ARBA00085337 cell redox homeostasis (GO:0045454)

View original ARBA rule on UniProt

Type: ARBA
Status: COMPLETE
Action: ACCEPT
Confidence: 0.70

Description

Assigns GO:0045454 (cell redox homeostasis) through 14 alternative condition sets, each one to three CATH FunFams with a taxon. The sets cover nitric oxide synthases in Primates, fungal and plant thioredoxins, peroxiredoxins, glutathione reductase, KRIT1, selenide water dikinase 1, the yeast mitochondrial porin and fungal SCO1-like proteins.

Analysis Summary

Condition-set counts describe the sets recorded in this review, which may omit the full rule.

5
Domain Pairs Analyzed
14
Recorded condition sets
3
Subset Relationships
0
Redundant Annotations

No domain overlap table is shown: the cached overlap analysis for this version of the review is not available. Run just analyze-rule ARBA00085337 and re-render to add it.

Review Summary

All 14 live condition sets were examined. Eleven match reviewed entries, 32 in total, and every one carries GO:0045454, 30 by manual evidence. The KRIT1, mitochondrial porin and SCO1 sets, which could look out of place beside thioredoxins and peroxiredoxins, each rest on an experimental annotation of the protein. The nitric oxide synthase set rests on a Reactome TAS annotation only and is the least supported. Three sets match no UniProtKB entry.

Action Rationale

Each set that matches reviewed proteins selects proteins already curated to cell redox homeostasis, most with experimental evidence. A protein does not need redox homeostasis as its main role for the annotation to be true. The counts are from Swiss-Prot, which is also what ARBA learns its rules from, so they show the condition sets are coherent rather than giving an independent error rate for unreviewed entries.

GO Annotations

GO:0045454 - cell redox homeostasis
Aspect: BP

Annotation Assessments

CORRECT GO_TERM GO:0045454 - cell redox homeostasis
Matched proteins: 32; incorrect: 0
Correct examples: P22217, P34760, O00522, P04840, P23833, P49903, Q96291, Q9XFH8, Q93379

Manual annotations to GO:0045454 on reviewed matches (QuickGO, retrieved 2026-11-09). Set 2: P22217 (TRX1), IGI, PMID:22561702. Set 4: O00522 (KRIT1), IMP, PMID:20668652. Set 6: P49903 (SEPHS1), IMP, PMID:31607477. Set 7: P04840 (POR1) and P40478 (POR2), IMP, PMID:18768136. Set 9: Q93379 (gsr-1), IMP, PMID:27117030. Set 11: P34760 (TSA1), IDA and IMP, PMID:8344960. Set 12: P23833 (SCO1) and P38072 (SCO2), IGI, PMID:30593977. Set 13: Q96291 (BAS1), IMP, PMID:30104347. Set 14: Q9XFH8, IGI, PMID:26842981. Set 1: P29474 (NOS3), P29475 (NOS1) and P35228 (NOS2) carry the term only as TAS from Reactome:R-HSA-1222556.

Rule Definition

Condition Sets

Condition Set 1

3 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3 of those by a manual-evidence GO annotation. 159 unreviewed entries match. The reviewed matches are human NOS1, NOS2 and NOS3, annotated by Reactome TAS only.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
3.40.50.80:FF:000003 3.90.1230.10:FF:000001 26 20 19 0.704 0.731 0.950 HIGH_OVERLAP

Condition Set 2

2 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3 of those by a manual-evidence GO annotation. 87 unreviewed entries match.

Condition Set 3

4 condition(s)
Notes:

UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0 of those by a manual-evidence GO annotation. 0 unreviewed entries match. No UniProtKB entry matches this set; it is one of three sets that repeat the same FunFam conditions for Archaea, Eukaryota and Bacteria.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
1.20.80.10:FF:000016 1.25.40.20:FF:000120 3 4 3 0.750 1.000 0.750 SUBSET
1.20.80.10:FF:000016 2.30.29.30:FF:000227 3 3 3 1.000 1.000 1.000 REDUNDANT
1.25.40.20:FF:000120 2.30.29.30:FF:000227 4 3 3 0.750 0.750 1.000 SUBSET

Condition Set 4

4 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3 of those by a manual-evidence GO annotation. 521 unreviewed entries match.

