ARBA00090252

View original ARBA rule on UniProt

Type: ARBA
Status: COMPLETE
Action: DEPRECATE
Confidence: 1.00

Description

Rule annotates ribosomal protein components (L40, L10a) in fungi with nuclear export of ribosomal large subunit. Contains two condition sets targeting ubiquitin-ribosomal protein fusions and ribosomal proteins in fungal taxa.

Analysis Summary

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

2
Domain Pairs Analyzed
2
Recorded condition sets
1
Subset Relationships
0
Redundant Annotations

Domain Overlap Analysis Table

Interactive prediction matrix showing how row entries PREDICT column entries. Cell (i,j) shows what fraction of proteins with row domain i also have column domain j. Click cells to view intersection in UniProt. Click domain IDs to view proteins with that domain.

CS 1
Fungi 		CS 2
Dikarya 		TGT EXT
ipr2go
Ubiquitin-60S ribosomal L...
3.10.20.90:FF:000014
(50) 		ubiquitin-60S ribosomal p...
4.10.1060.50:FF:000001
(40) 		Ribosomal protein
3.30.190.20:FF:000006
(28) 		Ribosomal protein L10a
3.30.190.20:FF:000009
(29) 		ribosomal large subunit e...
GO:0000055 []
(117) 		IPR027312
IPR027312
(14) 		IPR037700
IPR037700
(9)
CS 1
Fungi 		Ubiquitin-60S ribosomal L40 fusion
3.10.20.90:FF:000014 (50) 		100%
70%
J:64%
(35)
0%
J:0%
(0)
0%
J:0%
(0)
12%
J:4%
(6)
0%
J:0%
(0)
0%
J:0%
(0)
ubiquitin-60S ribosomal protein L40
4.10.1060.50:FF:000001 (40)
88%
J:64%
(35) 		100%
0%
J:0%
(0)
0%
J:0%
(0)
15%
J:4%
(6)
0%
J:0%
(0)
0%
J:0%
(0)
CS 2
Dikarya 		Ribosomal protein
3.30.190.20:FF:000006 (28)
0%
J:0%
(0)
0%
J:0%
(0) 		100%
96%
J:90%
(27)
29%
J:6%
(8)
0%
J:0%
(0)
0%
J:0%
(0)
Ribosomal protein L10a
3.30.190.20:FF:000009 (29)
0%
J:0%
(0)
0%
J:0%
(0)
93%
J:90%
(27) 		100%
28%
J:6%
(8)
0%
J:0%
(0)
0%
J:0%
(0)
TGT ribosomal large subunit export from nucleus
GO:0000055 [] (117)
5%
J:4%
(6)
5%
J:4%
(6)
7%
J:6%
(8)
7%
J:6%
(8) 		100%
12%
J:12%
(14)
8%
J:8%
(9)
EXT
ipr2go 		IPR027312
IPR027312 (14)
0%
J:0%
(0)
0%
J:0%
(0)
0%
J:0%
(0)
0%
J:0%
(0)
100%
J:12%
(14) 		100%
0%
J:0%
(0)
IPR037700
IPR037700 (9)
0%
J:0%
(0)
0%
J:0%
(0)
0%
J:0%
(0)
0%
J:0%
(0)
100%
J:8%
(9)
0%
J:0%
(0) 		100%

Legend: Each cell shows PREDICTS % (fraction of row entry proteins that also have column entry - row PREDICTS column), Jaccard similarity (J:%), and intersection count. CS = Condition Set(s), TGT = GO annotation target.

Review Summary

This rule exhibits a fundamental biological misconception by annotating structural ribosomal protein components with a transport process (nuclear export). Ribosomal proteins L40 and L10a are structural components of the large ribosomal subunit that are transported AS CARGO during nuclear export, but they do not mediate or perform the export process itself. The rule shows poor specificity with only 12-28% of targeted proteins actually overlapping with the GO term annotation. High domain overlap within condition sets indicates redundancy. The taxonomic restriction to fungi appears arbitrary given that ribosomal export occurs in all eukaryotes.

Action Rationale

This rule should be deprecated because it represents a fundamental misunderstanding of the biological process. It incorrectly annotates structural ribosomal proteins with a transport function they do not perform. The proteins are cargo in the export process, not the export machinery. Low coverage (12-28%) indicates poor specificity, and the rule would create numerous false positive annotations. InterPro entries IPR027312 and IPR037700 already provide more appropriate coverage for this GO term with 100% containment.

