HHsearch alignment for GI: 254780295 and conserved domain: cd00497

>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly ph
Probab=100.00  E-value=0  Score=514.10  Aligned_cols=219  Identities=34%  Similarity=0.499  Sum_probs=204.7

Q ss_pred             EEECCCCCEEEEECCCCCCHHHHHHHHHHHHH----CCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             99716687200487538778899999999970----99569997112138612223468864063211046899999861
Q gi|254780295|r    8 IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYL   83 (247)
Q Consensus         8 i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~----~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L   83 (247)
T Consensus         1 i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~i~~agRTDaGVHA~~qv~~f~~~~~~--~~~~~~lN~~L   78 (224)
T cd00497           1 IAYDGWKYHGFQRQPDVPTVEGELFKALLKTGLIESPKPSNYSRAGRTDKGVSALGQVVSLETRSKL--KPYPDILNGLL   78 (224)
T ss_pred             CEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCEEEEECCCCC--HHHHHHHHHHC
T ss_conf             9476888207877888989999999999973342378705899733566782415558999877772--77999998359


Q ss_pred             CCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECCCCC
Q ss_conf             88876543443226777550002100223556852443202333210244333335665565676520011001024565
Q gi|254780295|r   84 KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC  163 (247)
Q Consensus        84 ~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~~~~  163 (247)
T Consensus        79 --p~dI~v~~~~~v~~~FhaR~~a~~r~Y~Y~~~----------------~~~ld~~~m~~a~~~~~G~HDF~~F~~~~~  140 (224)
T cd00497          79 --PKDIRVLAWAPVPEDFHARFSCVSRTYRYYFP----------------GGDLDIEAMREAAKLLLGTHDFRNFCKKDG  140 (224)
T ss_pred             --CCCCEEEEEEECCCCCCCCCCCCCEEEEEEEC----------------CCCCCHHHHHHHHHHHCCCCCHHHHHCCCC
T ss_conf             --89878989999288766443787269999675----------------898779999999998048534786217688


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCC-CCCCCCCCCCCEEE
Q ss_conf             53332110331111233320011315888899999999999999976899888999998358821-16663698984763
Q gi|254780295|r  164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFD  242 (247)
Q Consensus       164 ~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~-~~~~~APa~GL~L~  242 (247)
T Consensus       141 ~~~~~vRtI~~~~v~~~~~~~~i~i~g~~FL~~mVR~mvGtl~~vg~gk~~~~~i~~~l~~~~~~~~~~~~APa~GL~L~  220 (224)
T cd00497         141 RKKNPVRTIISAEVEEVDDFYVFEVKGKSFLWHQVRRIVAALFLVGQGLEPPSIISRLLDEEKRPSKPQYPAPPEPLVLW  220 (224)
T ss_pred             CCCCCEEEEEEEEEEECCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEE
T ss_conf             89996599999999977989999980788999999999999999987999999999998478865569887899887893


Q ss_pred             EEEE
Q ss_conf             3043
Q gi|254780295|r  243 SVEY  246 (247)
Q Consensus       243 ~V~Y  246 (247)
T Consensus       221 ~V~Y  224 (224)
T cd00497         221 DCKY  224 (224)
T ss_pred             EEEC
T ss_conf             2499