Condition Set 5

4 condition(s)
Notes:

UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0 of those by a manual-evidence GO annotation. 0 unreviewed entries match. No UniProtKB entry matches this set; it is one of three sets that repeat the same FunFam conditions for Archaea, Eukaryota and Bacteria.

Condition Set 6

3 condition(s)
Notes:

UniProtKB release 2026_04: 7 reviewed entries match this set; 7 of them carry GO:0045454, 7 of those by a manual-evidence GO annotation. 757 unreviewed entries match.

Condition Set 7

2 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0045454, 2 of those by a manual-evidence GO annotation. 14 unreviewed entries match.

Condition Set 8

3 condition(s)
Notes:

UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0 of those by a manual-evidence GO annotation. 0 unreviewed entries match. No UniProtKB entry matches this set; it is one of three sets that repeat the same FunFam conditions for Archaea, Eukaryota and Bacteria.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
3.30.390.30:FF:000003 3.50.50.60:FF:000141 18 3 3 0.167 0.167 1.000 SUBSET

Condition Set 9

3 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3 of those by a manual-evidence GO annotation. 963 unreviewed entries match.

Condition Set 10

3 condition(s)
Notes:

UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0 of those by a manual-evidence GO annotation. 45 unreviewed entries match. No reviewed entry matches, so this set could not be checked against curated annotation.

Condition Set 11

2 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0045454, 2 of those by a manual-evidence GO annotation. 85 unreviewed entries match.

Condition Set 12

2 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 2 of those by a manual-evidence GO annotation. 1077 unreviewed entries match. The reviewed match without a manual annotation is O42899 (Schizosaccharomyces pombe sco1).

Condition Set 13

2 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3 of those by a manual-evidence GO annotation. 502 unreviewed entries match.

Condition Set 14

2 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 2 of those by a manual-evidence GO annotation. 47 unreviewed entries match.

Assessments

APPROPRIATE

GO:0045454 is the term carried by the reviewed members of every set, with experimental evidence codes for the thioredoxin, peroxiredoxin, glutathione reductase, KRIT1, SEPHS1, porin and SCO sets (accessions in annotation_assessments).

References (3)

