ARBA00004173 mitochondrion (GO:0005739)

id: ARBA00004173
description: >-
  Assigns the UniProt subcellular location Mitochondrion (SL-0173) through 1,525 alternative condition
  sets built from CATH FunFam, InterPro and PANTHER signatures, each with a taxon condition. UniProt converts
  the location to GO:0005739 (mitochondrion) by GO_REF:0000044.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00004173
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR005798
      curie: InterPro:IPR005798
      label: Cytochrome b/b6, C-terminal
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR027387
      curie: InterPro:IPR027387
      label: Cytochrome b/b6-like domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 1701; of these 1701 have the subcellular location
      Mitochondrion (SL-0173) (UniProtKB query, 2026-11-10). The set matches mitochondrially encoded cytochrome
      b, for example P00156 (human MT-CYB). In all of UniProtKB, 54,084 eukaryotic entries match both
      InterPro entries and 52,943 of them are encoded in the mitochondrion; one is plastid-encoded. The
      plastid cytochrome b6-f subunits do not match the conjunction: P56773 (Arabidopsis cytochrome b6)
      has IPR027387 but not IPR005798, and P56774 (Arabidopsis cytochrome b6-f complex subunit 4) has
      IPR005798 but not IPR027387.
  - number: 43
    conditions:
    - condition_type: INTERPRO
      value: IPR003439
      curie: InterPro:IPR003439
      label: ABC transporter-like, ATP-binding domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR003593
      curie: InterPro:IPR003593
      label: AAA+ ATPase domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: PANTHER
      value: PTHR24221:SF402
      curie: PANTHER:PTHR24221:SF402
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: true
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: true
    - condition_type: TAXON
      value: Viruses
      curie: NCBITaxon:10239
      label: Viruses
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 26; 25 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 1 do not (UniProtKB query, 2026-11-10). Those without it: 1 x ABC transporter
      B family member 5 (Swiss-Prot location: Membrane). Accessions: Q8T9W2.
  - number: 209
    conditions:
    - condition_type: INTERPRO
      value: IPR007667
      curie: InterPro:IPR007667
      label: Hypoxia induced protein, domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: true
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: true
    - condition_type: TAXON
      value: Viruses
      curie: NCBITaxon:10239
      label: Viruses
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 75; 69 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 6 do not (UniProtKB query, 2026-11-10). Those without it: 2 x HIG1
      domain family member 1C (Swiss-Prot location: Membrane); 2 x HIG1 domain family member 1B (Swiss-Prot
      location: Membrane); 1 x HIG1 domain family member 2B (Swiss-Prot location: Membrane); 1 x RING-H2
      finger protein ATL48 (Swiss-Prot location: Membrane). Accessions: A8MV81, Q4VC39, Q7X843, Q9P298,
      Q76I25, Q99JY6.
  - number: 251
    conditions:
    - condition_type: INTERPRO
      value: IPR000194
      curie: InterPro:IPR000194
      label: ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR000793
      curie: InterPro:IPR000793
      label: ATP synthase, alpha subunit, C-terminal
      interpro_type: DOMAIN
      negated: false
    - condition_type: TAXON
      value: rosids
      curie: NCBITaxon:71275
      label: rosids
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 41; 8 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 33 do not (UniProtKB query, 2026-11-10). Those without it: 33 x ATP
      synthase subunit alpha, chloroplastic (Swiss-Prot location: Plastid, chloroplast thylakoid membrane).
      Accessions: P56757, A4GGB2, A4QJI4, A4QKR6, A4QL04, Q09MJ3 and 27 more.
  - number: 365
    conditions:
    - condition_type: INTERPRO
      value: IPR003698
      curie: InterPro:IPR003698
      label: Lipoyl synthase
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR031691
      curie: InterPro:IPR031691
      label: Lipoyl synthase, N-terminal
      interpro_type: DOMAIN
      negated: false
    - condition_type: PANTHER
      value: PTHR10949:SF0
      curie: PANTHER:PTHR10949:SF0
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: true
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: true
    - condition_type: TAXON
      value: Viruses
      curie: NCBITaxon:10239
      label: Viruses
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 106; 102 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 4 do not (UniProtKB query, 2026-11-10). Those without it: 4 x Lipoyl
      synthase, apicoplast (Swiss-Prot location: Plastid, apicoplast). Accessions: Q8IDQ0, A5K883, Q7RBD6,
      B3L8F2.