External Mappings (ipr2go)

These InterPro domains also map to the rule's GO term(s) via InterPro2GO but are not part of any condition set in this rule. They may represent alternative domain signatures that predict the same function.

IPR027312
ipr2go
Maps to:
GO:0000055
14 proteins in Swiss-Prot
IPR037700
ipr2go
Maps to:
GO:0000055
9 proteins in Swiss-Prot

Rule Definition

Condition Sets

Condition Set 1

3 condition(s)

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
3.10.20.90:FF:000014 4.10.1060.50:FF:000001 50 40 35 0.636 0.700 0.875 HIGH_OVERLAP

Condition Set 2

3 condition(s)

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
3.30.190.20:FF:000006 3.30.190.20:FF:000009 28 29 27 0.900 0.964 0.931 SUBSET

Assessments

REDUNDANT

Condition set 2 shows 90% Jaccard similarity between ribosomal protein domains, indicating near-complete redundancy. Condition set 1 shows high overlap (64% Jaccard) between ubiquitin-fusion domains. The rule could be simplified, but fundamental biological issues make it unsuitable regardless.

CONTRADICTED

Literature clearly demonstrates that ribosomal proteins are structural components, not export factors. Nuclear export of ribosomal subunits is mediated by dedicated export machinery including Exportin-1/CRM1, Nmd3, and Lsg1. Ribosomal proteins are substrates (cargo) of this process, not mediators.

Supporting Evidence:

  • file:rules/arba/ARBA00090252/ARBA00090252-manual-research.md: Proteins actually involved in ribosomal large subunit nuclear export include Exportin-1, Nmd3, Lsg1, and nuclear pore components. Ribosomal proteins are structural components that become part of exported subunits but do not mediate export.
SIGNIFICANT

Condition set 2 shows 90% Jaccard similarity between ribosomal protein domains (3.30.190.20:FF:000006 and 3.30.190.20:FF:000009), indicating substantial redundancy. Condition set 1 shows 64% Jaccard overlap between ubiquitin-fusion domains. Cross-condition overlap is appropriately zero, indicating the sets target distinct protein families.

MISMATCHED

GO:0000055 describes a transport process (nuclear export), while the rule targets structural protein components. This is a categorical mismatch - the GO term describes a biological process performed by transport machinery, but the rule annotates structural components that are transported. The specificity level is irrelevant when the functional category is incorrect.

TOO_NARROW

Nuclear export of ribosomal large subunits occurs in all eukaryotes, yet this rule restricts annotations to Fungi (condition 1) and Dikarya (condition 2). If the biological annotation were correct, such taxonomic restriction would be unjustified. However, since the fundamental annotation is incorrect, the taxonomic scope issue is secondary.

References (2)

