id: ARBA00028584 description: >- Rule predicts GO:0005778 (peroxisomal membrane) localization for nine distinct protein families: fungal DysF-domain peroxins (PEX23-32), peroxisomal ABC transporters (ABCD1, ABCD3), peroxisomal import machinery (PEX13, PEX14), RING finger peroxins (PEX12), the peroxisomal solute carrier SLC25A17/PMP34, the autophagy cargo receptor NBR1, and peroxisomal 2,4-dienoyl-CoA reductase (DECR2). Each condition set uses different domain signatures with varying taxonomic restrictions. status: COMPLETE rule_type: ARBA rule: rule_id: ARBA00028584 condition_sets: - number: 1 conditions: - condition_type: INTERPRO value: IPR010482 curie: InterPro:IPR010482 label: TECPR1-like, DysF domain negated: false - condition_type: TAXON value: '4751' curie: NCBITaxon:4751 label: Fungi negated: false notes: >- Targets fungal DysF-domain peroxins PEX23, PEX24, PEX28, PEX29, PEX30, PEX31, and PEX32. UniProt search for IPR010482 + Fungi (reviewed) returns 10 proteins, all established peroxisomal membrane proteins in S. cerevisiae, O. parapolymorpha, and S. pombe. The DysF domain in fungi is diagnostic for this peroxin subfamily. However, IPR010482 also covers non-fungal TECPR1 (an autophagy protein localized to lysosomes, not peroxisomes), so the Fungi taxonomic restriction is essential for accuracy. WELL-FOUNDED. - number: 2 conditions: - condition_type: FUNFAM value: 3.40.50.300:FF:000800 curie: CATH.FunFam:3.40.50.300:FF:000800 label: ATP-binding cassette sub-family D member 1 negated: false - condition_type: TAXON value: '314147' curie: NCBITaxon:314147 label: Glires negated: false notes: >- Targets ABCD1 (adrenoleukodystrophy protein) in Glires (rodents + lagomorphs). ABCD1 is a well-established peroxisomal membrane ABC transporter that imports very long-chain fatty acyl-CoAs. Mutations cause X-linked adrenoleukodystrophy. The FunFam is specific to the ABCD1 NBD within the P-loop NTPase superfamily. The Glires restriction is overly narrow; ABCD1 is conserved across all vertebrates. WELL-FOUNDED but taxonomic scope should be broadened. - number: 3 conditions: - condition_type: FUNFAM value: 2.30.30.40:FF:000109 curie: CATH.FunFam:2.30.30.40:FF:000109 label: Peroxisomal biogenesis factor 13 negated: false - condition_type: TAXON value: '7711' curie: NCBITaxon:7711 label: Chordata negated: false notes: >- Targets PEX13, a component of the peroxisomal docking/translocation machinery for matrix protein import. PEX13 contains an SH3 domain (CATH superfamily 2.30.30.40) and is an integral peroxisomal membrane protein. The FunFam label explicitly identifies it as PEX13. Chordata restriction is reasonable as the FunFam is trained on chordate sequences. WELL-FOUNDED. - number: 4 conditions: - condition_type: FUNFAM value: 1.10.8.10:FF:000033 curie: CATH.FunFam:1.10.8.10:FF:000033 label: Next to BRCA1 gene 1 protein negated: false - condition_type: FUNFAM value: 2.60.40.10:FF:000199 curie: CATH.FunFam:2.60.40.10:FF:000199 label: next to BRCA1 gene 1 protein-like negated: false - condition_type: FUNFAM value: 3.30.60.90:FF:000007 curie: CATH.FunFam:3.30.60.90:FF:000007 label: Next to BRCA1 gene 1 protein negated: false notes: >- Targets NBR1 (Next to BRCA1 gene 1 protein) using three FunFam domains with no taxonomic restriction. NBR1 is primarily a cytoplasmic selective autophagy cargo receptor that is recruited to ubiquitinated peroxisomes during pexophagy. While NBR1 does associate with the peroxisomal surface during pexophagy (PMID:37493040, PMID:32388919), it is NOT an integral or peripheral peroxisomal membrane protein. Its primary localization is cytoplasm and autophagosomes. UniProt annotates human NBR1 (Q14596) with GO:0005778, but this annotation is debatable -- NBR1 transiently associates with peroxisomes as a signal for degradation, not as a resident membrane protein. PROBLEMATIC -- predicting peroxisomal membrane for an autophagy receptor risks false annotation of its primary function. - number: 5 conditions: - condition_type: FUNFAM value: 1.20.1560.10:FF:000036 curie: CATH.FunFam:1.20.1560.10:FF:000036 label: ATP-binding cassette sub-family D member 3 negated: false - condition_type: FUNFAM value: 3.40.50.300:FF:000636 curie: CATH.FunFam:3.40.50.300:FF:000636 label: ATP-binding cassette sub-family D member 