ARBA00089391 spermidine transmembrane transport (GO:1903711)

id: ARBA00089391
description: >-
  Assigns GO:1903711 (spermidine transmembrane transport) to fungal proteins in CATH FunFam 1.20.1730.10:FF:000006
  (Urea active transporter), the family of the DUR3 polyamine and urea transporter.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00089391
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 1.20.1730.10:FF:000006
      curie: CATH.FunFam:1.20.1730.10:FF:000006
      label: Urea active transporter
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      1445. Swiss-Prot matches: P33413 (DUR3), A0A1D8PDB5 (DUR3), O94469 (dur3-1). Experimental annotation
      to GO:1903711 spermidine transmembrane transport or an is_a/part_of descendant (QuickGO): A0A1D8PDB5
      DUR3 GO:0015606 spermidine transmembrane transporter activity IMP PMID:22033918 (CGD); P33413 DUR3
      GO:0015606 spermidine transmembrane transporter activity IDA PMID:17218313 (SGD).
  go_annotations:
  - go_id: GO:1903711
    go_label: spermidine transmembrane transport
    aspect: BP
  entries:
  - id: 1.20.1730.10:FF:000006
    type: FUNFAM
    label: Urea active transporter
    appears_in_condition_sets:
    - 1
    protein_count: 5
    related_entries:
    - relationship: PREDICTS
      target_id: GO:1903711
      containment: 0.6
      jaccard_similarity: 0.018
      intersection_count: 3
      exclusive_count: 2
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2025-03-21'
  modified_date: '2025-12-15'
  source_condition_set_count: 1
  retrieved_date: '2026-11-09'
review_summary: >-
  The live rule has one condition set, FunFam 1.20.1730.10:FF:000006 in Fungi, and it was examined. Its
  Swiss-Prot matches are S. cerevisiae DUR3 (P33413), C. albicans DUR3 (A0A1D8PDB5, named Spermidine transporter
  DUR3) and S. pombe dur3-1 (O94469). P33413 has spermidine transmembrane transporter activity by IDA
  and IMP from PMID:17218313, and A0A1D8PDB5 by IMP from PMID:22033918; GO:0015606 is part_of GO:1903711.
  The MFS multidrug transporter set that an earlier version of the rule contained (FunFam 1.20.1250.20:FF:000011
  in Taphrinomycotina) is no longer in the rule.
action: ACCEPT
action_rationale: >-
  The only condition set identifies fungal DUR3 orthologs, and two of the three reviewed matches have
  experimental evidence of spermidine transport. Confidence is limited because 1,445 unreviewed fungal
  entries match and S. pombe has several dur3 paralogs whose substrates have not been tested.
literature_support:
  assessment: MODERATE
  notes: >-
    PMID:17218313, "Polyamine uptake by DUR3 and SAM3 in Saccharomyces cerevisiae", is the source of the
    SGD IDA and IMP annotations of P33413 to GO:0015606. The paper is not in the local publication cache,
    so no quotation is given.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:1903711
  label: spermidine transmembrane transport
  assessment: CORRECT
  correct_examples:
  - P33413
  - A0A1D8PDB5
  notes: >-
    P33413 DUR3 GO:0015606 spermidine transmembrane transporter activity IDA and IMP PMID:17218313 (SGD),
    and GO:1903711 IEA GO_REF:0000108 derived from it; A0A1D8PDB5 DUR3 GO:0015606 IMP PMID:22033918 (CGD);
    O94469 dur3-1 GO:0015606 IBA GO_REF:0000033 (GO_Central).
confidence: 0.75
references:
- id: PMID:17218313
  title: Polyamine uptake by DUR3 and SAM3 in Saccharomyces cerevisiae.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    No literature supports the urea active transporter family having polyamine transport activity.
  correction: >-
    S. cerevisiae DUR3, a member of this FunFam, is an experimentally characterised spermidine transporter.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - UniProtKB:P33413 DUR3 GO:0015606 IDA PMID:17218313 (SGD)
  - UniProtKB:P33413 DUR3 GO:0015606 IMP PMID:17218313 (SGD)
  - >-
    UniProtKB:A0A1D8PDB5 recommended name: Spermidine transporter DUR3; GO:0015606 IMP PMID:22033918 (CGD)
- date: '2026-11-10'
  withdrawn_claim: >-
    Tpo1-5 belong to specific MFS subfamilies, not to the generic FunFam 1.20.1250.20:FF:000011 used in
    the rule.
  correction: >-
    TPO1, TPO2 and TPO3 are members of that FunFam. The set that used it is no longer part of the rule.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - >-
    UniProtKB FunFam cross-reference 1.20.1250.20:FF:000011 on Q07824 (TPO1), P53283 (TPO2) and Q06451
    (TPO3)
  - >-
    Live rule retrieved 2026-11-09 has one condition set: FunFam 1.20.1730.10:FF:000006 AND Fungi
- date: '2026-11-10'
  withdrawn_claim: >-
    Only 21.8% of proteins matching FunFam 1.20.1250.20:FF:000011 carry the term, which confirms poor
    specificity.
  correction: >-
    The figure counted existing annotations among Swiss-Prot members of the FunFam in all taxa, ignored
    the taxon condition of the set, and treated a missing annotation as evidence of absence.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    Previous entries block: protein_count 55, intersection_count 12 for the FunFam alone, with no taxon
    filter
- date: '2026-11-10'
  withdrawn_claim: >-
    If the FunFams predicted spermidine transport the function would be expected in broader taxa, so the
    taxon restrictions show ad hoc construction.
  correction: >-
    A taxon condition limits where the rule fires; it says nothing about whether the annotation is true
    where it does fire.
  error_type: TAXON_MISREAD
  evidence:
  - 'Live condition set 1 taxon: Fungi (NCBITaxon:4751)'
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule has two condition sets, an MFS multidrug transporter set and a urea active transporter set.
  correction: The live rule has only the urea active transporter (DUR3) set.
  error_type: STALE_RULE_VERSION
  evidence:
  - >-
    https://rest.uniprot.org/arba/ARBA00089391 retrieved 2026-11-09, modifiedDate 2025-12-15, one condition
    set