HHsearch alignment for GI: 254780289 and conserved domain: PRK12535
>PRK12535 RNA polymerase sigma factor; Provisional.
Probab=98.37 E-value=0.0001 Score=56.19 Aligned_cols=170 Identities=19% Similarity=0.136 Sum_probs=109.0
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 9 ~da~~~~Lv~~a~~GD~~A---f~~L~~r~~~~v~r~~~~l~~~-~~AeDl~QEtflk~~~~l~~f~~~~--~f~---tW 79 (195)
T PRK12535 9 NDAHVTELALAAGRGDRAA---LTEFIRATQDDVWRLLAHLGGH-DIADDLTQETYLRVMSALPRFAARS--SAR---TW 79 (195)
T ss_pred CHHHHHHHHHHHHHCCHHH---HHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HH
T ss_conf 8488999999998220999---9999999999999999893799-7799999999999999887707888--799---99
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 80 L~~Ia~n~~~-d~~R----------------~---~~~-------------------------------~~~~~~~~~-- 106 (195)
T PRK12535 80 LLSLARRVWV-DNIR----------------H---DMA-------------------------------RPRKSAVEY-- 106 (195)
T ss_pred HHHHHHHHHH-HHHH----------------H---HHC-------------------------------CCCCCCCCC--
T ss_conf 9999999999-9999----------------8---851-------------------------------666553332--
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 107 -~~~~~----~d--~~~~~~~~~----~~~l~~~l~~Lp~~~R~~l~L~~----~~g~s~~EIA~ilgi~~gTVKsRl~R 171 (195)
T PRK12535 107 -EDTGA----TD--ATNAGIWSE----WIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVAR 171 (195)
T ss_pred -CCCCC----CC--CCCCHHHHH----HHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf -23566----77--764035777----99999999849998879999999----82998999999989399999999999
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 172 Ar~~Lr~ 178 (195)
T PRK12535 172 ARADLVA 178 (195)
T ss_pred HHHHHHH
T ss_conf 9999999