  - number: 378
    conditions:
    - condition_type: INTERPRO
      value: IPR019775
      curie: InterPro:IPR019775
      label: WD40 repeat, conserved site
      interpro_type: CONSERVED_SITE
      negated: false
    - condition_type: PANTHER
      value: PTHR22847:SF637
      curie: PANTHER:PTHR22847:SF637
      negated: false
    - condition_type: TAXON
      value: Aspergillus
      curie: NCBITaxon:5052
      label: Aspergillus
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 8; 6 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 2 do not (UniProtKB query, 2026-11-10). Those without it: 1 x Nuclear
      distribution protein nudF 2 (Swiss-Prot location: Cytoplasm, cytoskeleton); 1 x Nuclear distribution
      protein nudF (Swiss-Prot location: Cytoplasm, cytoskeleton). Accessions: A1CF18, A2QP30.
  - number: 456
    conditions:
    - condition_type: INTERPRO
      value: IPR005294
      curie: InterPro:IPR005294
      label: ATP synthase, F1 complex, alpha subunit
      interpro_type: FAMILY
      negated: false
    - condition_type: PANTHER
      value: PTHR48082:SF2
      curie: PANTHER:PTHR48082:SF2
      negated: false
    - condition_type: TAXON
      value: Liliopsida
      curie: NCBITaxon:4447
      label: Liliopsida
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 10; 5 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 5 do not (UniProtKB query, 2026-11-10). Those without it: 5 x ATP synthase
      subunit alpha, chloroplastic (Swiss-Prot location: Plastid, chloroplast thylakoid membrane). Accessions:
      A6MMJ2, Q3V549, A9L981, A9LYH0, Q3BAQ7.
  - number: 484
    conditions:
    - condition_type: INTERPRO
      value: IPR020537
      curie: InterPro:IPR020537
      label: ATP synthase, F0 complex, subunit C, DCCD-binding site
      interpro_type: BINDING_SITE
      negated: false
    - condition_type: INTERPRO
      value: IPR035921
      curie: InterPro:IPR035921
      label: F/V-ATP synthase subunit C superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: Solanaceae
      curie: NCBITaxon:4070
      label: Solanaceae
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 12; 5 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 7 do not (UniProtKB query, 2026-11-10). Those without it: 7 x ATP synthase
      subunit c, chloroplastic (Swiss-Prot location: Plastid, chloroplast thylakoid membrane). Accessions:
      P06286, Q33C51, Q3C1H2, Q8RU61, Q2MIB3, Q2MIK0 and 1 more.
  - number: 549
    conditions:
    - condition_type: FUNFAM
      value: 1.20.1560.10:FF:000004
      curie: CATH.FunFam:1.20.1560.10:FF:000004
      label: ATP-binding cassette sub-family B member 7
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: true
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: true
    - condition_type: TAXON
      value: Viruses
      curie: NCBITaxon:10239
      label: Viruses
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 27; 26 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 1 do not (UniProtKB query, 2026-11-10). Those without it: 1 x ABC transporter
      B family member 5 (Swiss-Prot location: Membrane). Accessions: Q8T9W2.
  - number: 718
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000403
      curie: CATH.FunFam:3.40.50.300:FF:000403
      label: ATP-binding cassette sub-family B member 8, mitochondrial
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: true
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: true
    - condition_type: TAXON
      value: Viruses
      curie: NCBITaxon:10239
      label: Viruses
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 10; 8 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 2 do not (UniProtKB query, 2026-11-10). Those without it: 1 x ABC transporter
      B family member 28 (Swiss-Prot location: Membrane); 1 x ABC transporter B family member 1 (Swiss-Prot
      location: Membrane). Accessions: Q8LPQ6, Q54BU4.
