HHsearch alignment for GI: 254780313 and conserved domain: pfam05958

>pfam05958 tRNA_U5-meth_tr tRNA (Uracil-5-)-methyltransferase. This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.
Probab=96.01  E-value=0.047  Score=33.31  Aligned_cols=89  Identities=19%  Similarity=0.235  Sum_probs=56.1

Q ss_pred             HHHHHHHHHCCCCCCCCEEEEEECCCCHHHHHHHHHHCCCCCCEEEEEECCCC-----------CCCCCCCEEEECCCCH
Q ss_conf             99999986458313796788850455306899999706878832786411213-----------3346981783011220
Q gi|254780313|r   53 YKLLQINEKHQILQSNRRIVDLGSSPGSWSQVAARITGSNANNTRVVAIDILD-----------MEPILGVKFFKFDFLD  121 (227)
Q Consensus        53 fKL~eId~kf~l~k~g~~VlDLGaaPGgWsQva~~~~~~~~~~~~VigVDl~~-----------~~~i~gv~~~~gDi~~  121 (227)
T Consensus       184 ~~l~~~a~~~~~~~~~-~vlDlYcG~Gtfsl~lA~~~~------~V~GvE~~~~AV~~A~~Na~~N~i~Nv~f~~~~~~~  256 (353)
T pfam05958       184 IKMLEWACEVTQGSKG-DLLELYCGNGNFSLALAQNFR------RVLATEIAKPSVNAAQYNIAANNIDNVQIIRMSAEE  256 (353)
T ss_pred             HHHHHHHHHHHHCCCC-CEEEEECCCCHHHHHHHHHCC------EEEEEECCHHHHHHHHHHHHHCCCCCEEEEECCHHH
T ss_conf             9999999998626899-589984688888899986478------799996259999999998998699864999728999


Q ss_pred             HH-HHHHHHHH--C------CCCCCEEEECCCHHHCCC
Q ss_conf             79-99999973--1------388748975320211022
Q gi|254780313|r  122 LD-SWEFIRQA--I------GGNPDLVLSDMAYPTIGH  150 (227)
Q Consensus       122 ~~-~~~~i~~~--l------~~~~DlVlSDmapn~SG~  150 (227)
T Consensus       257 ~~~~~~~~~~~~~~~~i~~~~~~~d~vvlD--PPR~G~  292 (353)
T pfam05958       257 FTQAMNGVREFRRLKGIDLKSYNCSTIFVD--PPRAGL  292 (353)
T ss_pred             HHHHHHCCCHHHHCCCCCCCCCCCCCEEEC--CCCCCC
T ss_conf             999875242233203666322467725848--987777