Raw YAML

View Source YAML 
id: ARBA00085337
description: >-
  Assigns GO:0045454 (cell redox homeostasis) through 14 alternative condition sets, each one to three
  CATH FunFams with a taxon. The sets cover nitric oxide synthases in Primates, fungal and plant thioredoxins,
  peroxiredoxins, glutathione reductase, KRIT1, selenide water dikinase 1, the yeast mitochondrial
  porin and fungal SCO1-like proteins.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00085337
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.80:FF:000003
      curie: CATH.FunFam:3.40.50.80:FF:000003
      label: Nitric oxide synthase
      negated: false
    - condition_type: FUNFAM
      value: 3.90.1230.10:FF:000001
      curie: CATH.FunFam:3.90.1230.10:FF:000001
      label: Nitric oxide synthase, brain
      negated: false
    - condition_type: TAXON
      value: Primates
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3
      of those by a manual-evidence GO annotation. 159 unreviewed entries match. The reviewed matches
      are human NOS1, NOS2 and NOS3, annotated by Reactome TAS only.
    pairwise_overlap:
    - condition_a: 3.40.50.80:FF:000003
      condition_b: 3.90.1230.10:FF:000001
      protein_database: SWISSPROT
      count_a: 26
      count_b: 20
      intersection_count: 19
      a_minus_b_count: 7
      b_minus_a_count: 1
      jaccard_similarity: 0.7037037037037037
      containment_a_in_b: 0.7307692307692307
      containment_b_in_a: 0.95
      interpretation: HIGH_OVERLAP
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 3.40.30.10:FF:000104
      curie: CATH.FunFam:3.40.30.10:FF:000104
      label: Thioredoxin
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3
      of those by a manual-evidence GO annotation. 87 unreviewed entries match.
  - number: 3
    conditions:
    - condition_type: FUNFAM
      value: 1.20.80.10:FF:000016
      curie: CATH.FunFam:1.20.80.10:FF:000016
      label: Krev interaction trapped protein 1
      negated: false
    - condition_type: FUNFAM
      value: 1.25.40.20:FF:000120
      curie: CATH.FunFam:1.25.40.20:FF:000120
      label: krev interaction trapped protein 1 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 2.30.29.30:FF:000227
      curie: CATH.FunFam:2.30.29.30:FF:000227
      label: krev interaction trapped protein 1 isoform X1
      negated: false
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: false
    notes: >-
      UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0
      of those by a manual-evidence GO annotation. 0 unreviewed entries match. No UniProtKB entry
      matches this set; it is one of three sets that repeat the same FunFam conditions for Archaea,
      Eukaryota and Bacteria.
    pairwise_overlap:
    - condition_a: 1.20.80.10:FF:000016
      condition_b: 1.25.40.20:FF:000120
      protein_database: SWISSPROT
      count_a: 3
      count_b: 4
      intersection_count: 3
      a_minus_b_count: 0
      b_minus_a_count: 1
      jaccard_similarity: 0.75
      containment_a_in_b: 1.0
      containment_b_in_a: 0.75
      interpretation: SUBSET
    - condition_a: 1.20.80.10:FF:000016
      condition_b: 2.30.29.30:FF:000227
      protein_database: SWISSPROT
      count_a: 3
      count_b: 3
      intersection_count: 3
      a_minus_b_count: 0
      b_minus_a_count: 0
      jaccard_similarity: 1.0
      containment_a_in_b: 1.0
      containment_b_in_a: 1.0
      interpretation: REDUNDANT
    - condition_a: 1.25.40.20:FF:000120
      condition_b: 2.30.29.30:FF:000227
      protein_database: SWISSPROT
      count_a: 4
      count_b: 3
      intersection_count: 3
      a_minus_b_count: 1
      b_minus_a_count: 0
      jaccard_similarity: 0.75
      containment_a_in_b: 0.75
      containment_b_in_a: 1.0
      interpretation: SUBSET
  - number: 4
    conditions:
    - condition_type: FUNFAM
      value: 1.20.80.10:FF:000016
      curie: CATH.FunFam:1.20.80.10:FF:000016
      label: Krev interaction trapped protein 1
      negated: false
    - condition_type: FUNFAM
      value: 1.25.40.20:FF:000120
      curie: CATH.FunFam:1.25.40.20:FF:000120
      label: krev interaction trapped protein 1 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 2.30.29.30:FF:000227
      curie: CATH.FunFam:2.30.29.30:FF:000227
      label: krev interaction trapped protein 1 isoform X1
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3
      of those by a manual-evidence GO annotation. 521 unreviewed entries match.
  - number: 5
    conditions:
    - condition_type: FUNFAM
      value: 1.20.80.10:FF:000016
      curie: CATH.FunFam:1.20.80.10:FF:000016
      label: Krev interaction trapped protein 1
      negated: false
    - condition_type: FUNFAM
      value: 1.25.40.20:FF:000120
      curie: CATH.FunFam:1.25.40.20:FF:000120