3 negated: false - condition_type: TAXON value: '9989' curie: NCBITaxon:9989 label: Rodentia negated: false notes: >- Targets ABCD3 (PMP70) in Rodentia using both the transmembrane domain FunFam (ABC transporter type 1 TMD superfamily) and the NBD FunFam (P-loop NTPase superfamily). ABCD3 is a well-characterized peroxisomal membrane ABC transporter for branched-chain and long-chain fatty acyl-CoAs. The dual-FunFam requirement increases specificity. The Rodentia restriction is overly narrow; ABCD3 is conserved across vertebrates. Note partial overlap with CS2 (both target ABCD subfamily D but different members, ABCD1 vs ABCD3). WELL-FOUNDED but taxonomic scope should be broadened. - number: 6 conditions: - condition_type: FUNFAM value: 1.50.40.10:FF:000023 curie: CATH.FunFam:1.50.40.10:FF:000023 label: peroxisomal membrane protein PMP34 isoform X1 negated: false - condition_type: FUNFAM value: 1.50.40.10:FF:000045 curie: CATH.FunFam:1.50.40.10:FF:000045 label: peroxisomal membrane protein PMP34 isoform X1 negated: false - condition_type: TAXON value: '2759' curie: NCBITaxon:2759 label: Eukaryota negated: false notes: >- Targets SLC25A17/PMP34, the only member of the mitochondrial carrier family localized to peroxisomal membranes. Uses two FunFam domains from the mitochondrial carrier superfamily (1.50.40.10), both explicitly labeled as PMP34. The dual-FunFam requirement differentiates PMP34 from mitochondrial SLC25 family members. Eukaryota scope is appropriate as SLC25A17 is conserved across eukaryotes. PMID:22185573 demonstrates SLC25A17 is a peroxisomal transporter of CoA, FAD, and NAD+. WELL-FOUNDED. - number: 7 conditions: - condition_type: FUNFAM value: 1.10.10.10:FF:000296 curie: CATH.FunFam:1.10.10.10:FF:000296 label: Peroxisomal membrane protein PEX14 negated: false - condition_type: TAXON value: '10066' curie: NCBITaxon:10066 label: Muridae negated: false notes: >- Targets PEX14, a core component of the peroxisomal docking complex for matrix protein import. The FunFam is from the winged helix-like superfamily, explicitly labeled as PEX14. PEX14 is an integral peroxisomal membrane protein conserved across all eukaryotes. The Muridae taxonomic restriction is excessively narrow -- PEX14 is found across all eukaryotes (PMID:37493040 describes PEX14 variants in human patients). WELL-FOUNDED but taxonomic scope far too narrow. - number: 8 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: '89593' curie: NCBITaxon:89593 label: Craniata negated: false notes: >- Targets PEX12, a RING finger E3 ubiquitin ligase that is an integral peroxisomal membrane protein. PEX12 forms a complex with PEX2 and PEX10 in the peroxisomal membrane and is essential for matrix protein import. The FunFam is from the RING/zinc finger superfamily, explicitly labeled as PEX12. Craniata restriction is narrow but defensible for this specific FunFam. WELL-FOUNDED. - number: 9 conditions: - condition_type: FUNFAM value: 3.40.50.720:FF:000477 curie: CATH.FunFam:3.40.50.720:FF:000477 label: Peroxisomal 2,4-dienoyl-CoA reductase negated: false - condition_type: TAXON value: '33208' curie: NCBITaxon:33208 label: Metazoa negated: false notes: >- Targets DECR2 (peroxisomal 2,4-dienoyl-CoA reductase), a Rossmann-fold enzyme in the peroxisomal beta-oxidation pathway. DECR2 is a soluble peroxisomal enzyme. While UniProt Q9NUI1 carries GO:0005778 (peroxisomal membrane) via Reactome, DECR2 lacks transmembrane domains and is likely a peroxisomal matrix enzyme. The GO:0005778 annotation may be incorrect; GO:0005782 (peroxisomal matrix) may be more appropriate. DEBATABLE -- the protein is peroxisomal but may not be membrane-associated. go_annotations: - go_id: GO:0005778 go_label: peroxisomal membrane aspect: CC reviewed_protein_count: 0 unreviewed_protein_count: 0 created_date: '2021-10-20' modified_date: '2025-05-15' entries: [] review_summary: >- This rule predicts GO:0005778 (peroxisomal membrane) for nine protein families using diverse domain signatures. Contrary to the initial review that recommended deprecation based on "biological incoherence," enriched analysis of the actual condition sets reveals that 7 of 9 condition sets target well-established peroxisomal membrane proteins: fungal DysF-domain peroxins (CS1: PEX23-32), peroxisomal ABC transporters (CS2: ABCD1; CS5: ABCD3), peroxisomal import machinery (CS3: PEX13; CS7: PEX14), RING finger peroxins (CS8: PEX12), and the peroxisomal solute carrier (CS6: PMP34/ SLC25A17). Two condition sets are problematic: CS4 targets NBR1, a cytoplasmic autophagy receptor that transiently associates with peroxisomes during pexophagy but is not a resident peroxisomal membrane protein; and CS9 targets DECR2, a peroxisomal matrix enzyme that likely lacks membrane association. The taxonomic restrictions are inconsistent, with some being far too narrow (PEX14 restricted to Muridae, ABCD3 to Rodentia) for proteins conserved across all eukaryotes. The rule should be MODIFIED to remove CS4 (NBR1) and potentially CS9 (DECR2), and to broaden taxonomic restrictions where justified. The initial deprecation recommendation was based on a review that lacked actual condition set data and made factually incorrect claims about the proteins targeted. action: MODIFY action_rationale: >- The rule is fundamentally biologically sound for 7 of 9 condition sets. The FunFam labels and InterPro domains unambiguously identify well-characterized peroxisomal membrane proteins: PEX23-32 (CS1), ABCD1 (CS2), PEX13 (CS3), ABCD3 (CS5), PMP34 (CS6), PEX14 (CS7), and PEX12 (CS8). Two modifications are needed: (1) Remove CS4 (NBR1) because NBR1 is a cytoplasmic pexophagy receptor that transiently associates with peroxisomes for degradation signaling, not a resident peroxisomal membrane protein. While some GO databases include GO:0005778 for NBR1, this represents over-annotation of a transient association. (2) Review CS9 (DECR2), which is a soluble peroxisomal enzyme without transmembrane domains -- GO:0005782 (peroxisomal matrix) may be more accurate. (3) Broaden overly narrow taxonomic restrictions: PEX14 (Muridae to at least Mammalia or Eukaryota), ABCD1 (Glires to Vertebrata), ABCD3 (Rodentia to Vertebrata). suggested_modifications: - Remove condition set 4 (NBR1) -- NBR1 is a cytoplasmic autophagy receptor, not a peroxisomal membrane protein. Its transient recruitment to peroxisomes during pexophagy does not justify GO:0005778 annotation. - Review condition set 9 (DECR2) -- DECR2 lacks transmembrane domains and is a soluble peroxisomal enzyme. Consider changing the GO annotation to GO:0005782 (peroxisomal matrix) or GO:0005777 (peroxisome). - Broaden CS7 taxonomic scope from Muridae to at least Mammalia or Eukaryota, as PEX14 is conserved across all eukaryotes. - Broaden CS2 taxonomic scope from Glires to Vertebrata or broader, as ABCD1 is conserved across vertebrates. - Broaden CS5 taxonomic scope from Rodentia to Vertebrata, as ABCD3 is conserved across vertebrates. parsimony: assessment: ACCEPTABLE notes: >- The 9 condition sets target 7 distinct peroxisomal protein families using different domain architectures. Each condition set captures a structurally distinct protein family: DysF-domain peroxins, ABC transporter subfamily D members 1 and 3 (using different FunFam combinations), SH3-domain PEX13, PMP34 (mitochondrial carrier fold), winged-helix PEX14, RING-finger PEX12, and Rossmann-fold DECR2. The diversity of condition sets reflects the genuine structural diversity of peroxisomal membrane proteins, which span multiple unrelated protein folds. CS2 (ABCD1) and CS5 (ABCD3) both target ABCD family members but capture different paralogs using different FunFam signatures, which is appropriate. The only unnecessary complexity is CS4 (NBR1), which targets a non-membrane protein. supported_by: - reference_id: file:rules/arba/ARBA00028584/ARBA00028584.enriched.json supporting_text: >- Condition sets use distinct domain signatures from different CATH superfamilies: 2.30.30.40 (SH3 domains for PEX13), 1.50.40.10 (mitochondrial carrier for PMP34), 1.10.10.10 (winged helix for PEX14), 3.30.40.10 (RING finger for PEX12), 3.40.50.720 (Rossmann-like for DECR2), 1.20.1560.10 and 3.40.50.300 (ABC transporter domains). literature_support: assessment: STRONG notes: >- The peroxisomal membrane localization of the proteins targeted by 7 of 9 condition sets is supported by extensive literature spanning decades of research. PEX23-32 are established yeast peroxisomal membrane peroxins. ABCD1 and ABCD3 are well-characterized peroxisomal ABC transporters with cryo-EM