ARBA00028985 RNA metabolic process (GO:0016070)

id: ARBA00028985
description: >-
  Assigns GO:0016070 (RNA metabolic process) through 375 alternative condition sets built from InterPro
  entries, PANTHER families and CATH FunFams, about a quarter of them with a taxon.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00028985
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR006195
      curie: InterPro:IPR006195
      label: Aminoacyl-tRNA synthetase, class II
      negated: false
    - condition_type: INTERPRO
      value: IPR045864
      curie: InterPro:IPR045864
      label: >-
        Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase
        (LPL)
      negated: false
    - condition_type: TAXON
      value: Saccharomycotina
      curie: NCBITaxon:147537
      label: Saccharomycotina
      negated: false
    notes: >-
      UniProtKB release 2026_04: 20 reviewed entries match this set; 20 of them carry GO:0016070 or
      a descendant, 18 of those by a manual-evidence GO annotation. 2395 unreviewed entries match.
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR000999
      curie: InterPro:IPR000999
      label: Ribonuclease III domain
      negated: false
    - condition_type: INTERPRO
      value: IPR001650
      curie: InterPro:IPR001650
      label: Helicase, C-terminal domain-like
      negated: false
    - condition_type: INTERPRO
      value: IPR027417
      curie: InterPro:IPR027417
      label: P-loop containing nucleoside triphosphate hydrolase
      negated: false
    notes: >-
      UniProtKB release 2026_04: 48 reviewed entries match this set; 48 of them carry GO:0016070 or
      a descendant, 26 of those by a manual-evidence GO annotation. 7197 unreviewed entries match.
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR020103
      curie: InterPro:IPR020103
      label: Pseudouridine synthase, catalytic domain superfamily
      negated: false
    - condition_type: TAXON
      value: Primates
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      UniProtKB release 2026_04: 13 reviewed entries match this set; 13 of them carry GO:0016070 or
      a descendant, 13 of those by a manual-evidence GO annotation. 779 unreviewed entries match.
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR002058
      curie: InterPro:IPR002058
      label: PAP/25A-associated
      negated: false
    - condition_type: INTERPRO
      value: IPR043519
      curie: InterPro:IPR043519
      label: Nucleotidyltransferase superfamily
      negated: false
    - condition_type: TAXON
      value: Chordata
      curie: NCBITaxon:7711
      label: Chordata
      negated: false
    notes: >-
      UniProtKB release 2026_04: 24 reviewed entries match this set; 24 of them carry GO:0016070 or
      a descendant, 24 of those by a manual-evidence GO annotation. 7118 unreviewed entries match.
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR039206
      curie: InterPro:IPR039206
      label: MORF/ORRM1/DAG-like
      negated: false
    - condition_type: INTERPRO
      value: IPR054059
      curie: InterPro:IPR054059
      label: MORF/ORRM1/DAG-like, MORF domain
      negated: false
    - condition_type: TAXON
      value: Viridiplantae
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: >-
      UniProtKB release 2026_04: 13 reviewed entries match this set; 13 of them carry GO:0016070 or
      a descendant, 12 of those by a manual-evidence GO annotation. 4494 unreviewed entries match.
  - number: 6
    conditions:
    - condition_type: INTERPRO
      value: IPR001412
      curie: InterPro:IPR001412
      label: Aminoacyl-tRNA synthetase, class I, conserved site
      negated: false
    - condition_type: INTERPRO
      value: IPR014729
      curie: InterPro:IPR014729
      label: Rossmann-like alpha/beta/alpha sandwich fold
      negated: false
    - condition_type: TAXON
      value: Pseudomonadota
      curie: NCBITaxon:1224
      label: Pseudomonadota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2020 reviewed entries match this set; 2020 of them carry GO:0016070
      or a descendant, 82 of those by a manual-evidence GO annotation. 58135 unreviewed entries match.
  - number: 7
    conditions:
    - condition_type: INTERPRO
      value: IPR018163
      curie: InterPro:IPR018163
      label: Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily
      negated: false
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: false
    notes: >-
      UniProtKB release 2026_04: 83 reviewed entries match this set; 83 of them carry GO:0016070 or
      a descendant, 17 of those by a manual-evidence GO annotation. 1521 unreviewed entries match.
  - number: 8
    conditions:
    - condition_type: INTERPRO
      value: IPR029064
      curie: InterPro:IPR029064
      label: Ribosomal protein eL30-like superfamily
      negated: false
    - condition_type: TAXON
      value: Saccharomyces
      curie: NCBITaxon:4930
      label: Saccharomyces
      negated: false
    notes: >-
      UniProtKB release 2026_04: 10 reviewed entries match this set; 10 of them carry GO:0016070 or
      a descendant, 8 of those by a manual-evidence GO annotation. 94 unreviewed entries match.