      label: krev interaction trapped protein 1 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 2.30.29.30:FF:000227
      curie: CATH.FunFam:2.30.29.30:FF:000227
      label: krev interaction trapped protein 1 isoform X1
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: false
    notes: >-
      UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0
      of those by a manual-evidence GO annotation. 0 unreviewed entries match. No UniProtKB entry
      matches this set; it is one of three sets that repeat the same FunFam conditions for Archaea,
      Eukaryota and Bacteria.
  - number: 6
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1330.10:FF:000006
      curie: CATH.FunFam:3.30.1330.10:FF:000006
      label: Selenide water dikinase 1
      negated: false
    - condition_type: FUNFAM
      value: 3.90.650.10:FF:000003
      curie: CATH.FunFam:3.90.650.10:FF:000003
      label: Selenide, water dikinase 1
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 7 reviewed entries match this set; 7 of them carry GO:0045454, 7
      of those by a manual-evidence GO annotation. 757 unreviewed entries match.
  - number: 7
    conditions:
    - condition_type: FUNFAM
      value: 2.40.160.10:FF:000016
      curie: CATH.FunFam:2.40.160.10:FF:000016
      label: Por1p
      negated: false
    - condition_type: TAXON
      value: Dikarya
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0045454, 2
      of those by a manual-evidence GO annotation. 14 unreviewed entries match.
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 3.30.390.30:FF:000003
      curie: CATH.FunFam:3.30.390.30:FF:000003
      label: Glutathione reductase
      negated: false
    - condition_type: FUNFAM
      value: 3.50.50.60:FF:000141
      curie: CATH.FunFam:3.50.50.60:FF:000141
      label: Glutathione reductase
      negated: false
    - condition_type: TAXON
      value: Archaea
      curie: NCBITaxon:2157
      label: Archaea
      negated: false
    notes: >-
      UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0
      of those by a manual-evidence GO annotation. 0 unreviewed entries match. No UniProtKB entry
      matches this set; it is one of three sets that repeat the same FunFam conditions for Archaea,
      Eukaryota and Bacteria.
    pairwise_overlap:
    - condition_a: 3.30.390.30:FF:000003
      condition_b: 3.50.50.60:FF:000141
      protein_database: SWISSPROT
      count_a: 18
      count_b: 3
      intersection_count: 3
      a_minus_b_count: 15
      b_minus_a_count: 0
      jaccard_similarity: 0.16666666666666666
      containment_a_in_b: 0.16666666666666666
      containment_b_in_a: 1.0
      interpretation: SUBSET
  - number: 9
    conditions:
    - condition_type: FUNFAM
      value: 3.30.390.30:FF:000003
      curie: CATH.FunFam:3.30.390.30:FF:000003
      label: Glutathione reductase
      negated: false
    - condition_type: FUNFAM
      value: 3.50.50.60:FF:000141
      curie: CATH.FunFam:3.50.50.60:FF:000141
      label: Glutathione reductase
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3
      of those by a manual-evidence GO annotation. 963 unreviewed entries match.
  - number: 10
    conditions:
    - condition_type: FUNFAM
      value: 3.30.390.30:FF:000003
      curie: CATH.FunFam:3.30.390.30:FF:000003
      label: Glutathione reductase
      negated: false
    - condition_type: FUNFAM
      value: 3.50.50.60:FF:000141
      curie: CATH.FunFam:3.50.50.60:FF:000141
      label: Glutathione reductase
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: false
    notes: >-
      UniProtKB release 2026_04: 0 reviewed entries match this set; 0 of them carry GO:0045454, 0
      of those by a manual-evidence GO annotation. 45 unreviewed entries match. No reviewed entry
      matches, so this set could not be checked against curated annotation.
  - number: 11
    conditions:
    - condition_type: FUNFAM
      value: 3.40.30.10:FF:000003
      curie: CATH.FunFam:3.40.30.10:FF:000003
      label: Peroxiredoxin 1
      negated: false
    - condition_type: TAXON
      value: Saccharomycetes
      curie: NCBITaxon:4891
      label: Saccharomycetes
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0045454, 2
      of those by a manual-evidence GO annotation. 85 unreviewed entries match.
  - number: 12
    conditions:
    - condition_type: FUNFAM
      value: 3.40.30.10:FF:000013
      curie: CATH.FunFam:3.40.30.10:FF:000013
      label: Blast:Protein SCO1 homolog, mitochondrial
      negated: false
    - condition_type: TAXON
      value: Ascomycota
      curie: NCBITaxon:4890
      label: Ascomycota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 2
      of those by a manual-evidence GO annotation. 1077 unreviewed entries match. The reviewed match