structures confirming their membrane integration. PEX13 and PEX14 are core components of the peroxisomal import docking complex. SLC25A17/PMP34 was functionally characterized as the sole peroxisomal member of the mitochondrial carrier family. PEX12 is a RING finger E3 ligase integral to the peroxisomal membrane. The only weakly supported condition sets are CS4 (NBR1 is an autophagy receptor, not a membrane protein) and CS9 (DECR2 may be a matrix rather than membrane enzyme). supported_by: - reference_id: PMID:22185573 supporting_text: >- Recombinant and purified SLC25A17 was reconstituted into liposomes - reference_id: PMID:35908918 supporting_text: >- ABCD1-3 are localized to peroxisomal membranes and involved in the transport of various acyl-CoAs from the cytosol to the peroxisomal lumen. - reference_id: PMID:37493040 supporting_text: >- Inhibition of pexophagy by different autophagy inhibitors or genetic knockdown of the peroxisomal autophagy receptor NBR1 resulted in restoration of peroxisomal functions in the patients' fibroblasts. - reference_id: PMID:36541703 supporting_text: >- PEX13, a component of the peroxisomal matrix import system, is required to prevent the degradation of otherwise healthy peroxisomes. - reference_id: PMID:36462131 supporting_text: >- Pex30 is a peroxisomal protein whose role in peroxisome biogenesis via the endoplasmic reticulum has been established - reference_id: PMID:22342342 supporting_text: >- Strikingly, TECPR1 localizes to and recruits Atg5 to autolysosome membrane condition_overlap: assessment: MINOR notes: >- The 9 condition sets show minimal overlap because they target structurally distinct protein families using different CATH superfamily signatures. CS2 (ABCD1, Glires) and CS5 (ABCD3, Rodentia) both target peroxisomal ABC transporters but capture different paralogs: ABCD1 (adrenoleukodystrophy protein) and ABCD3 (PMP70). Their FunFam identifiers are from different CATH superfamilies or different FunFams within the same superfamily, indicating they target genuinely different protein sets. The taxonomic overlap (Rodentia is a subset of Glires) means some rodent ABCD1 proteins could be captured by both CS2 and CS5 in principle, but since they use different FunFam signatures, the same protein will not match both condition sets. No other condition set pairs show meaningful overlap. supported_by: - reference_id: file:rules/arba/ARBA00028584/ARBA00028584.enriched.json supporting_text: >- CS2 uses FunFam 3.40.50.300:FF:000800 (labeled ABCD1) while CS5 uses FunFams 1.20.1560.10:FF:000036 and 3.40.50.300:FF:000636 (both labeled ABCD3). These are different FunFam families targeting different ABC transporter paralogs. go_specificity: assessment: APPROPRIATE notes: >- GO:0005778 (peroxisomal membrane) is the correct cellular component term for 7 of 9 condition sets. The peroxisomal membrane is defined as "the lipid bilayer surrounding a peroxisome." Integral membrane proteins (ABCD1, ABCD3, PEX13, PEX14, PEX12, PMP34) and peripheral membrane proteins (PEX23-32 family) are all appropriately annotated with this term. Two condition sets may be better served by different GO terms: CS4 (NBR1) should use GO:0005776 (autophagosome) or a pexophagy-specific term; CS9 (DECR2) should potentially use GO:0005782 (peroxisomal matrix) if it lacks genuine membrane association. supported_by: - reference_id: PMID:35908918 supporting_text: >- ABCD1-3 are localized to peroxisomal membranes and involved in the transport of various acyl-CoAs from the cytosol to the peroxisomal lumen. - reference_id: PMID:22185573 supporting_text: >- In the present study we have functionally identified and characterized SLC25A17 (solute carrier family 25 member 17), which is the only member of the mitochondrial carrier family that has previously been shown to be localized in the peroxisomal membrane taxonomic_scope: assessment: TOO_NARROW notes: >- Several condition sets have taxonomic restrictions that are far too narrow relative to the biological conservation of their target proteins. PEX14 (CS7, Muridae) is conserved across all eukaryotes -- restricting to Muridae misses the vast majority of organisms with PEX14. ABCD1 (CS2, Glires) and ABCD3 (CS5, Rodentia) are conserved across vertebrates. In contrast, CS1 (IPR010482 + Fungi) is