HHsearch alignment for GI: 254780295 and conserved domain: cd02866
>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,. This group consists of archealpseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs.
Probab=100.00 E-value=0 Score=511.94 Aligned_cols=217 Identities=36% Similarity=0.591 Sum_probs=204.3
Q ss_pred EEEEECCCCCEEEEECCCCCCHHHHHHHHHHHH----HCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHH
Q ss_conf 999971668720048753877889999999997----0995699971121386122234688640632110468999998
Q gi|254780295|r 6 MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNA 81 (247)
Q Consensus 6 ~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~----~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~ 81 (247)
T Consensus 1 l~i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~~agRTDaGVHA~~qv~~f~~~~~~~----~~~lN~ 76 (221)
T cd02866 1 LKVAYDGTPYHGFQRQPDVRTVEGELIKALRRLGIIESPKRPRLYSAGRTDAGVSALGNVVAFETEKELT----PPAINN 76 (221)
T ss_pred CEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCEEEEEEEEECCCCCC----HHHHHH
T ss_conf 9899928982368888989899999999999723310598258998515778852000389995674013----899983
Q ss_pred HHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECCC
Q ss_conf 61888765434432267775500021002235568524432023332102443333356655656765200110010245
Q gi|254780295|r 82 YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161 (247)
Q Consensus 82 ~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~~ 161 (247)
T Consensus 77 ~L--p~dI~v~~~~~v~~~FhaR~~a~~r~Y~Y~~~----------------~~~ld~~~m~~a~~~~~G~HDF~~F~~~ 138 (221)
T cd02866 77 AL--PKDIRVWAWAKVPEDFHPRRDARRRYYRYYLG----------------AEDYDVEAMAEAAKKLIGTHDFSNFSKR 138 (221)
T ss_pred HC--CCCEEEEEEEEECCCCCCEEECCEEEEEEEEC----------------CCCCCHHHHHHHHHHHCCCCCHHHHHCC
T ss_conf 59--99889999999497978425234699999852----------------5767899999999983271576664111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEE
Q ss_conf 65533321103311112333200113158888999999999999999768998889999983588211666369898476
Q gi|254780295|r 162 HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241 (247)
Q Consensus 162 ~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L 241 (247)
T Consensus 139 --~~~~~vRtI~~~~v~~~~~~~~~~i~g~~FL~~mVR~mVg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L 216 (221)
T cd02866 139 --DGRDPVRTIERIEIRENGEFLVIDVVGESFLWNMVRRIVGALSLVGKGKRENEWVDKLLDGEFRKKDGVPAPPEGLIL 216 (221)
T ss_pred --CCCCCEEEEEEEEEEECCCEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEE
T ss_conf --589972599999999429899999608999999999999999999879999999999974788555888659987789
Q ss_pred EEEEE
Q ss_conf 33043
Q gi|254780295|r 242 DSVEY 246 (247)
Q Consensus 242 ~~V~Y 246 (247)
T Consensus 217 ~~V~Y 221 (221)
T cd02866 217 VDVKY 221 (221)
T ss_pred CCCCC
T ss_conf 21599