GI: 254780289 and conserved domain: PRK12534
>PRK12534 RNA polymerase sigma factor; Provisional.
Probab=98.96 E-value=2e-07 Score=77.55 Aligned_cols=177 Identities=18% Similarity=0.255 Sum_probs=131.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf 11268899999987653321124689998755578999887522356777887544367999988743854573120102
Q gi|254780289|r 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682)
Q Consensus 421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682)
T Consensus 6 ~~~~de~~~Li~~~~~GD~~---Af~~Ly~~y~~~l~~~~~~~~~~~~~AeDv~Qe~Fl~vw~~~~~~~~~~~~~~---- 78 (187)
T PRK12534 6 GHDDDETGRLLTATAGGDRH---AFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGL---- 78 (187)
T ss_pred CCCCHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH----
T ss_conf 99962899999999936899---99999999999999999998699999999999999999987533687522189----
Q ss_pred HHHHHH-HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf 898999-9999997228704614205889899999999987760889997899987099989999999860898755363
Q gi|254780289|r 501 MWWVKQ-AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579 (682)
Q Consensus 501 ~~~i~~-~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~ 579 (682)
T Consensus 79 -tWl~~IarN~~~-d~lR----------------~~~--------------------------------~~~~~~~~~~~ 108 (187)
T PRK12534 79 -TWLAMIARNKAI-DHLR----------------ANA--------------------------------PQRRNVALDDA 108 (187)
T ss_pred -HHHHHHHHHHHH-HHHH----------------HCC--------------------------------CCCCCCCCCCC
T ss_conf -999999999999-9999----------------624--------------------------------41357773411
Q ss_pred CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 58899860475623898899899999999999999997329988999999981879867468899989966789999999
Q gi|254780289|r 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659 (682)
Q Consensus 580 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi 659 (682)
T Consensus 109 ------~---~-~~-~~~~~~~e~~~~~~~~~~l~~al~~L~~~~r~vi~l~~----~eg~s~~EIA~~l~i~~gTVksr 173 (187)
T PRK12534 109 ------G---E-LR-AADASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSW 173 (187)
T ss_pred ------C---C-CC-CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf ------0---0-13-56898277899999999999999868998999999999----84999999999989199999999
Q ss_pred HHHHHHHHCC
Q ss_conf 9999998329
Q gi|254780289|r 660 EAKAIRKLKH 669 (682)
Q Consensus 660 ~~~a~~~l~~ 669 (682)
T Consensus 174 l~ra~~~Lr~ 183 (187)
T PRK12534 174 IRRGLAKLKA 183 (187)
T ss_pred HHHHHHHHHH
T ss_conf 9999999999