appropriately restricted because the DysF domain outside of fungi captures TECPR1, which is NOT a peroxisomal membrane protein. CS6 (PMP34, Eukaryota) has an appropriately broad scope. The inconsistency likely reflects the ARBA algorithm training on available annotation data rather than biological reality. supported_by: - reference_id: PMID:37493040 supporting_text: >- We identified 2 different single heterozygous de novo variants in the PEX14 genes of 2 patients diagnosed with ZSD. - reference_id: PMID:31187491 supporting_text: >- We found that the zebrafish genome contains two slc25a17 genes that function redundantly, but additively confidence: 0.8 references: - id: PMID:22185573 title: >- The human gene SLC25A17 encodes a peroxisomal transporter of coenzyme A, FAD and NAD+ findings: - statement: >- SLC25A17 is the only member of the mitochondrial carrier family localized to the peroxisomal membrane. It transports CoA, FAD, FMN, AMP, and to a lesser extent NAD+, PAP, and ADP into peroxisomes. - id: PMID:35908918 title: >- Substrate Specificity and the Direction of Transport in the ABC Transporters ABCD1-3 and ABCD4 findings: - statement: >- ABCD1-3 are localized to peroxisomal membranes and transport various acyl-CoAs from the cytosol to the peroxisomal lumen. ABCD4 is lysosomal. Mutations in ABCD1, ABCD3, and ABCD4 cause genetic diseases. - id: PMID:37493040 title: >- Autosomal dominant Zellweger spectrum disorder caused by de novo variants in PEX14 gene findings: - statement: >- PEX14 is a core peroxisomal membrane protein required for matrix protein import. Truncated PEX14 exerts dominant-negative effects on peroxisome function. Knockdown of NBR1 restored peroxisomal functions, confirming NBR1's role as a pexophagy signal rather than a structural membrane component. - id: PMID:36541703 title: >- PEX13 prevents pexophagy by regulating ubiquitinated PEX5 and peroxisomal ROS findings: - statement: >- PEX13 is a component of the peroxisomal matrix import system and is required to prevent degradation of healthy peroxisomes. Loss of PEX13 causes accumulation of ubiquitinated PEX5 on peroxisomes and induces pexophagy. - id: PMID:36462131 title: >- Characterization of the Multiple Domains of Pex30 Involved in Subcellular Localization of the Protein and Regulation of Peroxisome Number findings: - statement: >- Pex30 is a peroxisomal membrane protein with DysF domain that regulates peroxisome number. Lack of the DysF domain increases peroxisome number similar to PEX30 deletion. Pex30 facilitates contact site formation between peroxisomes and ER. - id: PMID:22342342 title: >- A mammalian autophagosome maturation mechanism mediated by TECPR1 and the Atg12-Atg5 conjugate findings: - statement: >- TECPR1 localizes to autolysosomes, NOT peroxisomes. This confirms that the DysF domain (IPR010482) in non-fungal organisms captures TECPR1 which has a different localization, justifying the Fungi restriction in CS1. - id: PMID:31187491 title: >- Slc25a17 acts as a peroxisomal coenzyme A transporter and regulates multiorgan development in zebrafish findings: - statement: >- SLC25A17/PMP34 is a peroxisomal CoA transporter conserved from zebrafish to mammals, demonstrating the broad phylogenetic distribution of this peroxisomal membrane protein. - id: PMID:32388919 title: 'Mycobacterium tuberculosis Rv3034c regulates mTORC1 and PPAR-γ dependant pexophagy mechanism to control redox levels in macrophages.' findings: - statement: >- NBR1 and p62/SQSTM1 are described as pexophagy-associated adaptor molecules. M. tuberculosis Rv3034c down-regulates expression of NBR1 and other pexophagy proteins to inhibit peroxisome degradation. - id: file:rules/arba/ARBA00028584/ARBA00028584.enriched.json title: Enriched rule data with CATH FunFam and InterPro labels findings: - statement: >- FunFam labels explicitly identify the target proteins for each condition set: ABCD1, PEX13, NBR1, ABCD3, PMP34, PEX14, PEX12, and DECR2. supported_by: - reference_id: file:rules/arba/ARBA00028584/ARBA00028584.enriched.json supporting_text: >- All 9 condition sets have been identified via enriched FunFam labels. Seven of nine target well-established peroxisomal membrane proteins. CS4 targets NBR1 (autophagy receptor) and CS9 targets DECR2 (likely matrix enzyme).