      without a manual annotation is O42899 (Schizosaccharomyces pombe sco1).
  - number: 13
    conditions:
    - condition_type: FUNFAM
      value: 3.40.30.10:FF:000063
      curie: CATH.FunFam:3.40.30.10:FF:000063
      label: 2-Cys peroxiredoxin BAS1, chloroplastic
      negated: false
    - condition_type: TAXON
      value: eudicotyledons
      curie: NCBITaxon:71240
      label: eudicotyledons
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 3
      of those by a manual-evidence GO annotation. 502 unreviewed entries match.
  - number: 14
    conditions:
    - condition_type: FUNFAM
      value: 3.40.30.10:FF:000250
      curie: CATH.FunFam:3.40.30.10:FF:000250
      label: Thioredoxin F-type, chloroplastic
      negated: false
    - condition_type: TAXON
      value: Viridiplantae
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0045454, 2
      of those by a manual-evidence GO annotation. 47 unreviewed entries match.
  go_annotations:
  - go_id: GO:0045454
    go_label: cell redox homeostasis
    aspect: BP
  entries:
  - id: 1.20.80.10:FF:000016
    type: FUNFAM
    label: Krev interaction trapped protein 1
    appears_in_condition_sets:
    - 3
    - 4
    - 5
    protein_count: 3
    related_entries:
    - relationship: EQUIV
      target_id: 3.40.50.80:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.90.1230.10:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000104
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: PREDICTS
      target_id: 1.25.40.20:FF:000120
      containment: 1.0
      jaccard_similarity: 0.75
      intersection_count: 3
      exclusive_count: 0
    - relationship: EQUIV
      target_id: 2.30.29.30:FF:000227
      containment: 1.0
      jaccard_similarity: 1.0
      intersection_count: 3
      exclusive_count: 0
    - relationship: EQUIV
      target_id: 3.30.390.30:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.50.50.60:FF:000141
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 2.40.160.10:FF:000016
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000013
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000063
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000250
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: PREDICTS
      target_id: GO:0045454
      containment: 1.0
      jaccard_similarity: 0.004
      intersection_count: 3
      exclusive_count: 0
  - id: 1.25.40.20:FF:000120
    type: FUNFAM
    label: krev interaction trapped protein 1 isoform X1
    appears_in_condition_sets:
    - 3
    - 4
    - 5
    protein_count: 4
    related_entries:
    - relationship: EQUIV
      target_id: 3.40.50.80:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 4
    - relationship: EQUIV
      target_id: 3.90.1230.10:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 4
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000104
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 4
    - relationship: PREDICTED_BY
      target_id: 1.20.80.10:FF:000016
      containment: 0.75
      jaccard_similarity: 0.75
      intersection_count: 3
      exclusive_count: 1
    - relationship: PREDICTED_BY
      target_id: 2.30.29.30:FF:000227
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    type: FUNFAM
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    type: FUNFAM
    label: Por1p
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    type: FUNFAM
    label: Glutathione reductase
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    type: FUNFAM
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    type: FUNFAM
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    type: FUNFAM
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      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000063
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: PREDICTS
      target_id: GO:0045454
      containment: 1.0
      jaccard_similarity: 0.004
      intersection_count: 3
      exclusive_count: 0
  - id: 3.40.50.80:FF:000003
    type: FUNFAM
    label: Nitric oxide synthase
    appears_in_condition_sets:
    - 1
    protein_count: 26
    related_entries:
    - relationship: PREDICTED_BY
      target_id: 3.90.1230.10:FF:000001
      containment: 0.95
      jaccard_similarity: 0.704
      intersection_count: 19
      exclusive_count: 1
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000104
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 1.20.80.10:FF:000016
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 1.25.40.20:FF:000120
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 2.30.29.30:FF:000227
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 3.30.390.30:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 3.50.50.60:FF:000141
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 2.40.160.10:FF:000016
