Bacterial aminoacyl-tRNA charging

Production of the twenty canonical aminoacyl-tRNAs used in bacterial protein synthesis, through direct aminoacyl-tRNA synthetases and species-matched indirect amino-acid conversion on tRNA. The reusable program distinguishes class I and class II LysRS, homodimeric and heterotetrameric GlyRS, heteromeric PheRS, direct versus GatCAB-dependent Asn/Gln formation, and the rare bacterial SepRS–SepCysS route to Cys-tRNA. The boundary ends at a correctly aminoacylated tRNA. It excludes ribosomal elongation, initiation-specific formylation, tRNA maturation, selenocysteine/pyrrolysine recoding and off-tRNA amino-acid synthesis. Editing improves fidelity but is not modeled as a universally obligatory independent enzyme for each output.

All 26 original proteins are retained in the 42-member panel. The historical cross-species THEVB GluRS–PSEPK GatCAB chain is replaced by a species-matched Bacillus indirect Gln route. A same-organism oracle is required when evaluating the reusable program; the generic Boolean compiler itself does not enforce taxonomy. Partial comparator panels cannot establish whole-genome absence of missing activities. All 22 disputed terms were verified individually on 2026-10-29 in the committed QuickGO snapshot and pinned GO source stanzas; see bacterial_aminoacyl_trna_charging-analysis/ontology-review.md. GO explicitly replaces the twenty substrate-specific charging BPs with GO:0006418; substrate specificity remains in the molecular functions. GO:0070681 has consider advice, not an automatic replacement. The eleven GatCAB rows use GO:0019988 after reviewing their charged-tRNA modification chemistry. No GOA row, protein name, provider prose or family label alone is used as biochemical evidence. Archived Parcubacteria identities are verified by literal UniSave/UniParc sequence matches to published clone accessions; deletion from the current reference-proteome collection is not biological loss.