HHsearch alignment for GI: 254780289 and conserved domain: PRK11923
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional.
Probab=99.07 E-value=3.5e-08 Score=83.56 Aligned_cols=188 Identities=19% Similarity=0.271 Sum_probs=134.4
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 3 t~~~D~~Li~~~~~GD~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDi~Qe~f~~~~~~~~~~~~~~--~f~~---W 74 (193)
T PRK11923 3 TQEEDQQLVERVQRGDKR---AFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAYRALGNFRGDS--AFYT---W 74 (193)
T ss_pred CCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCH--HHHH---H
T ss_conf 871099999999948699---9999999999999999999909999999999999999986132126504--6899---9
Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCC-CCCC
Q ss_conf 899999999972287046142058898999999999877608899978999870999899999998608987553-6358
Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIG 581 (682)
Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~-~~~~ 581 (682)
T Consensus 75 L~~Ia~n~~~-----------------~~~~~~--------~rr~~~~~----------------------~~~~~~~~~ 107 (193)
T PRK11923 75 LYRIAINTAK-----------------NHLVSR--------GRRPPDSD----------------------VSSEDAEFY 107 (193)
T ss_pred HHHHHHHHHH-----------------HHHHHH--------HCCCCCCC----------------------CCHHHHHHC
T ss_conf 9999999999-----------------999998--------65575333----------------------453466522
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 108 ~~~-----~~~~--~~~~~e~~~~~~e~~~~i~~~l~~Lp~~~R~v~~L~~----~egls~~EIA~~l~is~~tVk~rl~ 176 (193)
T PRK11923 108 DGD-----HALK--DIESPERALLRDEIEATVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIF 176 (193)
T ss_pred CCC-----CCCC--CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 554-----3223--4488889999999999999999817898999999999----9499999999998929999999999
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 177 RAr~~Lr~-----~L~~ll~ 191 (193)
T PRK11923 177 RAREAIDK-----ALQPLLQ 191 (193)
T ss_pred HHHHHHHH-----HHHHHHH
T ss_conf 99999999-----9899873