HHsearch alignment for GI: 254780414 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=99.63  E-value=1.2e-15  Score=131.95  Aligned_cols=158  Identities=28%  Similarity=0.385  Sum_probs=113.5

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCC--------CCHHHHHHHHHHCCCCCEEEEEHHHHHHH----
Q ss_conf             036640564047799999986223656999973895515--------62789999886236985799758899999----
Q gi|254780414|r  224 RVICAVSGGVDSTVAAFLIYEAIGINLTCVLVDHGFMRK--------NEVENIISLFKGYPNFPLRVVDASERFIR----  291 (520)
Q Consensus       224 kVi~~lSGGVDStV~A~Ll~kAig~~l~~vfVD~GllRk--------nE~~~v~~~~~~~~~~~l~~vda~~~Fl~----  291 (520)
T Consensus         1 kV~v~mSGGVDSsvaA~LL~~~-G~~V~gv~m~~w~~~~~~~~C~~~~d~~dA~~va-~~LgIp~~v~d~~~ef~~~V~~   78 (349)
T cd01998           1 KVVVAMSGGVDSSVAAALLKEQ-GYEVIGVFMKNWDEDDGKGGCCSEEDLKDARRVA-DQLGIPHYVVNFEKEYWEKVFE   78 (349)
T ss_pred             CEEEECCCCHHHHHHHHHHHHC-CCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHH-HHCCCCEEEECHHHHHHHHHHH
T ss_conf             9899907789999999999877-9957999999678876678988677899999999-9869967996809988688899


Q ss_pred             -----HHCCCC-CHHHHHHHHHHHHHHH--HHHHHHHCCCCEEEEECCCCCHHHHHHCC---CCCCCCEEEEEEC-CCCH
Q ss_conf             -----966898-8899998875658999--99999743997099864622024542024---6777630344302-3201
Q gi|254780414|r  292 -----KLKNIV-DPETKRKVIGQLFIEV--FEEEAKKIGGAQFLGQGTLYPDVIESISF---FGGPSSIIKSHHN-VGGL  359 (520)
Q Consensus       292 -----~L~gv~-DPE~KRkiIG~~Fi~v--f~~~a~~~~~~~~L~QGTlypDvIES~~~---~~~~~~~IKsHHN-vggl  359 (520)
T Consensus        79 ~f~~~Y~~G~TPNPc----v~CN~~IKF~~l~~~A~~~-g~d~iATGH-YAri~~~~~~~~~L~r~~D~~KDQSYfL~~l  152 (349)
T cd01998          79 PFLEEYKKGRTPNPD----ILCNKEIKFGALLDYAKKL-GADYIATGH-YARIEEDNNGRYRLLRGVDPNKDQSYFLSQL  152 (349)
T ss_pred             HHHHHHHCCCCCCCC----HHCCCEEEHHHHHHHHHHC-CCCEECCCC-EEEEEECCCCCEEEEECCCCCCCCCEEEECC
T ss_conf             999999748999876----2118735199999999875-998641351-4788975898489987689987820564012


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             132032022378987389999999981999
Q gi|254780414|r  360 PEHMDMKLVEPLKELFKDEVRLLGKELRLP  389 (520)
Q Consensus       360 p~~~~~~liEPl~~l~KdEVR~lg~~Lglp  389 (520)
T Consensus       153 ~~~~L~~~~FPLG~~~K~eVR~iA~~~gl~  182 (349)
T cd01998         153 SQEQLSRLIFPLGDLTKPEVREIAKELGLP  182 (349)
T ss_pred             CHHHHHHEECCCCCCCHHHHHHHHHHCCCC
T ss_conf             487661038788786538999999985999