id: ARBA00085337 description: 'Predicts GO:0045454 "cell redox homeostasis" for proteins across 9 condition sets covering diverse redox-related protein families including nitric oxide synthases, thioredoxins, glutathione reductases, peroxiredoxins, and other oxidative stress response proteins with taxonomic restrictions' status: IN_PROGRESS 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: 'LIKELY OVER-ANNOTATION: NOS enzymes produce nitric oxide, primarily a signaling molecule. NADPH consumption is a catalytic mechanism feature, not evidence of redox homeostasis function. NOS uncoupling produces superoxide but this is pathological, not homeostatic. Primary GO annotations should be nitric-oxide synthase activity and NO biosynthetic process. Candidate for REMOVAL from this rule.' 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: '' - 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 notes: 'OVER-ANNOTATION: KRIT1 primary function is vascular development. While KRIT1 contains a NUDIX domain shown to regulate SOD2 expression and mitochondrial ROS levels (Goitre et al., 2010; Antognelli et al., 2018), its effect on redox is indirect via transcriptional regulation of antioxidant genes, not direct redox homeostasis. Complete domain redundancy (Jaccard=1.0) between two FunFams further weakens this condition set. Candidate for REMOVAL.' 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: 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: '' 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: 5 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: 'OVER-ANNOTATION: Por1p/VDAC is the main channel for metabolite exchange across the mitochondrial outer membrane. Primary function is metabolite transport (GO:0008308 voltage-gated anion channel activity). While VDAC has been linked to ROS release from mitochondria, this is an indirect association, not a primary role in redox homeostasis. Candidate for REMOVAL.' - number: 6 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: '' - number: 7 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: 'LIKELY OVER-ANNOTATION: SCO1 is a copper chaperone for cytochrome c oxidase (Complex IV) assembly. While it has a thioredoxin-like fold with redox-active cysteines, the fold is used for copper binding, not disulfide reduction. Annotating SCO1 to cell redox homeostasis based on structural similarity to thioredoxins is a false positive. Candidate for REMOVAL.' - number: 8 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: '' - number: 9 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: '' go_annotations: - go_id: GO:0045454 go_label: cell redox homeostasis aspect: P reviewed_protein_count: 0 unreviewed_protein_count: 0 created_date: '' modified_date: '' entries: - id: 1.20.80.10:FF:000016 type: FUNFAM label: Krev interaction trapped protein 1 appears_in_condition_sets: - 3 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: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR046952 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 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 containment: 1.0 jaccard_similarity: 0.75 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: 4 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR046952 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.005 intersection_count: 4 exclusive_count: 0 - id: 2.30.29.30:FF:000227 type: FUNFAM label: krev interaction trapped protein 1 isoform X1 appears_in_condition_sets: - 3 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: 1.0 jaccard_similarity: 1.0 intersection_count: 3 exclusive_count: 0 - relationship: PREDICTS target_id: 1.25.40.20:FF:000120 containment: 0.75 jaccard_similarity: 0.75 intersection_count: 3 exclusive_count: 1 - 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: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 3 - relationship: EQUIV target_id: IPR046952 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: 2.40.160.10:FF:000016 type: FUNFAM label: Por1p appears_in_condition_sets: - 5 protein_count: 2 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.30.390.30:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: EQUIV target_id: IPR046952 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 2 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.003 intersection_count: 2 exclusive_count: 0 - id: 3.30.390.30:FF:000003 type: FUNFAM label: Glutathione reductase appears_in_condition_sets: - 4 protein_count: 18 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: PREDICTED_BY target_id: 3.50.50.60:FF:000141 containment: 1.0 jaccard_similarity: 0.167 intersection_count: 3 exclusive_count: 0 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: PREDICTS target_id: IPR046952 containment: 1.0 jaccard_similarity: 0.321 intersection_count: 18 exclusive_count: 0 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.023 intersection_count: 18 exclusive_count: 0 - id: 3.40.30.10:FF:000003 type: FUNFAM label: Peroxiredoxin 1 appears_in_condition_sets: - 6 protein_count: 38 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 