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000013
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000063
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000250
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 26
    - relationship: PREDICTS
      target_id: GO:0045454
      containment: 0.115
      jaccard_similarity: 0.004
      intersection_count: 3
      exclusive_count: 23
  - id: 3.50.50.60:FF:000141
    type: FUNFAM
    label: Glutathione reductase
    appears_in_condition_sets:
    - 8
    - 9
    - 10
    protein_count: 3
    related_entries:
    - relationship: EQUIV
      target_id: 3.40.50.80:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.90.1230.10:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000104
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 1.20.80.10:FF:000016
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 1.25.40.20:FF:000120
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 2.30.29.30:FF:000227
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: PREDICTS
      target_id: 3.30.390.30:FF:000003
      containment: 0.167
      jaccard_similarity: 0.167
      intersection_count: 3
      exclusive_count: 15
    - relationship: EQUIV
      target_id: 2.40.160.10:FF:000016
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000013
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000063
      containment: 0.0
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      intersection_count: 0
      exclusive_count: 3
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000250
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 3
    - relationship: PREDICTS
      target_id: GO:0045454
      containment: 1.0
      jaccard_similarity: 0.004
      intersection_count: 3
      exclusive_count: 0
  - id: 3.90.1230.10:FF:000001
    type: FUNFAM
    label: Nitric oxide synthase, brain
    appears_in_condition_sets:
    - 1
    protein_count: 20
    related_entries:
    - relationship: PREDICTS
      target_id: 3.40.50.80:FF:000003
      containment: 0.731
      jaccard_similarity: 0.704
      intersection_count: 19
      exclusive_count: 7
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000104
      containment: 0.0
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      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 1.20.80.10:FF:000016
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      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 1.25.40.20:FF:000120
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 2.30.29.30:FF:000227
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 3.30.390.30:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 3.50.50.60:FF:000141
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 2.40.160.10:FF:000016
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000013
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000063
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: EQUIV
      target_id: 3.40.30.10:FF:000250
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 20
    - relationship: PREDICTS
      target_id: GO:0045454
      containment: 0.15
      jaccard_similarity: 0.004
      intersection_count: 3
      exclusive_count: 17
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2025-03-21'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 14
review_summary: >-
  All 14 live condition sets were examined. Eleven match reviewed entries, 32 in total, and every
  one carries GO:0045454, 30 by manual evidence. The KRIT1, mitochondrial porin and SCO1 sets, which
  could look out of place beside thioredoxins and peroxiredoxins, each rest on an experimental annotation
  of the protein. The nitric oxide synthase set rests on a Reactome TAS annotation only and is the
  least supported. Three sets match no UniProtKB entry.
action: ACCEPT
action_rationale: >-
  Each set that matches reviewed proteins selects proteins already curated to cell redox homeostasis,
  most with experimental evidence. A protein does not need redox homeostasis as its main role for
  the annotation to be true. The counts are from Swiss-Prot, which is also what ARBA learns its rules
  from, so they show the condition sets are coherent rather than giving an independent error rate
  for unreviewed entries.
go_specificity:
  assessment: APPROPRIATE
  notes: >-
    GO:0045454 is the term carried by the reviewed members of every set, with experimental evidence
    codes for the thioredoxin, peroxiredoxin, glutathione reductase, KRIT1, SEPHS1, porin and SCO
    sets (accessions in annotation_assessments).
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0045454
  label: cell redox homeostasis
  assessment: CORRECT
  matched_protein_count: 32
  incorrect_protein_count: 0
  correct_examples:
  - P22217
  - P34760
  - O00522
