PA4178 (eftM, Q9HWK3) notes

Literature

No deep-research provider was available; research done by hand. PubMed
E-utilities returned HTTP 500 on 2026-11-05, so the search was limited to the
cached publications (grep of publications/ for EftM/PA4178).

PA4178 is EftM, the EF-Tu-modifying enzyme. Purified enzyme trimethylates
EF-Tu Lys5 with SAM PMID:26677219
Exclusively Lys5, distributive PMID:26677219.
Thermolabile, which explains why the modification appears at 25 but not at
37 degrees C PMID:26677219.
G50R (clinical isolate PAHM23) abolishes SAM binding and activity.
Trimethylated EF-Tu binds the host platelet-activating factor receptor and is
linked to adhesion and invasion (introduction of PMID:26677219, citing earlier
work).

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000010968	GO:0008168 methyltransferase activity	10	412 (77 taxa)	GO:0008168, IDA, PMID:26677219 (PseudoCAP)	SOUND	Full text read. Purified EftM methylates EF-Tu with SAM; MS maps trimethyl-Lys5. The seed is under-specific (the paper supports GO:0016279), but a descendant is valid IBD evidence for the generic node term.	E. coli UbiE P0A887, human COQ5 Q5HYK3, yeast COQ5 S000004578, Synechocystis MPBQ MTase P74388, A. nidulans LaeA C8VQG9, Candida CAL0000191608, three Arabidopsis loci	Yes. Several seeds are well-characterised methyltransferases; generic methyltransferase activity suits a broad class I MTase node. No GO_CENTRAL defect for this node.

Separate problem (not a PseudoCAP seed): PA4178 also receives UbiE/COQ5 IBAs
(GO:0008425, GO:0006744) from the child node PTN001297884. These are wrong for
EftM, a protein lysine methyltransferase. Both rows are REMOVE, with one
GO_CENTRAL defect (PROBABLE) recorded on the GO:0006744 row.

Decisions

GO:0008168 IDA: MODIFY to GO:0016279 protein-lysine N-methyltransferase activity.
NEW GO:0018023 peptidyl-lysine trimethylation (IDA, PMID:26677219). EftM is the
enzyme that does the step.
GO:0003824 IEA: TOO_GENERAL.
GO:0017000 antibiotic biosynthetic process (ARBA): REMOVE.