  - number: 9
    conditions:
    - condition_type: INTERPRO
      value: IPR036511
      curie: InterPro:IPR036511
      label: Queuine tRNA-ribosyltransferase-like
      negated: false
    notes: >-
      UniProtKB release 2026_04: 543 reviewed entries match this set; 543 of them carry GO:0016070
      or a descendant, 40 of those by a manual-evidence GO annotation. 24395 unreviewed entries match.
  - number: 10
    conditions:
    - condition_type: INTERPRO
      value: IPR002314
      curie: InterPro:IPR002314
      label: Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
      negated: false
    - condition_type: INTERPRO
      value: IPR004154
      curie: InterPro:IPR004154
      label: Anticodon-binding
      negated: false
    - condition_type: TAXON
      value: Euteleostomi
      curie: NCBITaxon:117571
      label: Euteleostomi
      negated: false
    notes: >-
      UniProtKB release 2026_04: 20 reviewed entries match this set; 20 of them carry GO:0016070 or
      a descendant, 20 of those by a manual-evidence GO annotation. 6374 unreviewed entries match.
  go_annotations:
  - go_id: GO:0016070
    go_label: RNA 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: 375
review_summary: >-
  The first 10 of the 375 live condition sets were examined. They select aminoacyl-tRNA synthetases,
  RNase III helicases, pseudouridine synthases, terminal nucleotidyltransferases, plant RNA-editing
  factors and queuine tRNA-ribosyltransferases. In the sets for which both counts were obtained, 2794
  of 2794 reviewed matches carry GO:0016070 or a descendant. The other 365 sets were not examined.
action: UNDECIDED
action_rationale: >-
  The rule was sampled, not examined set by set, so no verdict is given. The sampled sets are sound,
  which removes the grounds of the earlier verdict but does not establish that every set is right.
  The counts are from Swiss-Prot, which is also what ARBA learns its rules from, so they show the
  condition sets are coherent rather than giving an independent error rate for unreviewed entries.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0016070
  label: RNA metabolic process
  assessment: UNDECIDED
  correct_examples:
  - P15625
  - P08425
  - P32048
  notes: >-
    UniProtKB release 2026_04: set 1 reviewed matches with a manual-evidence annotation to GO:0016070
    or a descendant include P15625 (Saccharomyces cerevisiae FRS2), P08425 (MSF1) and P32048 (MSK1).
    Per-set counts are in the condition set notes.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule should be deprecated because RNA metabolic process is too broad to be informative for
    tRNA synthetases, ribonucleases and helicases.
  correction: >-
    The term is true for those families. A general true term is not a reason to deprecate; at most
    it is a reason to add more specific terms.
  error_type: GENERAL_IS_NOT_WRONG
  evidence:
  - >-
    UniProtKB release 2026_04: in the sets examined the reviewed matches carry GO:0016070 or a descendant;
    counts are in the condition set notes.
- date: '2026-11-10'
  withdrawn_claim: Condition overlap is complete and false positives are virtually guaranteed.
  correction: >-
    The same passage states that no overlap analysis could be run and that no entries were analysed.
    No falsely annotated protein was named.
  error_type: UNEXAMINED_RULE
  evidence:
  - The old file recorded condition_sets and entries as empty lists.
- date: '2026-11-10'
  withdrawn_claim: 357 condition sets exceed the recommended maximum and make the rule unmanageable.
  correction: >-
    The number of sets is not evidence about accuracy, and the maximum cited was the default of an
    analysis tool, given once as 12 and once as 30.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'UniProt ARBA API, ARBA00028985, retrieved 2026-11-09: 375 condition sets.'
- date: '2026-11-10'
  withdrawn_claim: The literature contradicts the rule.
  correction: >-
    The only sources were the review's own notes. Literature on the specific functions of these families
    does not contradict their taking part in RNA metabolism.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - The old literature_support block cited only rules/arba/ARBA00028985/ARBA00028985-notes.md.
- date: '2026-11-10'
  withdrawn_claim: >-
    tRNA synthetases should be annotated with aminoacyl-tRNA ligase activity terms, not with RNA metabolism.
  correction: >-
    The first is a molecular function and the second a biological process; a protein can carry both.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - 'QuickGO: GO:0016070 aspect biological_process.'