  - number: 789
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1050.10:FF:000001
      curie: CATH.FunFam:3.30.1050.10:FF:000001
      label: Putative Non-specific lipid-transfer protein
      negated: false
    - condition_type: FUNFAM
      value: 3.40.47.10:FF:000016
      curie: CATH.FunFam:3.40.47.10:FF:000016
      label: Non-specific lipid-transfer protein
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: true
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: true
    - condition_type: TAXON
      value: Viruses
      curie: NCBITaxon:10239
      label: Viruses
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 6 (P22307, P11915, P32020, P07857, O62742, Q07598;
      all sterol carrier protein 2 / SCPx); an entry-level search finds the location Mitochondrion in
      all 6, but the search does not see isoform scoping; unreviewed matches: 1,235 (UniProtKB query,
      2026-11-10). The isoform scoping was read for P32020 and P22307 only. In mouse P32020 and human
      P22307 the Mitochondrion location is recorded for isoform SCP2 only; isoform SCPx is recorded as
      Peroxisome. Isoform SCP2 of P32020 lacks residues 1-404 (VSP_018895), and the CATH-Gene3D 3.40.47.10
      match of P32020 spans residues 13-405, so the isoform that carries the mitochondrial location cannot
      match this set. Drosophila ScpX (Q9VJ43, unreviewed) matches both FunFams and receives Mitochondrion
      from this rule.
  - number: 1084
    conditions:
    - condition_type: FUNFAM
      value: 1.10.300.10:FF:000002
      curie: CATH.FunFam:1.10.300.10:FF:000002
      label: Adenylosuccinate synthetase, chloroplastic
      negated: false
    - condition_type: FUNFAM
      value: 3.90.170.10:FF:000001
      curie: CATH.FunFam:3.90.170.10:FF:000001
      label: Adenylosuccinate synthetase
      negated: false
    - condition_type: TAXON
      value: Amphibia
      curie: NCBITaxon:8292
      label: Amphibia
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 6; 3 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 3 do not (UniProtKB query, 2026-11-10). Those without it: 1 x Adenylosuccinate
      synthetase isozyme 1 A (Swiss-Prot location: Cytoplasm); 1 x Adenylosuccinate synthetase isozyme
      1 B (Swiss-Prot location: Cytoplasm); 1 x Adenylosuccinate synthetase isozyme 1 (Swiss-Prot location:
      Cytoplasm). Accessions: Q561L1, Q68F20, Q6DIW6.
  - number: 1312
    conditions:
    - condition_type: FUNFAM
      value: 3.40.640.10:FF:000003
      curie: CATH.FunFam:3.40.640.10:FF:000003
      label: Cysteine desulfurase IscS
      negated: false
    - condition_type: FUNFAM
      value: 3.90.1150.10:FF:000002
      curie: CATH.FunFam:3.90.1150.10:FF:000002
      label: Cysteine desulfurase IscS
      negated: false
    - condition_type: TAXON
      value: Candida/Lodderomyces clade
      curie: NCBITaxon:1535325
      label: Candida/Lodderomyces clade
      negated: false
    notes: No Swiss-Prot entry matches the whole conjunction (UniProtKB query, 2026-11-10).
  - number: 1384
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.450:FF:000010
      curie: CATH.FunFam:3.40.50.450:FF:000010
      label: ATP-dependent 6-phosphofructokinase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.460:FF:000008
      curie: CATH.FunFam:3.40.50.460:FF:000008
      label: ATP-dependent 6-phosphofructokinase
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: true
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: true
    - condition_type: TAXON
      value: Viruses
      curie: NCBITaxon:10239
      label: Viruses
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 8; 2 have the subcellular location Mitochondrion
      (SL-0173) at entry level and 6 do not (UniProtKB query, 2026-11-10). Those without it: 2 x ATP-dependent
      6-phosphofructokinase subunit alpha (Swiss-Prot location: Cytoplasm); 2 x ATP-dependent 6-phosphofructokinase
      (Swiss-Prot location: Cytoplasm); 1 x ATP-dependent 6-phosphofructokinase 1 (Swiss-Prot location:
      Cytoplasm); 1 x ATP-dependent 6-phosphofructokinase subunit beta (Swiss-Prot location: Cytoplasm).
