View original ARBA rule on UniProt
Assigns GO:0006139 nucleobase-containing compound metabolic process through 773 alternative condition sets of InterPro, PANTHER and CATH FunFam signatures, some with a taxon condition.
Condition-set counts describe the sets recorded in this review, which may omit the full rule.
No domain overlap table is shown: the cached overlap analysis for this version of the review is not available.
Run just analyze-rule ARBA00026572 and re-render to add it.
None of the 773 live condition sets has been examined, and no wrongly annotated protein has been identified. GO:0006139 is a high-level term; a set that selects DNA repair proteins, aminoacyl-tRNA synthetases or nucleotide biosynthesis enzymes would be annotated correctly but generally. The review is open.
There is no evidence in hand that any condition set gives a false annotation. That the term is general is not a reason to deprecate.
No condition set examined. GO:0006281 DNA repair, GO:0006418 tRNA aminoacylation for protein translation and GO:0009165 nucleotide biosynthetic process all have GO:0006139 among their ancestors (QuickGO).
id: ARBA00026572
description: Assigns GO:0006139 nucleobase-containing compound metabolic process through 773 alternative
condition sets of InterPro, PANTHER and CATH FunFam signatures, some with a taxon condition.
status: IN_PROGRESS
rule_type: ARBA
rule:
rule_id: ARBA00026572
condition_sets: []
go_annotations:
- go_id: GO:0006139
go_label: nucleobase-containing compound metabolic process
aspect: BP
entries: []
reviewed_protein_count: 0
unreviewed_protein_count: 0
created_date: '2021-10-20'
modified_date: '2026-07-18'
retrieved_date: '2026-11-09'
source_condition_set_count: 773
review_summary: None of the 773 live condition sets has been examined, and no wrongly annotated protein
has been identified. GO:0006139 is a high-level term; a set that selects DNA repair proteins, aminoacyl-tRNA
synthetases or nucleotide biosynthesis enzymes would be annotated correctly but generally. The review
is open.
action: UNDECIDED
action_rationale: There is no evidence in hand that any condition set gives a false annotation. That the
term is general is not a reason to deprecate.
annotation_assessments:
- annotation_kind: GO_TERM
value: GO:0006139
label: nucleobase-containing compound metabolic process
assessment: UNDECIDED
notes: No condition set examined. GO:0006281 DNA repair, GO:0006418 tRNA aminoacylation for protein
translation and GO:0009165 nucleotide biosynthetic process all have GO:0006139 among their ancestors
(QuickGO).
corrections:
- date: '2026-11-10'
withdrawn_claim: The rule should be deprecated because GO:0006139 is too broad; DNA repair, tRNA aminoacylation
and nucleotide biosynthesis terms should be used instead.
correction: The proposed terms are descendants of GO:0006139, so the rule's annotation would be true
for those proteins. A true general term is not grounds for removal.
error_type: GENERAL_IS_NOT_WRONG
evidence:
- QuickGO ancestors of GO:0006281, GO:0006418 and GO:0009165 each include GO:0006139
- date: '2026-11-10'
withdrawn_claim: The literature contradicts the rule.
correction: The only source cited was the reviewer's own manual notes file. No publication was cited.
error_type: UNSUPPORTED_SOURCE
evidence:
- Old literature_support cited only ARBA00026572-deep-research-manual.md
- date: '2026-11-10'
withdrawn_claim: Sampling shows heterogeneous functional classes; taxonomic restrictions are arbitrary.
correction: The review recorded no condition sets, so neither statement can be checked.
error_type: UNEXAMINED_RULE
evidence:
- 'Old review: rule.condition_sets empty, protein counts 0'
- date: '2026-11-10'
withdrawn_claim: Because GO:0006139 is a universal process, taxon restrictions on the condition sets
are inappropriate.
correction: A taxon condition narrows where a signature is trusted; it says nothing about how widespread
the process is.
error_type: TAXON_MISREAD
evidence:
- 'Live rule: 773 condition sets, each a conjunction (rest.uniprot.org/arba/ARBA00026572, 2026-11-09)'
- date: '2026-11-10'
withdrawn_claim: 781 condition sets make the rule unanalyzable and it should be rebuilt with at most
12 sets per rule.
correction: The number of alternative sets is not evidence that any of them is wrong.
error_type: SIZE_AS_EVIDENCE
evidence:
- 'src/ai_gene_review/etl/rule_analysis.py: max_condition_sets: int = 12 (default of the overlap-analysis
tool)'