HHsearch alignment for GI: 254780234 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=99.71  E-value=2.9e-16  Score=137.04  Aligned_cols=162  Identities=28%  Similarity=0.387  Sum_probs=115.2

Q ss_pred             EEEEEECCCHHHHHHHHHHHHHCCCEEEEEEEECCC----------CCHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHH
Q ss_conf             899991477259999999987189869999945787----------1106899999997398079982008999998799
Q gi|254780234|r    7 KVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQ----------GEELKIASDKARLLGAKEVYVKDLRREFVRDFVF   76 (404)
Q Consensus         7 kVvlaySGGLDTSv~i~~L~~e~g~eVi~~~~d~Gq----------~~d~~~~~~~A~~~Ga~~~~v~D~r~ef~~~~i~   76 (404)
T Consensus         1 kV~v~mSGGVDSsvaA~LL~-~~G~~V~gv~m~~w~~~~~~~~C~~~~d~~dA~~va~~LgI-p~~v~d~~~ef~~~V~~   78 (349)
T cd01998           1 KVVVAMSGGVDSSVAAALLK-EQGYEVIGVFMKNWDEDDGKGGCCSEEDLKDARRVADQLGI-PHYVVNFEKEYWEKVFE   78 (349)
T ss_pred             CEEEECCCCHHHHHHHHHHH-HCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCC-CEEEECHHHHHHHHHHH
T ss_conf             98999077899999999998-77995799999967887667898867789999999998699-67996809988688899


Q ss_pred             HHHHCCCCCCCCCCCCCC-HHHHHHHHHHHHHHHHCCCCEEECHHHC-------------CC----CHHHHHHHHHHHHC
Q ss_conf             997368654787420130-1243359999999885689287500111-------------68----21567999999858
Q gi|254780234|r   77 PMFRANALYEGYYLLGTA-IARPLIAKYLVDIANETGADAIAHGSTG-------------KG----NDQVRFELSAYSLN  138 (404)
Q Consensus        77 ~~I~ana~Yeg~Ypl~ts-laRplia~~lv~~a~~~ga~~iaHG~Tg-------------kG----NDQvRFe~~~~~l~  138 (404)
T Consensus        79 ~f~~~Y--~~G~TPNPcv~CN~~IKF~~l~~~A~~~g~d~iATGHYAri~~~~~~~~~L~r~~D~~KDQSYfL---~~l~  153 (349)
T cd01998          79 PFLEEY--KKGRTPNPDILCNKEIKFGALLDYAKKLGADYIATGHYARIEEDNNGRYRLLRGVDPNKDQSYFL---SQLS  153 (349)
T ss_pred             HHHHHH--HCCCCCCCCHHCCCEEEHHHHHHHHHHCCCCEECCCCEEEEEECCCCCEEEEECCCCCCCCCEEE---ECCC
T ss_conf             999999--74899987621187351999999998759986413514788975898489987689987820564---0124


Q ss_pred             CC--CEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCH
Q ss_conf             79--7077441006876379999999970896756656788641572
Q gi|254780234|r  139 SD--IEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFSIDT  183 (404)
Q Consensus       139 P~--l~viaP~Rd~~~~sRe~~i~ya~~~gIpv~~~~~~~~~yS~D~  183 (404)
T Consensus       154 ~~~L~~~~FPLG--~~-~K~eVR~iA~~~gl~~a-~----K~dSq~I  192 (349)
T cd01998         154 QEQLSRLIFPLG--DL-TKPEVREIAKELGLPVA-K----KKDSQGI  192 (349)
T ss_pred             HHHHHHEECCCC--CC-CHHHHHHHHHHCCCCCC-C----CCCCCCE
T ss_conf             876610387887--86-53899999998599989-9----7777760