ARBA00026708 peroxisome organization (GO:0007031)

id: ARBA00026708
description: >-
  Assigns GO:0007031 (peroxisome organization) through 12 alternative condition sets that identify peroxins
  (PEX5, PEX7, PEX11, PEX12, PEX14/PEX33, the PEX28-PEX32 family), the dynamin-related fission GTPases
  DNM1/DRP3/DNM1L and VPS1, plant FIS1, and the fungal kinases KIN4 and FRK1.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00026708
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR006845
      curie: InterPro:IPR006845
      label: Pex, N-terminal
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR013083
      curie: InterPro:IPR013083
      label: Zinc finger, RING/FYVE/PHD-type
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR017375
      curie: InterPro:IPR017375
      label: Peroxisome assembly protein 12
      interpro_type: FAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 14 (UniProtKB query, 2026-11-10); unreviewed
      entries: 2858. Swiss-Prot matches: O00623 (PEX12), Q9M841 (PEX12), Q04370 (PEX12), O88177 (Pex12),
      Q19189 (prx-12), Q9VPT5 (Pex12), Q8VC48 (Pex12), C8VCP8 (PEX12), and 6 more. Experimental annotation
      to GO:0007031 peroxisome organization or an is_a/part_of descendant (QuickGO): O00623 PEX12 GO:0007031
      peroxisome organization IDA PMID:9354782 (UniProt); O88177 Pex12 GO:0007031 peroxisome organization
      IMP PMID:9632816 (RGD); Q01961 PEX12 GO:0016562 protein import into peroxisome matrix, receptor
      recycling IMP PMID:23344950 (UniProt); Q04370 PEX12 GO:0016558 protein import into peroxisome matrix
      IMP PMID:11370741 (SGD); Q19189 prx-12 GO:0007031 peroxisome organization IMP PMID:12181365 (WB).
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR006785
      curie: InterPro:IPR006785
      label: Peroxisome membrane anchor protein Pex14/PEX33, N-terminal
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR025655
      curie: InterPro:IPR025655
      label: Peroxisomal membrane protein 14
      interpro_type: FAMILY
      negated: false
    - condition_type: TAXON
      value: Pezizomycotina
      curie: NCBITaxon:147538
      label: Pezizomycotina
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      1610. Swiss-Prot matches: G4NCT7 (PEX14), G4NCH6 (PEX33), A0ABQ8WBK9 (PEX33), Q1K602 (PEX14), Q7RY61
      (PEX33). Experimental annotation to GO:0007031 peroxisome organization or an is_a/part_of descendant
      (QuickGO): A0ABQ8WBK9 PEX33 GO:0016558 protein import into peroxisome matrix IMP PMID:20597979 (UniProt);
      G4NCH6 PEX33 GO:0016558 protein import into peroxisome matrix IMP PMID:27571711 (UniProt); G4NCT7
      PEX14 GO:0016560 protein import into peroxisome matrix, docking IMP PMID:30905264 (UniProt); Q1K602
      PEX14 GO:0016560 protein import into peroxisome matrix, docking IMP PMID:17461798 (UniProt); Q7RY61
      PEX33 GO:0016560 protein import into peroxisome matrix, docking IMP PMID:20728240 (UniProt).
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR008733
      curie: InterPro:IPR008733
      label: Peroxisomal biogenesis factor 11
      interpro_type: FAMILY
      negated: false
    - condition_type: PANTHER
      value: PTHR12652
      curie: PANTHER:PTHR12652
      label: PEROXISOMAL BIOGENESIS FACTOR 11
      negated: false
    - condition_type: TAXON
      value: Viridiplantae
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 12 (UniProtKB query, 2026-11-10); unreviewed
      entries: 1979. Swiss-Prot matches: Q9FZF1 (PEX11A), Q84JW1 (PEX11E), O80845 (PEX11D), Q9LQ73 (PEX11C),
      Q9STY0 (PEX11B), Q10SM7 (PEX11-1), Q5VRJ8 (PEX11-5), Q10MN2 (PEX11-3), and 4 more. Experimental
      annotation to GO:0007031 peroxisome organization or an is_a/part_of descendant (QuickGO): O80845
      PEX11D GO:0007031 peroxisome organization IMP PMID:17478547 (TAIR); Q84JW1 PEX11E GO:0007031 peroxisome
      organization IMP PMID:17478547 (TAIR); Q9FZF1 PEX11A GO:0007031 peroxisome organization IMP PMID:17478547
      (TAIR); Q9LQ73 PEX11C GO:0007031 peroxisome organization IMP PMID:17478547 (TAIR); Q9STY0 PEX11B
      GO:0007031 peroxisome organization IMP PMID:17478547 (TAIR).