3.30.390.30:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: EQUIV target_id: IPR046952 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 38 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.048 intersection_count: 38 exclusive_count: 0 - id: 3.40.30.10:FF:000013 type: FUNFAM label: Blast:Protein SCO1 homolog, mitochondrial appears_in_condition_sets: - 7 protein_count: 18 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 18 - 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relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - relationship: EQUIV target_id: 3.30.390.30:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 13 - 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relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.016 intersection_count: 13 exclusive_count: 0 - id: IPR011902 type: INTERPRO source: ipr2go protein_count: 6 asserted_predicted_go_terms: - GO:0045454 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.30.390.30:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: EQUIV target_id: IPR046952 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 6 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.008 intersection_count: 6 exclusive_count: 0 - id: IPR011909 type: INTERPRO source: ipr2go protein_count: 7 asserted_predicted_go_terms: - GO:0045454 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.30.390.30:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR046952 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.009 intersection_count: 7 exclusive_count: 0 - id: IPR014223 type: INTERPRO source: ipr2go protein_count: 4 asserted_predicted_go_terms: - GO:0045454 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: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.30.390.30:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: EQUIV target_id: IPR046952 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 4 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.005 intersection_count: 4 exclusive_count: 0 - id: IPR044182 type: INTERPRO source: ipr2go protein_count: 7 asserted_predicted_go_terms: - GO:0045454 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.30.390.30:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.50.50.60:FF:000141 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: EQUIV target_id: IPR046952 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 7 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.009 intersection_count: 7 exclusive_count: 0 - id: IPR046952 type: INTERPRO source: ipr2go protein_count: 56 asserted_predicted_go_terms: - GO:0045454 related_entries: - relationship: EQUIV target_id: 3.40.50.80:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 3.90.1230.10:FF:000001 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 3.40.30.10:FF:000104 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 1.20.80.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 1.25.40.20:FF:000120 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 2.30.29.30:FF:000227 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: PREDICTED_BY target_id: 3.30.390.30:FF:000003 containment: 0.321 jaccard_similarity: 0.321 intersection_count: 18 exclusive_count: 38 - relationship: PREDICTED_BY target_id: 3.50.50.60:FF:000141 containment: 0.054 jaccard_similarity: 0.054 intersection_count: 3 exclusive_count: 53 - relationship: EQUIV target_id: 2.40.160.10:FF:000016 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 3.40.30.10:FF:000003 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 3.40.30.10:FF:000013 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 3.40.30.10:FF:000063 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: 3.40.30.10:FF:000250 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: IPR004502 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: IPR011900 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: IPR011902 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: IPR011909 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: IPR014223 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: EQUIV target_id: IPR044182 containment: 0.0 jaccard_similarity: 0.0 intersection_count: 0 exclusive_count: 56 - relationship: PREDICTS target_id: GO:0045454 containment: 1.0 jaccard_similarity: 0.071 intersection_count: 56 exclusive_count: 0 review_summary: 'This rule contains a mix of legitimate and problematic condition sets. Core redox homeostasis proteins (glutathione reductase, thioredoxins, peroxiredoxins - sets 2, 4, 6, 8, 9) are appropriately annotated to GO:0045454. However, 4 of 9 condition sets target proteins whose primary function is NOT redox homeostasis: NOS (set 1, primarily NO signaling), KRIT1 (set 3, primarily vascular development with indirect transcriptional redox effects), Por1p/VDAC (set 5, primarily metabolite transport), and SCO1 (set 7, copper chaperone with thioredoxin fold used for copper binding not disulfide reduction). These 4 condition sets should be removed. The rule also has domain redundancy (Jaccard=1.0 in set 3) and fragmented taxonomic