HHsearch alignment for GI: 254780289 and conserved domain: PRK12514
>PRK12514 RNA polymerase sigma factor; Provisional.
Probab=98.89 E-value=3.6e-07 Score=75.54 Aligned_cols=174 Identities=14% Similarity=0.243 Sum_probs=127.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf 26889999998765332112468999875557899988752235677788754436799998874385457312010289
Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682)
Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682)
T Consensus 2 ~p~d~~~Li~~~~~GD~~---Af~~L~~~y~~~l~~~a~~~~~d~~~AeDi~Qe~fl~~~~~~~~~~~~~-~~~~~---w 74 (179)
T PRK12514 2 QPDDIEKLIVRVSLGDRD---AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMT---W 74 (179)
T ss_pred CCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC-CCHHH---H
T ss_conf 971099999999965899---9999999999999999999909999999999999999998875157665-53999---9
Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682)
Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682)
T Consensus 75 L~~iarN~~i-d~----------------~R~----------~~~~------------------------~~~~~~---- 99 (179)
T PRK12514 75 LITIARNHAI-DR----------------LRA----------RKAV------------------------AVDIDE---- 99 (179)
T ss_pred HHHHHHHHHH-HH----------------HHH----------CCCC------------------------CCCHHH----
T ss_conf 9999999999-99----------------986----------3777------------------------787456----
Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682)
Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682)
T Consensus 100 -----~~~~~-~-~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~~~~l~~----~eg~s~~EIA~~l~is~~tVk~~l~r 168 (179)
T PRK12514 100 -----AHDLA-D-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRR 168 (179)
T ss_pred -----HHHHC-C-CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf -----76512-4-6898699999889999999999875599999999996----06998999999889099999999999
Q ss_pred HHHHHCC
Q ss_conf 9998329
Q gi|254780289|r 663 AIRKLKH 669 (682)
Q Consensus 663 a~~~l~~ 669 (682)
T Consensus 169 A~~~Lr~ 175 (179)
T PRK12514 169 SLLKLRE 175 (179)
T ss_pred HHHHHHH
T ss_conf 9999999