HHsearch alignment for GI: 254780289 and conserved domain: PRK12526
>PRK12526 RNA polymerase sigma factor; Provisional.
Probab=98.70 E-value=2e-06 Score=69.77 Aligned_cols=174 Identities=14% Similarity=0.162 Sum_probs=117.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682)
Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682)
T Consensus 26 ~~Lv~~A~~GD---~~AF~~Ly~~y~~~l~~~~~r~l~d~~~AEDvvQetFlkvw~~~~~~~~~~~-~f~tW----L~~I 97 (206)
T PRK12526 26 QWLILVAISRD---KQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTW----VYTV 97 (206)
T ss_pred HHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHH----HHHH
T ss_conf 99999999658---9999999999999999999999199999999999999999983876586425-29999----9999
Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682)
Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682)
T Consensus 98 arN~~~d~----------------lRk~~~~---------------------------------~~~~~----~~-d~~~ 123 (206)
T PRK12526 98 MRNAAFDM----------------LRKIKAK---------------------------------KEQNL----GD-DIWP 123 (206)
T ss_pred HHHHHHHH----------------HHHHHCC---------------------------------CCCCC----CC-HHCH
T ss_conf 99999999----------------9865312---------------------------------22232----10-0000
Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682)
Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682)
T Consensus 124 ~~~~~~~-~~-~~~~~~~~~~~~~~l~~~l~~LP~~~R~vi~L~~----~egls~~EIA~~l~is~~TVksrl~rAlk~L 197 (206)
T PRK12526 124 IEQALAE-SQ-SESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206)
T ss_pred HHHCCCC-CC-CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 4430145-78-8357899899999999999868999888989999----8599999999998939999999999999999
Q ss_pred CC
Q ss_conf 29
Q gi|254780289|r 668 KH 669 (682)
Q Consensus 668 ~~ 669 (682)
T Consensus 198 R~ 199 (206)
T PRK12526 198 KV 199 (206)
T ss_pred HH
T ss_conf 99