HHsearch alignment for GI: 254780611 and conserved domain: PRK12518
>PRK12518 RNA polymerase sigma factor; Provisional.
Probab=99.64 E-value=3.9e-14 Score=113.98 Aligned_cols=171 Identities=14% Similarity=0.192 Sum_probs=119.6
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99999982859999999994307787565555799998889999998889989862185345689997577899999985
Q gi|254780611|r 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302)
Q Consensus 37 l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302)
T Consensus 1 Li~~~~-~Gd~~Af~~ly~~y~~~l~~~~~~~~~~-~~AEDi~Qd~fik~~~~~~~~~~~-~-~~~~wl~~ia~N~~~d~ 76 (175)
T PRK12518 1 LIQRCQ-RGDRQAFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP-A-YFSTWLYRITWNVATDA 76 (175)
T ss_pred CHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHCCCCCCCC-C-HHHHHHHHHHHHHHHHH
T ss_conf 989898-6589999999999999999999997799-889999999999998711127982-3-59999999999999999
Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345
Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302)
Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302)
T Consensus 77 ~Rk~----------------------~r~~~-------~~~~------------------------~~~~~-------~- 95 (175)
T PRK12518 77 RRQF----------------------AKRPS-------RIQQ------------------------DSSLD-------Q- 95 (175)
T ss_pred HHHH----------------------HCCCC-------CCCC------------------------CCCCC-------C-
T ss_conf 9998----------------------70243-------2332------------------------10002-------4-
Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999
Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
T Consensus 96 --------~~~~~~~~~-~~~----~~~~~~l~~~l~~Lp~~~r~vi~l~~~~~--~s~~EIA~~l~is~~tVk~~l~Ra 160 (175)
T PRK12518 96 --------PSRPSDEPD-LMQ----LHYQDLVQQGLATLSLEHRAVLVLHDLED--LPQKEIAEILNIPVGTVKSRLFYA 160 (175)
T ss_pred --------CCCCCCCHH-HHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf --------567889769-999----99999999999769999999999999929--999999999895999999999999
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999974
Q gi|254780611|r 277 FKKVQESIQKQ 287 (302)
Q Consensus 277 L~kLR~~l~~~ 287 (302)
T Consensus 161 ~k~Lr~~L~~e 171 (175)
T PRK12518 161 RRQLRKFLQQQ 171 (175)
T ss_pred HHHHHHHHHHC
T ss_conf 99999999986