HHsearch alignment for GI: 254780289 and conserved domain: PRK12519
>PRK12519 RNA polymerase sigma factor; Provisional.
Probab=99.15 E-value=9.3e-09 Score=88.11 Aligned_cols=184 Identities=18% Similarity=0.276 Sum_probs=129.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682)
Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682)
T Consensus 11 m~~~tD~eLi~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDlvQe~fl~~~~~~~-~~~~~~-~~~~wL~ 85 (194)
T PRK12519 11 LSSRSDAELFSALKAGQS---AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRG-SLSSYLL 85 (194)
T ss_pred CCCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH-CCCCCC-CHHHHHH
T ss_conf 999609999999993859---99999999999999999999939999999999999999998633-166624-2999999
Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682)
Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682)
T Consensus 86 ~ia~n~~~d~~R~~~~~~~---------------------------~~~~----------------------------~~ 110 (194)
T PRK12519 86 TLTRSRAIDRLRSRRSRQR---------------------------LLER----------------------------WQ 110 (194)
T ss_pred HHHHHHHHHHHHHHHCCCC---------------------------HHHH----------------------------HH
T ss_conf 9999999999998632012---------------------------2444----------------------------44
Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 89986047562389889989999999999999999732998899999998187986746889998996678999999999
Q gi|254780289|r 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661 (682)
Q Consensus 582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~ 661 (682)
T Consensus 111 ~-------~~~~~~~~~~~~~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tVk~rl~ 179 (194)
T PRK12519 111 Q-------ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred H-------HHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 5-------4114677898588998999999999999819988756889999----8199999999998949999999999
Q ss_pred HHHHHHCCHHHHHHHHHHHC
Q ss_conf 99998329677787566517
Q gi|254780289|r 662 KAIRKLKHPSRSKKLRSFLD 681 (682)
Q Consensus 662 ~a~~~l~~~~~~~~l~~~~~ 681 (682)
T Consensus 180 rA~~~Lr-----~~L~e~le 194 (194)
T PRK12519 180 QGLLKLR-----ELLQDLLE 194 (194)
T ss_pred HHHHHHH-----HHHHHHHC
T ss_conf 9999999-----99898739