HHsearch alignment for GI: 254780546 and conserved domain: cd01998

>cd01998 tRNA_Me_trans tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs. This family of enzyme only presents in bacteria and eukaryote. The archaeal counterpart of this enzyme performs same function, but is completely unrelated in sequence.
Probab=99.48  E-value=8.9e-14  Score=116.45  Aligned_cols=168  Identities=18%  Similarity=0.237  Sum_probs=117.0

Q ss_pred             EEEEEECCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCC---C---CCCHHHHHHHHHHHHHHCCCCEEEEEEEC---
Q ss_conf             39999669424899999999999864899729999996677---9---87846899999999987189889999750---
Q gi|254780546|r   21 HILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHC---L---RETAKDEVRYVSDVCSRLRIAHSVVSWKN---   91 (423)
Q Consensus        21 ~i~vAvSGG~DS~aLl~ll~~~~~~~~~~~~~l~a~~vdHg---l---r~~s~~e~~~v~~~~~~lgi~~~~~~~~~---   91 (423)
T Consensus         1 kV~v~mSGGVDSsvaA~LL~~~-------G~~V~gv~m~~w~~~~~~~~C~~~~d~~dA~~va~~LgIp~~v~d~~~ef~   73 (349)
T cd01998           1 KVVVAMSGGVDSSVAAALLKEQ-------GYEVIGVFMKNWDEDDGKGGCCSEEDLKDARRVADQLGIPHYVVNFEKEYW   73 (349)
T ss_pred             CEEEECCCCHHHHHHHHHHHHC-------CCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHHHH
T ss_conf             9899907789999999999877-------995799999967887667898867789999999998699679968099886


Q ss_pred             --------------CCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH-HHHHHHHHCCCCC--C-CCCCCCC
Q ss_conf             --------------47877803788854555543200123442012345666566-8999986236544--4-3322357
Q gi|254780546|r   92 --------------SKPQTGLMAAAREARYALISEHAKTINATLIMTAHTFDDQL-ETVYMRSQRDYAE--K-GMGLSGM  153 (423)
Q Consensus        92 --------------~~~~~~~~~~ar~~r~~~~~~~~~~~~~~~l~~ah~~dD~~-Et~l~rl~r~sg~--~-g~~l~~~  153 (423)
T Consensus        74 ~~V~~~f~~~Y~~G~TPNPcv~CN-~~IKF~~l~~~A~~~g~d~iATGHYAri~~~~~~~~~L~r~~D~~KDQSYfL~~l  152 (349)
T cd01998          74 EKVFEPFLEEYKKGRTPNPDILCN-KEIKFGALLDYAKKLGADYIATGHYARIEEDNNGRYRLLRGVDPNKDQSYFLSQL  152 (349)
T ss_pred             HHHHHHHHHHHHCCCCCCCCHHCC-CEEEHHHHHHHHHHCCCCEECCCCEEEEEECCCCCEEEEECCCCCCCCCEEEECC
T ss_conf             888999999997489998762118-7351999999998759986413514788975898489987689987820564012


Q ss_pred             CCCCCCCCCCEEECCHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             64100357968710121042899999899818932026678642210
Q gi|254780546|r  154 CDTILYDLNLWISRPFLRCRREDIRSFLLQRNISWCEDPSNTDDRFE  200 (423)
Q Consensus       154 ~~~~~~~~~~~i~RPLL~~~r~~l~~~~~~~~i~wveDpSN~d~~f~  200 (423)
T Consensus       153 ~~~~L----~~~~FPLG~~~K~eVR~iA~~~gl~~a~K~dSq~ICFi  195 (349)
T cd01998         153 SQEQL----SRLIFPLGDLTKPEVREIAKELGLPVAKKKDSQGICFI  195 (349)
T ss_pred             CHHHH----HHEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEE
T ss_conf             48766----10387887865389999999859998997777760331