Fix bacterial (E. coli) tRNA identity elements#35
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Corrects several errors in the bundled E. coli identity element data, verified against Giege & Eriani (2023, NAR 51(4):1528), GtRNAdb K-12 sequences, and primary aminoacylation literature. Determinants: - tRNA-Asn: add the missing G34 anticodon determinant and set the discriminator to G73 (was unspecified). - tRNA-Gly: fix the acceptor-stem 2:71 pair orientation to C2-G71 (was encoded G2-C71, i.e. flipped) and add the G3-C70 pair. - tRNA-Glu and tRNA-Thr: remove the position-73 "discriminator" determinant rows. N73 is explicitly NOT an identity element for these two E. coli tRNAs (the stated exceptions in Giege & Eriani 2023); the E. coli tRNA-Thr discriminator is A73, not U73. Antideterminants: - Remove "A73 in tRNA-Met blocks IleRS" and "U73 in tRNA-Thr blocks ValRS"; neither appears in Table 3, and both premises are false (Met/Ile separation is via lysidine k2C34 in tRNA-Ile, already encoded; tRNA-Thr is A73, the same as Val). Regenerated determinants.rds and antideterminants.rds from data-raw/identity.R. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
A review of the bundled E. coli (
"Escherichia coli"/ Bacteria domain) tRNA aminoacylation identity elements inidentity_elements()surfaced several factual errors. This corrects them, verified against Giegé & Eriani 2023, NAR 51(4):1528 (Tables 1, 3, 4 — the dataset's cited source), GtRNAdb K-12 sequences, and primary aminoacylation literature.All anticodon (positions 35/36) bases and most discriminators were already correct; the fixes below target discriminators, an acceptor-stem pair orientation, and two antideterminants.
Changes
Determinants
G2-C71, i.e. the 5′ base flipped; C2×G71 is the central GlyRS determinant) and add the G3-C70 pair. (PMID 9171287)Antideterminants
determinants.rds(211 rows) andantideterminants.rds(10 rows) regenerated fromdata-raw/identity.R.Not included (medium-confidence, left for discussion)
Testing
Data-level
identity_elements()assertions (20 AAs present, column types, Ala G3-U70 universal flag, organism filtering, error handling) pass against the regenerated data. The error snapshots are unaffected (functions unchanged). Plotting tests require Bioconductor deps not available in this sandbox.🤖 Generated with Claude Code