HHsearch alignment for GI: 254780611 and conserved domain: PRK12539
>PRK12539 RNA polymerase sigma factor; Provisional.
Probab=99.64 E-value=7.3e-14 Score=112.19 Aligned_cols=176 Identities=17% Similarity=0.224 Sum_probs=120.9
Q ss_pred CCHHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf 998999-99999999828599999999943077875655557----9999888999999888998986218534568999
Q gi|254780611|r 29 LEKQEE-YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103 (302)
Q Consensus 29 Lt~eee-~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~----~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsT 103 (302)
T Consensus 2 ~~~~~~~~~Lv~~~~-~GD~~Af~~L~~r~~~~l~~~~~~~l~r~~~~~~dAeDlvQe~fl~~~~~~~~~~~~~--~~~~ 78 (184)
T PRK12539 2 MSKENELKALMLASL-DGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTP 78 (184)
T ss_pred CCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH
T ss_conf 997799999999998-0889999999999899999999999998439998999999999999998377559998--5799
Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 75778999999853202460011023003589999999978878662447888246778886189832110000001223
Q gi|254780611|r 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183 (302)
Q Consensus 104 YA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~ 183 (302)
T Consensus 79 WL~~Ia~n~~~d~~R----------------------~~~~~~~-------------------~---------------- 101 (184)
T PRK12539 79 WVYAIARYKLIDHLR----------------------RTRASLA-------------------D---------------- 101 (184)
T ss_pred HHHHHHHHHHHHHHH----------------------HCCCCCC-------------------C----------------
T ss_conf 999999999999998----------------------5145534-------------------4----------------
Q ss_pred CCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf 43355202323453200000123568705655666666677799999962199999999999827888889899999977
Q gi|254780611|r 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302)
Q Consensus 184 ~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302)
T Consensus 102 ~~~~~----~~~-------~~~~~~--~-~~~----e---~~~~l~~~l~~Lp~~~r~v~~L~~~eg--~s~~EIA~~lg 158 (184)
T PRK12539 102 VPIDD----ADE-------LVAHDD--A-AAV----E---STLDLGRLLARLPEKMRLAIQAVKLDG--LSVAEAATRSG 158 (184)
T ss_pred CCCCC----CCC-------CCCCCC--H-HHH----H---HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHC
T ss_conf 88443----444-------567851--3-318----8---999999999849999999999999949--99999999989
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999999999999999999974
Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
T Consensus 159 is~~tVks~l~Rark~Lr~~L~~e 182 (184)
T PRK12539 159 MSESAVKVSVHRGLKALAALIGRE 182 (184)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 199999999999999999998650