ARBA00026708 peroxisome organization (GO:0007031)

id: ARBA00026708
description: Rule predicting peroxisome organization (GO:0007031) based on multiple
  InterPro domains and CATH FunFam classifications across different taxonomic groups.
  The rule uses 10 condition sets targeting various peroxisomal proteins including
  peroxins and peroxisome division factors.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00026708
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR006845
      curie: InterPro:IPR006845
      label: Unknown function (peroxisomal)
      negated: false
    - condition_type: INTERPRO
      value: IPR013083
      curie: InterPro:IPR013083
      label: Unknown function (peroxisomal)
      negated: false
    - condition_type: INTERPRO
      value: IPR017375
      curie: InterPro:IPR017375
      label: Unknown function (peroxisomal)
      negated: false
    notes: Multi-domain condition set without taxonomic restriction. The combination
      of three InterPro domains suggests a complex peroxisomal protein requiring
      multiple functional domains for proper peroxisome organization.
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR008733
      curie: InterPro:IPR008733
      label: Unknown function (plant peroxisomal)
      negated: false
    - condition_type: PANTHER
      value: PTHR12652
      curie: PANTHER:PTHR12652
      label: Peroxisomal protein (plant)
      negated: false
    - condition_type: TAXON
      value: '33090'
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: Plant-specific peroxisomal proteins combining InterPro and PANTHER
      classifications. Plants have unique peroxisomal functions including glyoxylate
      cycle enzymes not found in animals.
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR010482
      curie: InterPro:IPR010482
      label: Unknown function (fungal peroxisomal)
      negated: false
    - condition_type: TAXON
      value: '4751'
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: Fungal-specific peroxisomal protein domain with taxonomic restriction.
      Fungi have specialized peroxisomal functions for fatty acid beta-oxidation.
  - number: 4
    conditions:
    - condition_type: FUNFAM
      value: 2.130.10.10:FF:000372
      curie: CATH.FunFam:2.130.10.10:FF:000372
      label: Peroxisomal protein family
      negated: false
    - condition_type: TAXON
      value: '2759'
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: Eukaryotic CATH FunFam for peroxisomal organization proteins.
  - number: 5
    conditions:
    - condition_type: FUNFAM
      value: 3.30.40.10:FF:000266
      curie: CATH.FunFam:3.30.40.10:FF:000266
      label: Peroxisomal protein family (metazoan)
      negated: false
    - condition_type: TAXON
      value: '33208'
      curie: NCBITaxon:33208
      label: Metazoa
      negated: false
    notes: Animal-specific peroxisomal organization proteins.
  - number: 6
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000397
      curie: CATH.FunFam:1.10.510.10:FF:000397
      label: Peroxisomal protein family (fungal)
      negated: false
    - condition_type: TAXON
      value: '4751'
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: Additional fungal-specific CATH FunFam for peroxisome organization.
  - number: 7
    conditions:
    - condition_type: FUNFAM
      value: 1.25.40.10:FF:000167
      curie: CATH.FunFam:1.25.40.10:FF:000167
      label: Peroxisomal protein family (plant)
      negated: false
    - condition_type: TAXON
      value: '33090'
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: Plant-specific CATH FunFam for peroxisome organization proteins.
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 1.25.40.10:FF:000218
      curie: CATH.FunFam:1.25.40.10:FF:000218
      label: Peroxisomal protein family (Dikarya)
      negated: false
    - condition_type: TAXON
      value: '451864'
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
    notes: Dikarya-specific (higher fungi) peroxisomal organization proteins.
  - number: 9
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000473
      curie: CATH.FunFam:3.40.50.300:FF:000473
      label: Peroxisomal protein family (Ascomycota)
      negated: false
    - condition_type: TAXON
      value: '4890'
      curie: NCBITaxon:4890
      label: Ascomycota
      negated: false
    notes: Ascomycota-specific peroxisomal organization proteins.
  - number: 10
    conditions:
    - condition_type: FUNFAM
      value: 1.20.120.1240:FF:000002
      curie: CATH.FunFam:1.20.120.1240:FF:000002
      label: Universal peroxisomal protein family
      negated: false
    notes: Universal CATH FunFam for peroxisome organization without taxonomic
      restriction, suggesting a highly conserved peroxisomal function.
