HHsearch alignment for GI: 254780611 and conserved domain: PRK12529
>PRK12529 RNA polymerase sigma factor; Provisional.
Probab=98.94 E-value=1.7e-07 Score=69.59 Aligned_cols=165 Identities=13% Similarity=0.118 Sum_probs=102.0
Q ss_pred HCCHHHHHHHHHHHHHHH-HHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 285999999999430778-75655557999-9888999999888998986218534568999757789999998532024
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLV-VKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV-~~iA~~y~~~g-~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~ 121 (302)
T Consensus 9 ~~D~~a~~~Ly~~h~~~L~~~l~~Rl~~~~~~~AeDl~QDvFlrl~~~~~~~~~~~i~~p~a~L~rIA~Nl~id------ 82 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVS------ 82 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH------
T ss_conf 44799999999999999999999982899835469999999999997344456432334899999999999999------
Q ss_pred CCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHH
Q ss_conf 60011023003589999999978878662447888246778886189832110000001223433552023234532000
Q gi|254780611|r 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201 (302)
Q Consensus 122 ~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~ 201 (302)
T Consensus 83 ----------------~~Rr~~~~~~~----------le~~------------------------~-------------- 98 (178)
T PRK12529 83 ----------------WRRRQSLELAW----------LEAL------------------------A-------------- 98 (178)
T ss_pred ----------------HHHHHHHHHHH----------HHHH------------------------H--------------
T ss_conf ----------------99988889878----------9988------------------------6--------------
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 00123568705655666666677799999962199999999999827888889899999977899999999999999999
Q gi|254780611|r 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 202 d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
T Consensus 99 ~~~~~~~pspE~~~~~~----e~l~~l~~al~~Lp~r~R~vF~L~r~eG--ls~~EIAe~LgiS~~tV~~~l~rAl~~C~ 172 (178)
T PRK12529 99 TLPEPLHPSPEQQSVIL----ETLHEIDALLDTLRPRVKQAFLMATLDG--MKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred CCCCCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 47866689989999999----9999999998569978889987998829--99999999989599999999999999999
Q ss_pred HHH
Q ss_conf 999
Q gi|254780611|r 282 ESI 284 (302)
Q Consensus 282 ~~l 284 (302)
T Consensus 173 ~~~ 175 (178)
T PRK12529 173 SLM 175 (178)
T ss_pred HHC
T ss_conf 867