HHsearch alignment for GI: 254780226 and conserved domain: TIGR00450

>TIGR00450 thdF tRNA modification GTPase TrmE; InterPro: IPR004520 The GTP-binding domain of all TrmE/ThdF orthologues is found in the C-terminal portion of the molecule. The N-terminal half can be removed without affecting the GTP-binding/hydrolysis function of the GTP-binding domain. The last four amino acids of all orthologues of ThdF/TrmE are highly conserved, being either CIGK or CLGK. This matches the Caax (where 'a' represents an aliphatic amino acid, and 'x' represents any amino acid) motif for isoprenylation that anchors small GTP-binding proteins to cell membranes in eukaryotic cells. However, protein isoprenylation has never been shown to occur in bacteria. Interestingly, biochemical experiments have shown that the Escherichia coli TrmE protein peripherally associates with the membrane fraction . Although the biochemical properties of TrmE have been investigated for the E. coli and Thermotoga maritima proteins, nothing is known about the relationship of this protein to tRNA modification. Orthologues of TrmE are present in eukaryotes and bacteria, but are not present in archaea. In Saccharomyces cerevisiae, Mss1p is a nuclear-encoded mitochondrial protein that is the yeast orthologue of TrmE. Mss1p interacts with the 15S rRNA of the yeast mitochondria, which is equivalent to the 16S rRNA of bacteria. Subsequent analysis of the S. cerevisiae MTO1 gene suggests that MSS1 and MTO1 act together in a pathway involved in optimizing mitochondrial protein synthesis. TrmE may play a role in tRNA processing and may be directly or indirectly involved in regulating ribosome function.; GO: 0003924 GTPase activity, 0005525 GTP binding, 0006400 tRNA modification, 0005622 intracellular.
Probab=99.23  E-value=5.1e-11  Score=94.08  Aligned_cols=92  Identities=34%  Similarity=0.479  Sum_probs=78.7

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHCCCCEEEEEEEEEEECCCCCCCC
Q ss_conf             82486752888788899998740489873666867448833799768555877764218650233579998512235432
Q gi|254780226|r    2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVPTRMSFVDIAGLVRGA   81 (367)
Q Consensus         2 ~~kiGlvG~pn~GKST~f~alT~~~~~~~~~ypFtTi~pn~g~~~v~d~~~~~l~~~~~~~~~~p~~i~~iDvaGLv~gA   81 (367)
T Consensus       225 g~k~ai~G~~NvGKSSLLNa~l~~DrAiVS~~kGtTRD~vE~~~~L~-----------------G~~~~~lDTAGiR~~~  287 (473)
T TIGR00450       225 GFKLAIVGKPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELN-----------------GILVKLLDTAGIREHA  287 (473)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHCCCEEEECCCCCCCCEEEEEEEEC-----------------CEEEEEEECCCCCCCH
T ss_conf             94799964788757899998762287055276688320442057774-----------------6789985146751020


Q ss_pred             CCCCCCH-HHHHHHHHCCCEEEEEECCCCC
Q ss_conf             2246632-8999987303747885012345
Q gi|254780226|r   82 SKGEGLG-NQFLAHIREVDAIIHVLRCFKD  110 (367)
Q Consensus        82 ~~G~GlG-N~FL~~ir~aDalihVVdaf~~  110 (367)
T Consensus       288 ~~~E~~GiekS~~~i~~A~LVi~~~D~~~~  317 (473)
T TIGR00450       288 DKVERLGIEKSFKAIKQADLVIYVLDASQP  317 (473)
T ss_pred             HHHHHHHHHHHHHHHHHCCEEEEEEECCCC
T ss_conf             046677689989998605734788874789