  go_annotations:
  - go_id: GO:0007031
    go_label: peroxisome organization
    aspect: BP
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2025-09-20'
  entries:
  - id: IPR006845
    type: INTERPRO
    label: Unknown function (peroxisomal)
    appears_in_condition_sets:
    - 1
    protein_count: 0
    related_entries: []
  - id: IPR013083
    type: INTERPRO
    label: Unknown function (peroxisomal)
    appears_in_condition_sets:
    - 1
    protein_count: 0
    related_entries: []
  - id: IPR017375
    type: INTERPRO
    label: Unknown function (peroxisomal)
    appears_in_condition_sets:
    - 1
    protein_count: 0
    related_entries: []
  - id: IPR008733
    type: INTERPRO
    label: Unknown function (plant peroxisomal)
    appears_in_condition_sets:
    - 2
    protein_count: 0
    related_entries: []
  - id: PTHR12652
    type: PANTHER
    label: Peroxisomal protein (plant)
    appears_in_condition_sets:
    - 2
    protein_count: 0
    related_entries: []
  - id: IPR010482
    type: INTERPRO
    label: Unknown function (fungal peroxisomal)
    appears_in_condition_sets:
    - 3
    protein_count: 0
    related_entries: []
  - id: 2.130.10.10:FF:000372
    type: FUNFAM
    label: Peroxisomal protein family
    appears_in_condition_sets:
    - 4
    protein_count: 0
    related_entries: []
  - id: 3.30.40.10:FF:000266
    type: FUNFAM
    label: Peroxisomal protein family (metazoan)
    appears_in_condition_sets:
    - 5
    protein_count: 0
    related_entries: []
  - id: 1.10.510.10:FF:000397
    type: FUNFAM
    label: Peroxisomal protein family (fungal)
    appears_in_condition_sets:
    - 6
    protein_count: 0
    related_entries: []
  - id: 1.25.40.10:FF:000167
    type: FUNFAM
    label: Peroxisomal protein family (plant)
    appears_in_condition_sets:
    - 7
    protein_count: 0
    related_entries: []
  - id: 1.25.40.10:FF:000218
    type: FUNFAM
    label: Peroxisomal protein family (Dikarya)
    appears_in_condition_sets:
    - 8
    protein_count: 0
    related_entries: []
  - id: 3.40.50.300:FF:000473
    type: FUNFAM
    label: Peroxisomal protein family (Ascomycota)
    appears_in_condition_sets:
    - 9
    protein_count: 0
    related_entries: []
  - id: 1.20.120.1240:FF:000002
    type: FUNFAM
    label: Universal peroxisomal protein family
    appears_in_condition_sets:
    - 10
    protein_count: 0
    related_entries: []
review_summary: ARBA00026708 presents significant concerns regarding annotation accuracy
  and rule design. The rule uses 10 condition sets to predict GO:0007031 (peroxisome
  organization) but suffers from multiple issues. First, many InterPro domains lack
  specific functional annotation, increasing false positive risk. Second, the broad
  taxonomic scope may lead to over-annotation of organisms with reduced or absent
  peroxisomes. Third, the rule lacks negative conditions to exclude proteins from
  other organellar systems (mitochondria, ER) that may share similar domains. Fourth,
  GO:0007031 is a very broad organizational term that may capture proteins with
  indirect roles rather than direct peroxisome organization functions. The rule would
  benefit from more specific GO terms and additional constraints to reduce false
  positives.
action: MODIFY
action_rationale: While peroxisome organization is a legitimate biological process
  and the rule attempts to capture genuine peroxisomal proteins, the current design
  has significant specificity issues. Many condition sets use poorly annotated
  InterPro domains, and the broad GO term increases risk of over-annotation. The
  rule should be refined with (1) more specific GO terms for distinct aspects of
  peroxisome organization (e.g., GO:0016559 peroxisome fission, GO:0016558 peroxisome
  fusion), (2) negative conditions to exclude mitochondrial/ER proteins, (3) validation
  that annotated organisms actually possess peroxisomes, and (4) replacement of
  poorly annotated InterPro domains with more specific alternatives.
suggested_modifications:
- Replace broad GO:0007031 with more specific child terms based on protein function
- Add negative conditions to exclude non-peroxisomal organellar proteins
- Validate taxonomic scope to exclude organisms lacking peroxisomes
- Replace poorly annotated InterPro domains with better characterized alternatives
- Consider splitting into separate rules for different aspects of peroxisome organization
- Add literature-validated positive examples to guide refinement
parsimony:
  assessment: OVERLY_COMPLEX
  notes: The rule contains 10 condition sets targeting the same broad biological
    process. While kingdom-specific peroxisome differences exist, many condition
    sets likely identify the same core peroxisomal proteins through different domain
    classification systems. The rule would benefit from consolidation and validation
    of unique coverage provided by each condition set.
