HHsearch alignment for GI: 254780295 and conserved domain: cd02569

>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like. This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.
Probab=100.00  E-value=0  Score=500.32  Aligned_cols=223  Identities=28%  Similarity=0.416  Sum_probs=196.2

Q ss_pred             EEEEECCCCCEEEEECCCC-CCHHHHHHHHHHHHH----CCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCH-------
Q ss_conf             9999716687200487538-778899999999970----9956999711213861222346886406321104-------
Q gi|254780295|r    6 MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV-------   73 (247)
Q Consensus         6 ~~i~YdGt~y~G~q~Q~~~-~TVq~~le~aL~~~~----~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~-------   73 (247)
T Consensus         1 L~i~YdGt~f~G~Q~Q~~~~~TVqg~Le~aL~k~~~i~~~~~~~~~~agRTDaGVHA~~qv~~f~~~~~~~~~~~~~~~~   80 (256)
T cd02569           1 LRFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDRQTSNYSRCGRTDKGVSAFGQVISLDVRSNLKPEDGLDPST   80 (256)
T ss_pred             CEEEEECCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             98999589800785789999788999999999722645786068983366652432135579999504677521123322


Q ss_pred             -----------HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHH
Q ss_conf             -----------689999986188876543443226777550002100223556852443202333210244333335665
Q gi|254780295|r   74 -----------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM  142 (247)
Q Consensus        74 -----------~~~~~lN~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l  142 (247)
T Consensus        81 ~~~~~~~~~~~~~~~~LN~~L--P~dIrv~~~~~v~~~FhaR~~a~~R~Y~Y~~~~----------------~~ld~~~m  142 (256)
T cd02569          81 DVKSTADEEELPYCKILNRVL--PPDIRILAWAPVPPDFSARFSCVSRTYRYFFPK----------------GDLDIELM  142 (256)
T ss_pred             CCCCCCCCHHHHHHHHHHHCC--CCCEEEEEEEECCCCCCCCCCCCCEEEEEEECC----------------CCCCHHHH
T ss_conf             222122202567999998149--997599999988998885523431699997059----------------98799999


Q ss_pred             HHHHHHHHCCHHEEEECCCCC--CCCCCCCCCCCCCCCCC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             565676520011001024565--53332110331111233------3200113158888999999999999999768998
Q gi|254780295|r  143 RIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT  214 (247)
Q Consensus       143 ~~a~~~l~G~HdF~~F~~~~~--~~~~~~R~I~~~~v~~~------~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~  214 (247)
T Consensus       143 ~~a~~~f~GtHDF~~F~~~~~~~~~~~~~R~i~~~~v~~~~~~~~~~~~~~~~i~g~~FL~~mVR~mVGtL~~vg~G~~~  222 (256)
T cd02569         143 RKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEP  222 (256)
T ss_pred             HHHHHHCCCCCCHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEECHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999714861667627778899888874699999999855656887389999993056899899999999999779999


Q ss_pred             HHHHHHHHHCCCCCC--CCCCCCCCCCEEEEEEE
Q ss_conf             889999983588211--66636989847633043
Q gi|254780295|r  215 STDLEKALQAQDRKE--CGPLAPPEGLYFDSVEY  246 (247)
Q Consensus       215 ~~~i~~~L~~~~r~~--~~~~APa~GL~L~~V~Y  246 (247)
T Consensus       223 ~~~i~~~L~~~~~~~~~~~~~AP~~GL~L~~V~Y  256 (256)
T cd02569         223 PSVISQLLDVEKNPRKPQYTMASEVPLVLYDCGF  256 (256)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             8999999865567667886789998738998589