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR010482
      curie: InterPro:IPR010482
      label: TECPR1-like, DysF domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: TAXON
      value: Saccharomycetes
      curie: NCBITaxon:4891
      label: Saccharomycetes
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      261. Swiss-Prot matches: P53203 (PEX31), Q06169 (PEX30), Q03370 (PEX29), P38848 (PEX28), P38292
      (PEX32). Experimental annotation to GO:0007031 peroxisome organization or an is_a/part_of descendant
      (QuickGO): P38292 PEX32 GO:0007031 peroxisome organization IMP PMID:14617799 (SGD); P38848 PEX28
      GO:0007031 peroxisome organization IDA PMID:12707309 (SGD); P53203 PEX31 GO:0007031 peroxisome organization
      IMP PMID:14617799 (SGD); Q03370 PEX29 GO:0007031 peroxisome organization IDA PMID:12707309 (SGD);
      Q06169 PEX30 GO:0007031 peroxisome organization IMP PMID:14617799 (SGD).
  - number: 5
    conditions:
    - condition_type: FUNFAM
      value: 2.130.10.10:FF:000372
      curie: CATH.FunFam:2.130.10.10:FF:000372
      label: Peroxisomal biogenesis factor 7
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      149. Swiss-Prot matches: O00628 (PEX7), P97865 (Pex7), Q8R537 (PEX7). Experimental annotation to
      GO:0007031 peroxisome organization or an is_a/part_of descendant (QuickGO): O00628 PEX7 GO:0007031
      peroxisome organization IMP PMID:10022913 (UniProt); P97865 Pex7 GO:0016558 protein import into
      peroxisome matrix IMP PMID:12915479 (UniProt); Q8R537 PEX7 GO:0016558 protein import into peroxisome
      matrix IDA PMID:10767286 (UniProt).
  - number: 6
    conditions:
    - condition_type: FUNFAM
      value: 3.30.40.10:FF:000266
      curie: CATH.FunFam:3.30.40.10:FF:000266
      label: Peroxisome assembly protein 12
      negated: false
    - condition_type: TAXON
      value: Metazoa
      curie: NCBITaxon:33208
      label: Metazoa
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 8 (UniProtKB query, 2026-11-10); unreviewed entries:
      631. Swiss-Prot matches: O00623 (PEX12), O88177 (Pex12), Q19189 (prx-12), Q8VC48 (Pex12), A0A1L8H814
      (pex12.S), Q6DFK1 (pex12.L), A4FUD4 (PEX12), Q9ET67 (PEX12). Experimental annotation to GO:0007031
      peroxisome organization or an is_a/part_of descendant (QuickGO): O00623 PEX12 GO:0007031 peroxisome
      organization IDA PMID:9354782 (UniProt); O88177 Pex12 GO:0007031 peroxisome organization IMP PMID:9632816
      (RGD); Q19189 prx-12 GO:0007031 peroxisome organization IMP PMID:12181365 (WB).
  - number: 7
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:001027
      curie: CATH.FunFam:3.40.50.300:FF:001027
      label: dynamin-related protein 3A
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      1574. Swiss-Prot matches: P54861 (DNM1), Q8LFT2 (DRP3B), Q8S944 (DRP3A), S8EYU3 (DRPA). Experimental
      annotation to GO:0007031 peroxisome organization or an is_a/part_of descendant (QuickGO): P54861
      DNM1 GO:0007031 peroxisome organization IGI PMID:16968746 (SGD); Q8LFT2 DRP3B GO:0016559 peroxisome
      fission IMP PMID:18785999 (TAIR); Q8S944 DRP3A GO:0016559 peroxisome fission IMP PMID:18539750 (TAIR).
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000397
      curie: CATH.FunFam:1.10.510.10:FF:000397
      label: Serine/threonine-protein kinase KIN4
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      922. Swiss-Prot matches: Q03002 (FRK1), Q01919 (KIN4). Experimental annotation to GO:0007031 peroxisome
      organization or an is_a/part_of descendant (QuickGO): Q01919 KIN4 GO:0045033 peroxisome inheritance
      IGI PMID:37509134 (SGD); Q03002 FRK1 GO:0045033 peroxisome inheritance IGI PMID:37509134 (SGD).