      Accessions: O94201, P78985, Q4W9B8, Q9HGZ1, C4QXA5, Q03215.
  go_annotations:
  - go_id: GO:0005739
    go_label: mitochondrion
    aspect: C
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 562320
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  source_condition_set_count: 1525
  retrieved_date: '2026-11-09'
review_summary: >-
  All 1,525 live condition sets were screened with two UniProtKB queries each (2026-11-10): the Swiss-Prot
  entries that match the whole conjunction, and how many of them have the subcellular location Mitochondrion
  (SL-0173). 1,524 sets match at least one Swiss-Prot entry and 1 match none. In 1,513 sets every Swiss-Prot
  match has the location and in 11 sets some do not (sets 43, 209, 251, 365, 378, 456, 484, 549, 718,
  1084, 1384); set 1312 matches no Swiss-Prot entry. The search is at entry level and does not see locations
  scoped to one isoform. Summed over sets there are 18,954 set-level matches, 18,884 with the location.
  Sets 1 and 789 were read in detail; they and the sets with incomplete agreement are recorded in the
  rule block. Set 1 (cytochrome b) is sound. Three sets match plastid-encoded ATP synthase subunits whose
  curated location is the chloroplast thylakoid membrane: set 251 (33 of 41 Swiss-Prot matches, in rosids),
  set 456 (5 of 10, in Liliopsida) and set 484 (7 of 12, in Solanaceae). Set 1384 matches ATP-dependent
  6-phosphofructokinases, 6 of 8 recorded as Cytoplasm, and set 1084 matches amphibian adenylosuccinate
  synthetase isozyme 1, 3 of 6 recorded as Cytoplasm; in both cases the Swiss-Prot location comes from
  a HAMAP rule, not an experiment. Set 365 also matches four apicoplast lipoyl synthases. Set 789 is defective
  in a different way: it requires the thiolase-type FunFam 3.40.47.10:FF:000016 together with the SCP2
  FunFam 3.30.1050.10:FF:000001, but in the reviewed mouse and human entries the mitochondrial location
  belongs to the short SCP2 isoform, which lacks the region matched by the first FunFam, while the full-length
  SCPx isoform is recorded as Peroxisome only. The rule therefore gives Mitochondrion to full-length SCPx
  proteins such as Drosophila ScpX (Q9VJ43). In sets 43, 209, 378, 549 and 718 the entries without the
  location have only a generic or rule-derived location comment, which does not show the protein is absent
  from mitochondria. ARBA rules are mined from Swiss-Prot annotation, and precision on the 562,320 unreviewed
  entries the rule annotates was not measured.
action: MODIFY
action_rationale: >-
  Specific condition sets are defective. Sets 251, 456 and 484 match chloroplast ATP synthase subunits,
  and set 789 transfers a location that the source entries record for a different isoform than the one
  the set detects. These four sets should be removed or narrowed; sets 1384, 1084 and 365 need a closer
  look. The remaining sets were not shown to be wrong: 1,513 of 1,525 sets agree fully with Swiss-Prot
  locations at entry level, so the rule as a whole is kept.
suggested_modifications:
- >-
  Remove condition set 789 (FunFam 3.30.1050.10:FF:000001 AND FunFam 3.40.47.10:FF:000016 AND NOT Bacteria,
  Archaea, Viruses), or stop it from emitting Mitochondrion. In P32020 and P22307 the Mitochondrion location
  is scoped to isoform SCP2, which lacks residues 1-404 and so cannot match FunFam 3.40.47.10:FF:000016;
  isoform SCPx is recorded as Peroxisome.
- >-
  When rules are mined from subcellular location comments that are scoped to a named isoform, do not transfer
  the location through a signature set that the named isoform cannot match.