  supported_by:
  - reference_id: file:rules/arba/ARBA00026708/ARBA00026708-deep-research-manual.md
    supporting_text: The rule covers All eukaryotes (some condition sets), Viridiplantae
      (plants), Fungi and subgroups (Dikarya, Ascomycota), Metazoa (animals). Potential
      Issues include Over-broad annotation peroxisome organization mechanisms may
      differ significantly between kingdoms, Domain promiscuity Some domains might
      appear in non-peroxisomal contexts, Missing specificity Lack of negative
      conditions to exclude false positives
literature_support:
  assessment: MODERATE
  notes: Peroxisome organization is a well-established biological process with strong
    literature support. However, the specific domains and proteins targeted by this
    rule lack detailed functional characterization in many cases. Known peroxins
    (PEX proteins) and peroxisome division factors are well-studied, but the InterPro
    domains in this rule often have unclear functional annotations.
  supported_by:
  - reference_id: file:rules/arba/ARBA00026708/ARBA00026708-deep-research-manual.md
    supporting_text: The major players in peroxisome biogenesis include PEX1, PEX6
      AAA+ ATPases involved in peroxisome matrix protein import, PEX3, PEX16, PEX19
      Membrane protein insertion machinery, PEX5, PEX7 Peroxisome targeting signal
      (PTS) receptors, PEX11 Peroxisome division protein, PEX13, PEX14 Docking complex
      components
condition_overlap:
  assessment: SIGNIFICANT
  notes: Without quantitative analysis, it's likely that many condition sets identify
    overlapping protein sets through different classification systems (InterPro vs
    CATH FunFam). The taxonomic restrictions may provide some separation, but core
    peroxisomal proteins are often conserved across kingdoms and could be captured
    by multiple condition sets.
  supported_by:
  - reference_id: file:rules/arba/ARBA00026708/ARBA00026708-deep-research-manual.md
    supporting_text: Basic peroxisome machinery is conserved across eukaryotes,
      Kingdom-specific adaptations exist, particularly in plants vs animals vs fungi,
      Some organisms (certain parasites) have lost peroxisomes entirely
go_specificity:
  assessment: TOO_BROAD
  notes: GO:0007031 (peroxisome organization) is a very broad term that encompasses
    multiple distinct processes including peroxisome biogenesis, fission, fusion,
    inheritance, and degradation. More specific child terms would be more appropriate
    for different classes of peroxisomal proteins (e.g., GO:0016559 for fission
    proteins, GO:0016560 for protein import).
  supported_by:
  - reference_id: file:rules/arba/ARBA00026708/ARBA00026708-deep-research-manual.md
    supporting_text: Peroxisome organization is a highly conserved process involving
      (1) Membrane biogenesis Formation of peroxisomal membranes, (2) Matrix protein
      import PTS1 and PTS2 pathway proteins, (3) Division/proliferation Peroxisome
      fission machinery, (4) Quality control Protein degradation and organelle
      maintenance
taxonomic_scope:
  assessment: TOO_BROAD
  notes: The rule covers very broad taxonomic ranges including all eukaryotes for
    some condition sets. This risks annotating organisms that have lost peroxisomes
    (certain parasites, some anaerobic organisms) or have highly reduced peroxisomal
    systems. Taxonomic restrictions should be validated against known peroxisome
    distribution.
  supported_by:
  - reference_id: file:rules/arba/ARBA00026708/ARBA00026708-deep-research-manual.md
    supporting_text: Very broad taxonomic scope may lead to over-annotation, Different
      mechanisms of peroxisome organization across kingdoms, Risk of annotating
      organisms that lack peroxisomes
confidence: 0.45
references:
- id: file:rules/arba/ARBA00026708/ARBA00026708-deep-research-manual.md
  title: Manual deep research analysis of ARBA00026708
  findings:
  - statement: Rule targets peroxisome organization through multiple condition sets
      but suffers from domain specificity issues and overly broad taxonomic scope
  - statement: Many InterPro domains lack detailed functional annotation, increasing
      risk of false positives from proteins with other primary functions
  - statement: Rule lacks negative conditions to exclude mitochondrial or ER proteins
      that might share similar domains
- id: GO:0007031
  title: peroxisome organization GO term definition
  findings:
  - statement: A process that is carried out at the cellular level which results
      in the assembly, arrangement of constituent parts, or disassembly of a peroxisome
  - statement: Very broad term encompassing multiple distinct processes that would
      benefit from more specific child term usage
supported_by:
- reference_id: file:rules/arba/ARBA00026708/ARBA00026708-deep-research-manual.md
  supporting_text: This rule annotates proteins with GO:0007031 (peroxisome organization)
    based on multiple condition sets targeting different taxonomic groups