  - number: 9
    conditions:
    - condition_type: FUNFAM
      value: 1.25.40.10:FF:000167
      curie: CATH.FunFam:1.25.40.10:FF:000167
      label: Mitochondrial fission 1 protein
      negated: false
    - condition_type: TAXON
      value: Streptophyta
      curie: NCBITaxon:35493
      label: Streptophyta
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      816. Swiss-Prot matches: Q9M1J1 (FIS1A), Q94CK3 (FIS1B). Experimental annotation to GO:0007031 peroxisome
      organization or an is_a/part_of descendant (QuickGO): Q94CK3 FIS1B GO:0016559 peroxisome fission
      IMP PMID:14730085 (TAIR); Q9M1J1 FIS1A GO:0016559 peroxisome fission IMP PMID:18785999 (TAIR).
  - number: 10
    conditions:
    - condition_type: FUNFAM
      value: 1.25.40.10:FF:000218
      curie: CATH.FunFam:1.25.40.10:FF:000218
      label: Peroxisomal targeting signal receptor
      negated: false
    - condition_type: TAXON
      value: Saccharomycotina
      curie: NCBITaxon:147537
      label: Saccharomycotina
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      71. Swiss-Prot matches: P35056 (PEX5), Q99144 (PAY32), O74711 (PEX5), Q6FM42 (PEX5), Q6BM14 (PEX5).
      Experimental annotation to GO:0007031 peroxisome organization or an is_a/part_of descendant (QuickGO):
      O74711 PEX5 GO:0016558 protein import into peroxisome matrix IMP PMID:18832312 (CGD); P35056 PEX5
      GO:0016558 protein import into peroxisome matrix IDA PMID:15283676 (UniProt).
  - number: 11
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000473
      curie: CATH.FunFam:3.40.50.300:FF:000473
      label: Vacuolar sorting-associated 1 protein
      negated: false
    - condition_type: TAXON
      value: Dikarya
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      1327. Swiss-Prot matches: P21576 (VPS1), Q9URZ5 (vps1). Experimental annotation to GO:0007031 peroxisome
      organization or an is_a/part_of descendant (QuickGO): P21576 VPS1 GO:0007031 peroxisome organization
      IDA PMID:12707309 (SGD); Q9URZ5 vps1 GO:0007031 peroxisome organization IGI PMID:18088324 (PomBase).
  - number: 12
    conditions:
    - condition_type: FUNFAM
      value: 1.20.120.1240:FF:000002
      curie: CATH.FunFam:1.20.120.1240:FF:000002
      label: Dynamin-1-like protein isoform 1
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      2016. Swiss-Prot matches: Q8K1M6 (Dnm1l), P54861 (DNM1). Experimental annotation to GO:0007031 peroxisome
      organization or an is_a/part_of descendant (QuickGO): P54861 DNM1 GO:0007031 peroxisome organization
      IGI PMID:16968746 (SGD); Q8K1M6 Dnm1l GO:0016559 peroxisome fission IMP PMID:29853636 (UniProt).
  go_annotations:
  - go_id: GO:0007031
    go_label: peroxisome organization
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  source_condition_set_count: 12
  retrieved_date: '2026-11-09'
review_summary: >-
  All 12 live condition sets were examined by retrieving the Swiss-Prot entries that match the whole conjunction
  and looking up their curated annotations. Every set has at least one Swiss-Prot match with an experimental
  annotation to GO:0007031 or an is_a/part_of descendant (protein import into peroxisome matrix and its
  steps, peroxisome fission, peroxisome inheritance). The dynamin, VPS1 and FIS1 sets match proteins that
  also act in mitochondrial fission; their peroxisome annotations are experimental. Set 8 matches S. cerevisiae
  KIN4 and FRK1, annotated to peroxisome inheritance by IGI from one paper. Sets 7 and 12 have no taxon
  condition; set 7 also matches Toxoplasma gondii DrpA (S8EYU3), which has no curated annotation to the
  term. The check uses Swiss-Prot, the source ARBA rules are mined from, and does not measure precision
  on unreviewed entries.
