family_id: PANTHER:PTHR13195
family_name: PSEUDOURIDINE SYNTHASE-RELATED
preferred_name: TRUB2-related RNA pseudouridylation proteins
summary: TRUB2-related proteins are associated with mitochondrial RNA pseudouridylation. Family membership
  supports an RNA-modification hypothesis but does not identify the RNA substrate or guarantee catalytic
  competence of a fragment.
functional_coherence: MOSTLY_COHERENT
coherence_reason: The pigeon protein is only 142 residues with an N-terminal pseudouridine-synthase annotation.
  Published TRUB2 evidence concerns specific mitochondrial mRNA residues; it does not by itself establish
  tRNA pseudouridine synthase activity for this short sequence. Full-domain completeness and substrate
  assignment remain unresolved.
subfamilies:
- subfamily_id: PANTHER:PTHR13195:SF0
  label: PSEUDOURIDYLATE SYNTHASE TRUB2, MITOCHONDRIAL
  description: Recorded placement of A0A2I0M3K7. The pigeon protein is only 142 residues with an N-terminal
    pseudouridine-synthase annotation. Published TRUB2 evidence concerns specific mitochondrial mRNA residues;
    it does not by itself establish tRNA pseudouridine synthase activity for this short sequence. Full-domain
    completeness and substrate assignment remain unresolved.
  representative_members:
  - id: UniProtKB:A0A2I0M3K7
    gene_symbol: A0A2I0M3K7
    organism: Columba livia
    gene_review: genes/COLLI/A0A2I0M3K7/A0A2I0M3K7-ai-review.yaml
term_assessments:
- assessed_term:
    id: GO:0106029
    label: tRNA pseudouridine synthase activity
  scope: UNRESOLVED
  scope_reason: The cited human TRUB2 depletion and pseudouridine-Seq study identifies specific mitochondrial
    mRNA targets, not a tRNA substrate. It therefore supports RNA pseudouridylation while leaving this
    particular tRNA activity unestablished. The pigeon product is only 142 residues with an N-terminal
    synthase-associated region, adding a domain-completeness problem independent of RNA substrate choice.
  supported_by:
  - reference_id: PMID:27974379
    supporting_text: "TRUB2/RPUSD3 were similarly involved in pseudouridylating specific residues in \n\
      mitochondrial mRNAs"
  - reference_id: file:genes/COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt
    supporting_text: DR   InterPro; IPR039048; Trub2.
  - reference_id: file:genes/COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt
    supporting_text: FT   DOMAIN          1..54
  - reference_id: file:genes/COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt
    supporting_text: FT                   /note="Pseudouridine synthase II N-terminal"
references:
- id: PMID:27974379
  title: A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability.
- id: file:genes/COLLI/A0A2I0M3K7/A0A2I0M3K7-uniprot.txt
- id: file:interpro/panther/PTHR13195/PTHR13195-entries.csv
- id: file:interpro/panther/PTHR13195/PTHR13195-paint.tsv
review_status: COMPLETE
reviewed_by: codex
review_date: '2026-09-10'
notes: 'COLLI/A0A2I0M3K7: requested accession A0A2I0M3K7; current record A0A2I0M3K7; sequence length 142;
  source cohort ARGO50. Family boundaries were assessed using the fetched member set and the cited domain,
  literature and analytical evidence. Gene-review verdicts and ARBA assertions are not independent validation.
  PANTHER subfamily labels and membership are recorded from the frozen UniProt records and panther.obo;
  they do not by themselves prove functional uniformity within a subfamily. PAINT rows were inspected
  as ancestral assertions, but node placement is not adjudicated without the relevant descendant tree/alignment.
  No residue requirement is encoded without a verified sequence-version anchor. A target-level refutation
  is not a family-wide NOT_APPLICABLE judgment. Exact protein-name-only predictions are treated as family-identification
  hypotheses rather than invented GO predictions.'