HHsearch alignment for GI: 254780151 and conserved domain: pfam03054

>pfam03054 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.
Probab=100.00  E-value=0  Score=962.16  Aligned_cols=347  Identities=46%  Similarity=0.793  Sum_probs=325.4

Q ss_pred             CEEEEEECCCHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEECCHHHHHHHHC
Q ss_conf             88999960985799999999886984999998704787665555778818999999999998099589817078866322
Q gi|254780151|r   21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCDTINVSHYVFDYEERFRNAV  100 (408)
Q Consensus        21 ~kV~va~SGGVDSsvaa~lL~~~G~~V~g~~m~~~~~~~~~~~~~~c~~~~d~~~a~~va~~LgI~~~~~d~~~~f~~~V  100 (408)
T Consensus         1 mkV~VamSGGVDSsVaA~LL~~~Gy~V~Gv~m~~w~~~~--~~~~~C~~~~d~~dA~~va~~LgIp~~v~d~~~~f~~~V   78 (354)
T pfam03054         1 MKVVVAMSGGVDSSVAAYLLKEQGYEVIGVFMKNWDEED--EFGHGCCSEEDLADAQRVCEQLGIPLYVVNFEKEYWEKV   78 (354)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHCCCCEEEEEEECCCCCC--CCCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHH
T ss_conf             969999047899999999999779963999999566887--667889988999999999998699789978799875899


Q ss_pred             CCCCHHHHHCCCCCCCEECCCCEEEHHHHHHHHCC-CCCCEECCCCCCCEEEECCCCCCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             44112678708861200001541105888887401-68764522531102541267877316885315787873189863
Q gi|254780151|r  101 IVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQ-LGADVLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFA  179 (408)
Q Consensus       101 ~~~~~~~y~~G~TPNPc~~CN~~iKF~~l~~~a~~-~g~~~iATGHYar~~~~~~~~~~~~~~L~r~~D~~KDQSYfL~~  179 (408)
T Consensus        79 i~~fv~~Y~~G~TPNPcv~CN~~IKFg~l~~~A~~~lGad~iATGHYAri~~~-----~~~~~L~r~~D~~KDQSYfL~~  153 (354)
T pfam03054        79 FEPFLDEYKNGRTPNPDILCNREIKFGALLDYAKQVLGADYLATGHYARVSLN-----ENESELLRGKDKNKDQSYFLSG  153 (354)
T ss_pred             HHHHHHHHHCCCCCCCCHHHCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEEC-----CCEEEEEECCCCCCCCCEEEEC
T ss_conf             99999999769999841441896438999999998669981044742899904-----9938999899999980178610


Q ss_pred             ECCHHHCEEECCCCCCCHHHHHHHHHHCCCCCCCHHHCCCEEECCCCCCHHHHHHCCCCCCCCCCEECC-CCCEEEEECC
Q ss_conf             020221003342568997898999974125435511102301112775103455307664346711037-7432233578
Q gi|254780151|r  180 TTQQQLCDLRFPLGDMKKESVRDLAREMGLDIADKSDSQDICFVQQGKYFDVVKRINAGIALEGDIVHL-NGQILGRHNG  258 (408)
Q Consensus       180 l~~~~L~~~~FPlg~~~K~eVR~~A~~~gl~~a~K~eSqgICFi~~~~~~~Fl~~~~~~~~~~G~ivd~-~G~viG~H~G  258 (408)
T Consensus       154 l~q~~L~~~lFPLG~~~K~eVR~iA~~~gL~~a~K~dSq~ICFi~~~~~~~Fl~~~~~--~~pG~ivd~~~G~vlG~H~G  231 (354)
T pfam03054       154 LSQEQLEKLLFPLGDLTKEEVRKIAKEAGLPTAKKKDSQGICFIGKRNFKDFLKKYLP--VKPGDIIDIDTGEVLGEHEG  231 (354)
T ss_pred             CCHHHHHHEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCHHHHHHHHCC--CCCCCEEECCCCCEEEEECC
T ss_conf             7898764318287688528999999976998899877787033058877999997478--99987698879929788869


Q ss_pred             CEEEEECCCCCCCCC-CCCCCEEEECCCCCCEEEEEC---CCCCCCCCEEECCCEECCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             315310233433565-778613763175531256523---5554222112002230377655544568718999980178
Q gi|254780151|r  259 IINYTIGQRRGLGVA-MGEPLFVVYLDKNSSRVIVGP---RESLEVHRIYLREINWLGDGLFEDAVVDGFKCFVKIRSSQ  334 (408)
Q Consensus       259 ~~~yTIGQRkGL~i~-~~eP~YVv~id~~~N~ViVg~---~~~L~~~~i~l~d~nWi~~~~~~~~~~~~~~~~vkiR~~~  334 (408)
T Consensus       232 ~~~yTIGQRkGlgi~g~~~p~yV~~~d~~~N~v~Vg~~~~~~~L~~~~~~~~~~nw~~~~~~~---~~~~~~~vkiRy~~  308 (354)
T pfam03054       232 IWFYTIGQRKGLGIGGYGEPWYVVEKDPEKNTVYVGRGEDHEDLYSDGLRAKDLNWLGPELPT---GEVLRCTVKVRHRQ  308 (354)
T ss_pred             EEEEEECCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCCCHHHHCCEEEEEEEEECCCCCCC---CCCEEEEEEECCCC
T ss_conf             068982542546658888618999981778889996698855562787999831888898888---99649999985698


Q ss_pred             CCCEEEEEEE-CCEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             8700899982-997999975972000696389997388866588876897
Q gi|254780151|r  335 DPVPVFVQRN-DDGVYVDFEKSEVGVASGQACVFYTSDSNEARVLGGGII  383 (408)
Q Consensus       335 ~pvp~~i~~~-~~~~~V~f~eP~~aiAPGQ~~VfY~~D~~~~~vLGGGiI  383 (408)
T Consensus       309 ~~~~~~v~~~~~~~~~v~f~~p~~avtPGQ~~V~Y~~d----~vLGGG~I  354 (354)
T pfam03054       309 PPVPCKVKLLDDNTIEVHFDEPVRAVTPGQAAVFYDGD----RCLGGGII  354 (354)
T ss_pred             CCCCEEEEEECCCEEEEEECCCCCCCCCCCEEEEEECC----EEEEEEEC
T ss_conf             29386999916998999949998777857089999699----99987789