action: ACCEPT
action_rationale: >-
  Each condition set identifies a characterised peroxisome biogenesis, fission or inheritance factor,
  and each has reviewed members with experimental support for the term or a descendant. Confidence is
  reduced by set 8, which rests on one genetic-interaction paper, and by the two dynamin sets without
  a taxon condition.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0007031
  label: peroxisome organization
  assessment: CORRECT
  correct_examples:
  - O00623
  - O00628
  - P35056
  - Q9FZF1
  - P38848
  - P54861
  - P21576
  - Q9M1J1
  - Q01919
  notes: >-
    O00623 PEX12 GO:0007031 IDA PMID:9354782; O00628 PEX7 GO:0007031 IMP PMID:10022913; P35056 PEX5 GO:0016558
    protein import into peroxisome matrix IDA PMID:15283676; Q9FZF1 PEX11A GO:0007031 IMP PMID:17478547;
    P38848 PEX28 GO:0007031 IDA PMID:12707309; P54861 DNM1 GO:0007031 IGI PMID:16968746; P21576 VPS1 GO:0007031
    IDA PMID:12707309; Q9M1J1 FIS1A GO:0016559 peroxisome fission IMP PMID:18785999; Q01919 KIN4 GO:0045033
    peroxisome inheritance IGI PMID:37509134. Per-set receipts are in the condition set notes.
confidence: 0.7
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    Many of the InterPro domains used lack specific functional annotation; conditions were labelled "Unknown
    function (peroxisomal)" or "Peroxisomal protein family".
  correction: >-
    The labels were placeholders, not the entry names. The entries are named peroxin and fission-factor
    signatures.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'InterPro IPR006845: Pex, N-terminal'
  - 'InterPro IPR017375: Peroxisome assembly protein 12'
  - 'InterPro IPR008733: Peroxisomal biogenesis factor 11'
  - 'InterPro IPR006785: Peroxisome membrane anchor protein Pex14/PEX33, N-terminal'
  - 'InterPro IPR010482: TECPR1-like, DysF domain'
  - >-
    CATH FunFam 2.130.10.10:FF:000372: Peroxisomal biogenesis factor 7; 1.25.40.10:FF:000218: Peroxisomal
    targeting signal receptor
- date: '2026-11-10'
  withdrawn_claim: The rule has 10 condition sets, including IPR010482 in Fungi.
  correction: >-
    The live rule has 12 sets; IPR010482 is restricted to Saccharomycetes, and the Pex14/PEX33 set and
    the dynamin-related protein 3A set were not recorded.
  error_type: STALE_RULE_VERSION
  evidence:
  - >-
    https://rest.uniprot.org/arba/ARBA00026708 retrieved 2026-11-09, modifiedDate 2026-07-18, 12 condition
    sets
- date: '2026-11-10'
  withdrawn_claim: >-
    Negative conditions are needed to exclude mitochondrial and ER proteins that share these domains.
  correction: >-
    The proteins shared with mitochondria (DNM1, DNM1L, VPS1, FIS1) have experimental peroxisome fission
    or organization annotations, so excluding them would remove correct annotations.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - UniProtKB:P54861 DNM1 GO:0007031 IGI PMID:16968746 (SGD)
  - UniProtKB:Q8K1M6 Dnm1l GO:0016559 IMP PMID:29853636 (UniProt)
  - UniProtKB:P21576 VPS1 GO:0007031 IDA PMID:12707309 (SGD)
  - UniProtKB:Q94CK3 FIS1B GO:0016559 IMP PMID:14730085 (TAIR)
- date: '2026-11-10'
  withdrawn_claim: GO:0016558 is peroxisome fusion and GO:0016560 is protein import.
  correction: >-
    GO:0016558 is protein import into peroxisome matrix; GO:0016560 is protein import into peroxisome
    matrix, docking.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'QuickGO GO:0016558 label: protein import into peroxisome matrix'
  - 'QuickGO GO:0016560 label: protein import into peroxisome matrix, docking'
- date: '2026-11-10'
  withdrawn_claim: >-
    Condition sets overlap significantly and the taxonomic scope is too broad, risking annotation of organisms
    without peroxisomes.
  correction: >-
    Neither was measured: the overlap was stated without any count and no organism lacking peroxisomes
    was shown to be annotated. Both blocks were removed.
  error_type: UNEXAMINED_RULE
  evidence:
  - >-
    Previous condition_overlap note began "Without quantitative analysis"; all previous entries had protein_count
    0