- >-
  Remove or narrow set 251 (IPR000194 AND IPR000793 AND rosids), set 456 (IPR005294 AND PTHR48082:SF2
  AND Liliopsida) and set 484 (IPR020537 AND IPR035921 AND Solanaceae): 33 of 41, 5 of 10 and 7 of 12
  of their Swiss-Prot matches are chloroplast ATP synthase subunits curated to the chloroplast thylakoid
  membrane (for example A6MMJ2, P06286).
- >-
  Review set 1384 (FunFams 3.40.50.450:FF:000010 AND 3.40.50.460:FF:000008): 6 of 8 Swiss-Prot matches
  are ATP-dependent 6-phosphofructokinases recorded as Cytoplasm by HAMAP rule MF_03184 (for example O94201,
  P78985). Review set 1084 (Amphibia adenylosuccinate synthetase, 3 of 6 recorded as Cytoplasm by HAMAP
  rule MF_03126) and set 365 (4 of 106 matches are apicoplast lipoyl synthases, for example Q8IDQ0).
go_specificity:
  assessment: APPROPRIATE
  notes: >-
    The rule emits the UniProt location Mitochondrion (SL-0173), which UniProt converts to GO:0005739
    mitochondrion; for example Q9VJ43 carries GO:0005739 IEA GO_REF:0000044 assigned by UniProt. The term
    matches the location it is derived from.
annotation_assessments:
- annotation_kind: OTHER
  value: SL-0173
  label: Mitochondrion
  assessment: PARTIALLY_CORRECT
  correct_examples:
  - P00156
  - P00158
  incorrect_examples:
  - Q9VJ43
  - A6MMJ2
  - P06286
  notes: >-
    Correct examples: P00156 and P00158 (cytochrome b of human and mouse) match set 1. P56757 (Arabidopsis
    ATP synthase subunit alpha, chloroplastic; set 251) is not listed as incorrect, because it carries
    GO:0005739 mitochondrion HDA PMID:22923678 (TAIR), a proteomics annotation; whether that is a real
    second location or organelle carry-over is not settled here. Swiss-Prot entries
    that match a condition set but are located in the chloroplast thylakoid membrane: A6MMJ2 (ATP synthase subunit alpha, chloroplastic; set 456),
    P06286 (ATP synthase subunit c, chloroplastic; set 484). ARBA does not annotate reviewed entries,
    so these show what the sets would assign to unreviewed orthologs. Annotated unreviewed example: Q9VJ43
    (Drosophila ScpX, unreviewed) has SUBCELLULAR LOCATION Mitochondrion with evidence ECO:0000256 ARBA:ARBA00004173
    and GO:0005739 IEA GO_REF:0000044; it carries FunFams 3.40.47.10:FF:000016 and 3.30.1050.10:FF:000001
    and so matches set 789. P32020: location Mitochondrion scoped to Isoform SCP2 (ECO:0000269 PMID:11003606,
    PMID:26901662), Isoform SCPx Peroxisome (ECO:0000269 PMID:26901662). P22307: Mitochondrion scoped
    to Isoform SCP2 (ECO:0000269 PMID:17157249), Isoform SCPx Peroxisome.
  supported_by:
  - reference_id: PMID:26901662
    supporting_text: >-
      the N-terminal mitochondrial targeting sequence is not powerful enough to localize the SCPX and
      SCP2 proteins to the mitochondria.
  - reference_id: PMID:26901662
    supporting_text: >-
      The Scp2 gene contains two transcription initiation sites, giving rise to the 58 kDa sterol carrier
      protein-x (SCPX) and 15 kDa pro-SCP2 proteins
confidence: 0.75
references:
- id: PMID:26901662
  title: >-
    Sterol Carrier Protein-2, a Nonspecific Lipid-Transfer Protein, in Intracellular Cholesterol Trafficking
    in Testicular Leydig Cells.