scope.' action: MODIFY action_rationale: 'MODIFY rather than REMOVE because 5 of 9 condition sets correctly identify core redox homeostasis proteins. The 4 problematic condition sets (NOS, KRIT1, Por1p, SCO1) should be removed: NOS produces NO as a signaling molecule (NADPH consumption is catalytic, not homeostatic); KRIT1 affects redox indirectly via SOD2 transcriptional regulation; Por1p is a metabolite transporter; SCO1 uses its thioredoxin fold for copper binding not disulfide reduction. Retained sets (thioredoxins, glutathione reductase, peroxiredoxins) have strong mechanistic basis for GO:0045454.' suggested_modifications: - 'REMOVE condition set 1 (NOS): NOS produces nitric oxide as a signaling molecule; NADPH consumption is catalytic, not evidence of redox homeostasis. Over-annotation.' - 'REMOVE condition set 3 (KRIT1): primary function is vascular development; redox involvement is indirect via transcriptional regulation of antioxidant genes, not direct redox homeostasis. Also has complete domain redundancy (Jaccard=1.0).' - 'REMOVE condition set 5 (Por1p/VDAC): primary function is metabolite transport; ROS release link is indirect.' - 'REMOVE condition set 7 (SCO1): copper chaperone with thioredoxin-like fold used for copper binding, not disulfide reduction. Structural similarity to thioredoxins does not imply functional equivalence.' - 'RETAIN condition sets 2, 4, 6, 8, 9 (thioredoxins, glutathione reductase, peroxiredoxins, chloroplastic thioredoxin F-type): these are core redox homeostasis proteins with direct roles.' - 'Evaluate taxonomic restrictions on retained sets: some FunFam-level restrictions may be narrower than biological distribution warrants.' parsimony: assessment: OVERLY_COMPLEX notes: 'Rule has 9 condition sets mixing mechanistically diverse proteins. Redundancy exists within condition sets (set 3 has Jaccard=1.0 between two FunFams, set 1 has 70% overlap), not between sets. After removing 4 inappropriate condition sets, the remaining 5 sets cover genuinely distinct protein families and should be retained.' literature_support: assessment: WEAK notes: 'Literature support is strong for core redox proteins (sets 2, 4, 6, 8, 9) but absent or contradictory for 4 condition sets: NOS literature supports NO signaling not redox homeostasis; KRIT1 literature shows indirect transcriptional effects; Por1p literature shows transport function; SCO1 literature shows copper chaperone function. The deep research file lacks actual citations (no PMIDs/DOIs), making claims unverifiable. Additional literature review needed.' supported_by: - reference_id: file:rules/arba/ARBA00085337/ARBA00085337-deep-research-manual.md supporting_text: 'Strong candidates: Glutathione reductase, thioredoxins, peroxiredoxins - these are core redox homeostasis proteins. Questionable candidates: KRIT1 (developmental protein with oxidative stress sensitivity), Por1p (transporter with indirect redox involvement)' condition_overlap: assessment: SIGNIFICANT notes: 'Analysis reveals concerning overlap patterns: Set 3 contains completely redundant domains (Jaccard=1.0), Set 1 has high overlap (Jaccard=0.70), and Set 4 shows subset relationships. This indicates poor curation and unnecessary complexity.' supported_by: [] go_specificity: assessment: MISMATCHED notes: 'GO:0045454 is APPROPRIATE for condition sets 2, 4, 6, 8, 9 (thioredoxins, glutathione reductase, peroxiredoxins) but MISMATCHED for sets 1, 3, 5, 7 (NOS, KRIT1, Por1p, SCO1) whose primary functions are not redox homeostasis. The term itself is correct; the issue is that 4 condition sets identify proteins that do not primarily perform this function.' supported_by: [] taxonomic_scope: assessment: TOO_NARROW notes: 'Fragmented taxonomic restrictions across condition sets. However, this assessment needs nuance: some restrictions may reflect FunFam scope rather than biological distribution (e.g., thioredoxin FunFam FF:000104 may only capture fungal members). For condition sets recommended for removal (NOS Primates-only, etc.), taxonomic scope is moot. For retained sets, the question is whether the specific FunFams are taxon-limited or whether orthologs in other taxa are missed.' supported_by: [] confidence: 0.5 references: - id: file:rules/arba/ARBA00085337/ARBA00085337-deep-research-manual.md title: Manual deep research analysis of ARBA00085337 findings: - statement: 'Core redox proteins (glutathione reductase, thioredoxins, peroxiredoxins) strongly support GO:0045454 annotation' - statement: 'KRIT1 and Por1p show questionable relevance - primarily developmental and transport functions respectively' - statement: 'Domain redundancy indicates poor curation, particularly complete overlap in condition set 3' - statement: 'Fragmented taxonomic scope suggests annotation bias rather than biological restriction' supported_by: - reference_id: file:rules/arba/ARBA00085337/ARBA00085337-deep-research-manual.md supporting_text: 'Analysis reveals concerning overlap patterns with complete redundancy (Jaccard=1.0) in condition set 3 and significant overlaps requiring consolidation'