  - P04840
  - P23833
  - P49903
  - Q96291
  - Q9XFH8
  - Q93379
  notes: >-
    Manual annotations to GO:0045454 on reviewed matches (QuickGO, retrieved 2026-11-09). Set 2: P22217
    (TRX1), IGI, PMID:22561702. Set 4: O00522 (KRIT1), IMP, PMID:20668652. Set 6: P49903 (SEPHS1),
    IMP, PMID:31607477. Set 7: P04840 (POR1) and P40478 (POR2), IMP, PMID:18768136. Set 9: Q93379
    (gsr-1), IMP, PMID:27117030. Set 11: P34760 (TSA1), IDA and IMP, PMID:8344960. Set 12: P23833
    (SCO1) and P38072 (SCO2), IGI, PMID:30593977. Set 13: Q96291 (BAS1), IMP, PMID:30104347. Set 14:
    Q9XFH8, IGI, PMID:26842981. Set 1: P29474 (NOS3), P29475 (NOS1) and P35228 (NOS2) carry the term
    only as TAS from Reactome:R-HSA-1222556.
confidence: 0.7
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The KRIT1 set is an over-annotation and should be removed, because the main role of KRIT1 is vascular
    development and its effect on redox state is indirect.
  correction: >-
    Human KRIT1 is curated to GO:0045454 with experimental evidence, and PAINT propagates the term
    in the family. Whether redox homeostasis is the main role of the protein does not decide whether
    the annotation is true.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - >-
    QuickGO: UniProtKB:O00522 (KRIT1), GO:0045454, IMP, PMID:20668652, assigned by UniProt; also IBA,
    GO_REF:0000033.
  - >-
    PMID:20668652, title: KRIT1 regulates the homeostasis of intracellular reactive oxygen species.
- date: '2026-11-10'
  withdrawn_claim: >-
    The Por1p set is an over-annotation and should be removed, because the porin is a metabolite channel
    and its link to redox is indirect.
  correction: Both yeast porins are curated to GO:0045454 by SGD from a mutant phenotype.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - >-
    QuickGO: UniProtKB:P04840 (POR1) and UniProtKB:P40478 (POR2), GO:0045454, IMP, PMID:18768136,
    assigned by SGD.
  - >-
    PMID:18768136, title: Redox regulation of protein expression in Saccharomyces cerevisiae mitochondria:
    possible role of VDAC.
- date: '2026-11-10'
  withdrawn_claim: >-
    The SCO1 set is a false positive that arises from structural similarity to thioredoxins, and should
    be removed.
  correction: >-
    Yeast SCO1 and SCO2 are curated to GO:0045454 by SGD from genetic interaction evidence. No source
    was given for the statement that the association comes from fold similarity.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - >-
    QuickGO: UniProtKB:P23833 (SCO1) and UniProtKB:P38072 (SCO2), GO:0045454, IGI, PMID:30593977,
    assigned by SGD.
  - 'PMID:30593977, title: Mitochondrial Sco proteins are involved in oxidative stress defense.'
- date: '2026-11-10'
  withdrawn_claim: The nitric oxide synthase set is an over-annotation and should be removed.
  correction: >-
    No source was cited for this. The three human NOS isoforms carry GO:0045454 as a Reactome TAS
    annotation; there is no experimental annotation, so this set is the least supported, but nothing
    checked shows it to be wrong.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - 'QuickGO: UniProtKB:P29474, P29475 and P35228, GO:0045454, TAS, Reactome:R-HSA-1222556.'
- date: '2026-11-10'
  withdrawn_claim: >-
    Two FunFams in the KRIT1 set match exactly the same proteins (Jaccard 1.0), which weakens the
    set and shows poor curation.
  correction: >-
    The FunFams are combined with AND within one set. Complete overlap between them leaves the set's
    meaning unchanged and has no bearing on accuracy.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    UniProt ARBA API, ARBA00085337 sets 3 to 5: three FunFam conditions and one taxon condition, all
    required.
- date: '2026-11-10'
  withdrawn_claim: The rule has 9 condition sets.
  correction: >-
    The live rule has 14. A selenide water dikinase 1 set was added, and the KRIT1 and glutathione
    reductase sets now appear once each for Archaea, Eukaryota and Bacteria.
  error_type: STALE_RULE_VERSION
  evidence:
  - >-
    UniProt ARBA API, ARBA00085337, modified 2026-07-18, retrieved 2026-11-09: 14 condition sets.
references:
- id: PMID:20668652
  title: KRIT1 regulates the homeostasis of intracellular reactive oxygen species
  findings:
  - statement: Reference for the IMP annotation of GO:0045454 on human KRIT1.
- id: PMID:18768136
  title: >-
    Redox regulation of protein expression in Saccharomyces cerevisiae mitochondria: possible role
    of VDAC
  findings:
  - statement: Reference for the SGD IMP annotations of GO:0045454 on POR1 and POR2.
- id: PMID:30593977
  title: Mitochondrial Sco proteins are involved in oxidative stress defense
  findings:
  - statement: Reference for the SGD IGI annotations of GO:0045454 on SCO1 and SCO2.