- id: PMID:11003606
  title: >-
    Sterol carrier protein-2 localization in endoplasmic reticulum and role in phospholipid formation.
  full_text_unavailable: true
supported_by:
- reference_id: PMID:26901662
  supporting_text: >-
    the N-terminal mitochondrial targeting sequence is not powerful enough to localize the SCPX and SCP2
    proteins to the mitochondria.
- reference_id: PMID:11003606
  supporting_text: detected SCP-2 in peroxisomes > endoplasmic reticulum > mitochondria >
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The broad NOT Bacteria/Archaea/Viruses taxon condition, combined with single-FunFam sets, is the principal
    false-positive generator and is exactly how the Drosophila ScpX case arises.
  correction: >-
    The ScpX case comes from a two-FunFam set and from an isoform-scoped source annotation; no taxon condition
    within eukaryotes would prevent it, and no false-positive rate was measured for any class of set.
    The taxonomic scope block was removed.
  error_type: OTHER
  evidence:
  - >-
    Live set 789: FunFam 3.30.1050.10:FF:000001 AND FunFam 3.40.47.10:FF:000016 AND NOT (Bacteria, Archaea,
    Viruses)
  - >-
    UniProtKB:P32020 SUBCELLULAR LOCATION: Mitochondrion scoped to Isoform SCP2; Isoform SCPx Peroxisome
- date: '2026-11-10'
  withdrawn_claim: >-
    About 96% of the InterPro conditions assert a mitochondrial location that InterPro curators did not
    assert.
  correction: >-
    The conditions act as conjunctions, so a single InterPro entry need not imply the location, and InterPro2GO
    maps few cellular component terms; the figure is not evidence against the rule.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    Live set 1 is IPR005798 AND IPR027387 AND Eukaryota: 54,084 UniProtKB entries match, 52,943 of them
    mitochondrion-encoded (UniProtKB, 2026-11-09)
- date: '2026-11-10'
  withdrawn_claim: >-
    Single-FunFam sets whose FunFam label does not mention mitochondria, or has no resolved label, should
    be dropped.
  correction: >-
    A label is not evidence about location. Agreement with Swiss-Prot locations was measured instead.
  error_type: UNEXAMINED_RULE
  evidence:
  - >-
    717 live sets consist of one FunFam plus taxon conditions; in 715 of them every Swiss-Prot match has
    the location Mitochondrion (UniProtKB, 2026-11-10)
- date: '2026-11-10'
  withdrawn_claim: The rule annotates zero reviewed proteins, so no reviewed proteins act as controls.
  correction: >-
    The ARBA API reports a reviewed count of zero for every rule because ARBA annotates unreviewed entries;
    reviewed entries do match the condition sets.
  error_type: OTHER
  evidence:
  - >-
    1,524 of 1,525 live sets match at least one Swiss-Prot entry; 18,954 set-level Swiss-Prot matches
    in total
  - >-
    reviewedProteinCount is 0 for all 15 live ARBA rules retrieved on 2026-11-09 for this group of reviews
- date: '2026-11-10'
  withdrawn_claim: >-
    A rule with 1,490 condition sets, about 124 times the 12-set threshold of the analysis tool, cannot
    be reviewed and is overly complex.
  correction: >-
    The number of condition sets is not evidence about correctness; every set was screened. The parsimony
    and overlap blocks were removed.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'All 1,525 live sets screened: 1,513 agree fully with Swiss-Prot locations'
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule has 1,490 condition sets and annotates 536,854 proteins; the SCPx set is number 779.
  correction: The live rule has more sets and the SCPx set is number 789.
  error_type: STALE_RULE_VERSION
  evidence:
  - >-
    https://rest.uniprot.org/arba/ARBA00004173 retrieved 2026-11-09: 1,525 condition sets, unreviewedProteinCount
    562,320, modifiedDate 2026-07-18
- date: '2026-11-10'
  withdrawn_claim: Assessments were supported by quotations from an AI-generated deep-research report.
  correction: >-
    That report is not literature; those supporting entries were removed and the two cached papers are
    cited directly.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - >-
    Previous supported_by entries cited rules/arba/ARBA00004173/ARBA00004173-deep-research-falcon.md