Raw YAML

View Source YAML 
id: ARBA00090252
description: 'Rule annotates ribosomal protein components (L40, L10a) in fungi with nuclear export of ribosomal large subunit. Contains two condition sets targeting ubiquitin-ribosomal protein fusions and ribosomal proteins in fungal taxa.'
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00090252
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 3.10.20.90:FF:000014
      curie: CATH.FunFam:3.10.20.90:FF:000014
      label: Ubiquitin-60S ribosomal L40 fusion
      negated: false
    - condition_type: FUNFAM
      value: 4.10.1060.50:FF:000001
      curie: CATH.FunFam:4.10.1060.50:FF:000001
      label: ubiquitin-60S ribosomal protein L40
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: ''
    pairwise_overlap:
    - condition_a: 3.10.20.90:FF:000014
      condition_b: 4.10.1060.50:FF:000001
      protein_database: SWISSPROT
      count_a: 50
      count_b: 40
      intersection_count: 35
      a_minus_b_count: 15
      b_minus_a_count: 5
      jaccard_similarity: 0.6363636363636364
      containment_a_in_b: 0.7
      containment_b_in_a: 0.875
      interpretation: HIGH_OVERLAP
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 3.30.190.20:FF:000006
      curie: CATH.FunFam:3.30.190.20:FF:000006
      label: Ribosomal protein
      negated: false
    - condition_type: FUNFAM
      value: 3.30.190.20:FF:000009
      curie: CATH.FunFam:3.30.190.20:FF:000009
      label: Ribosomal protein L10a
      negated: false
    - condition_type: TAXON
      value: Dikarya
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
    notes: ''
    pairwise_overlap:
    - condition_a: 3.30.190.20:FF:000006
      condition_b: 3.30.190.20:FF:000009
      protein_database: SWISSPROT
      count_a: 28
      count_b: 29
      intersection_count: 27
      a_minus_b_count: 1
      b_minus_a_count: 2
      jaccard_similarity: 0.9
      containment_a_in_b: 0.9642857142857143
      containment_b_in_a: 0.9310344827586207
      interpretation: SUBSET
  go_annotations: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: ''
  modified_date: ''
  entries:
  - id: 3.10.20.90:FF:000014
    type: FUNFAM
    label: Ubiquitin-60S ribosomal L40 fusion
    appears_in_condition_sets:
    - 1
    protein_count: 50
    related_entries:
    - relationship: PREDICTED_BY
      target_id: 4.10.1060.50:FF:000001
      containment: 0.875
      jaccard_similarity: 0.636
      intersection_count: 35
      exclusive_count: 5
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000006
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 50
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000009
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 50
    - relationship: EQUIV
      target_id: IPR027312
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 50
    - relationship: EQUIV
      target_id: IPR037700
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 50
    - relationship: PREDICTS
      target_id: GO:0000055
      containment: 0.12
      jaccard_similarity: 0.037
      intersection_count: 6
      exclusive_count: 44
  - id: 3.30.190.20:FF:000006
    type: FUNFAM
    label: Ribosomal protein
    appears_in_condition_sets:
    - 2
    protein_count: 28
    related_entries:
    - relationship: EQUIV
      target_id: 3.10.20.90:FF:000014
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 28
    - relationship: EQUIV
      target_id: 4.10.1060.50:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 28
    - relationship: PREDICTS
      target_id: 3.30.190.20:FF:000009
      containment: 0.964
      jaccard_similarity: 0.9
      intersection_count: 27
      exclusive_count: 1
    - relationship: EQUIV
      target_id: IPR027312
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 28
    - relationship: EQUIV
      target_id: IPR037700
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 28
    - relationship: PREDICTS
      target_id: GO:0000055
      containment: 0.286
      jaccard_similarity: 0.058
      intersection_count: 8
      exclusive_count: 20
  - id: 3.30.190.20:FF:000009
    type: FUNFAM
    label: Ribosomal protein L10a
    appears_in_condition_sets:
    - 2
    protein_count: 29
    related_entries:
    - relationship: EQUIV
      target_id: 3.10.20.90:FF:000014
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 29
    - relationship: EQUIV
      target_id: 4.10.1060.50:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 29
    - relationship: PREDICTED_BY
      target_id: 3.30.190.20:FF:000006
      containment: 0.931
      jaccard_similarity: 0.9
      intersection_count: 27
      exclusive_count: 2
    - relationship: EQUIV
      target_id: IPR027312
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 29
    - relationship: EQUIV
      target_id: IPR037700
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 29
    - relationship: PREDICTS
      target_id: GO:0000055
      containment: 0.276
      jaccard_similarity: 0.058
      intersection_count: 8
      exclusive_count: 21
  - id: 4.10.1060.50:FF:000001
    type: FUNFAM
    label: ubiquitin-60S ribosomal protein L40
    appears_in_condition_sets:
    - 1
    protein_count: 40
    related_entries:
    - relationship: PREDICTS
      target_id: 3.10.20.90:FF:000014
      containment: 0.7
      jaccard_similarity: 0.636
      intersection_count: 35
      exclusive_count: 15
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000006
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 40
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000009
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 40
    - relationship: EQUIV
      target_id: IPR027312
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 40
    - relationship: EQUIV
      target_id: IPR037700
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 40
    - relationship: PREDICTS
      target_id: GO:0000055
      containment: 0.15
      jaccard_similarity: 0.04
      intersection_count: 6
      exclusive_count: 34
  - id: IPR027312
    type: INTERPRO
    source: ipr2go
    protein_count: 14
    asserted_predicted_go_terms:
    - GO:0000055
    related_entries:
    - relationship: EQUIV
      target_id: 3.10.20.90:FF:000014
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 14
    - relationship: EQUIV
      target_id: 4.10.1060.50:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 14
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000006
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 14
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000009
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 14
    - relationship: EQUIV
      target_id: IPR037700
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 14
    - relationship: PREDICTS
      target_id: GO:0000055
      containment: 1.0
      jaccard_similarity: 0.12
      intersection_count: 14
      exclusive_count: 0
  - id: IPR037700
    type: INTERPRO
    source: ipr2go
    protein_count: 9
    asserted_predicted_go_terms:
    - GO:0000055
    related_entries:
    - relationship: EQUIV
      target_id: 3.10.20.90:FF:000014
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 9
    - relationship: EQUIV
      target_id: 4.10.1060.50:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 9
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000006
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 9
    - relationship: EQUIV
      target_id: 3.30.190.20:FF:000009
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 9
    - relationship: EQUIV
      target_id: IPR027312
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 9
    - relationship: PREDICTS
      target_id: GO:0000055
      containment: 1.0
      jaccard_similarity: 0.077
      intersection_count: 9
      exclusive_count: 0
review_summary: 'This rule exhibits a fundamental biological misconception by annotating structural ribosomal protein components with a transport process (nuclear export). Ribosomal proteins L40 and L10a are structural components of the large ribosomal subunit that are transported AS CARGO during nuclear export, but they do not mediate or perform the export process itself. The rule shows poor specificity with only 12-28% of targeted proteins actually overlapping with the GO term annotation. High domain overlap within condition sets indicates redundancy. The taxonomic restriction to fungi appears arbitrary given that ribosomal export occurs in all eukaryotes.'
action: DEPRECATE
action_rationale: 'This rule should be deprecated because it represents a fundamental misunderstanding of the biological process. It incorrectly annotates structural ribosomal proteins with a transport function they do not perform. The proteins are cargo in the export process, not the export machinery. Low coverage (12-28%) indicates poor specificity, and the rule would create numerous false positive annotations. InterPro entries IPR027312 and IPR037700 already provide more appropriate coverage for this GO term with 100% containment.'
suggested_modifications: []
parsimony:
  assessment: REDUNDANT
  notes: 'Condition set 2 shows 90% Jaccard similarity between ribosomal protein domains, indicating near-complete redundancy. Condition set 1 shows high overlap (64% Jaccard) between ubiquitin-fusion domains. The rule could be simplified, but fundamental biological issues make it unsuitable regardless.'
literature_support:
  assessment: CONTRADICTED
  notes: 'Literature clearly demonstrates that ribosomal proteins are structural components, not export factors. Nuclear export of ribosomal subunits is mediated by dedicated export machinery including Exportin-1/CRM1, Nmd3, and Lsg1. Ribosomal proteins are substrates (cargo) of this process, not mediators.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00090252/ARBA00090252-manual-research.md
    supporting_text: 'Proteins actually involved in ribosomal large subunit nuclear export include Exportin-1, Nmd3, Lsg1, and nuclear pore components. Ribosomal proteins are structural components that become part of exported subunits but do not mediate export.'
condition_overlap:
  assessment: SIGNIFICANT
  notes: 'Condition set 2 shows 90% Jaccard similarity between ribosomal protein domains (3.30.190.20:FF:000006 and 3.30.190.20:FF:000009), indicating substantial redundancy. Condition set 1 shows 64% Jaccard overlap between ubiquitin-fusion domains. Cross-condition overlap is appropriately zero, indicating the sets target distinct protein families.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00090252/ARBA00090252-analysis.yaml
    supporting_text: 'jaccard_similarity: 0.9, containment_a_in_b: 0.964, containment_b_in_a: 0.931, interpretation: SUBSET for domains 3.30.190.20:FF:000006 and 3.30.190.20:FF:000009'
go_specificity:
  assessment: MISMATCHED
  notes: 'GO:0000055 describes a transport process (nuclear export), while the rule targets structural protein components. This is a categorical mismatch - the GO term describes a biological process performed by transport machinery, but the rule annotates structural components that are transported. The specificity level is irrelevant when the functional category is incorrect.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00090252/ARBA00090252-manual-research.md
    supporting_text: 'The rule annotates ribosomal protein components with ribosomal large subunit export from nucleus. However, ribosomal proteins are COMPONENTS of the ribosome, not export factors.'
taxonomic_scope:
  assessment: TOO_NARROW
  notes: 'Nuclear export of ribosomal large subunits occurs in all eukaryotes, yet this rule restricts annotations to Fungi (condition 1) and Dikarya (condition 2). If the biological annotation were correct, such taxonomic restriction would be unjustified. However, since the fundamental annotation is incorrect, the taxonomic scope issue is secondary.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00090252/ARBA00090252-manual-research.md
    supporting_text: 'Nuclear export of ribosomal subunits occurs in all eukaryotes. If this were a valid annotation, taxonomic restriction seems arbitrary.'
confidence: 1.0
references:
- id: file:rules/arba/ARBA00090252/ARBA00090252-manual-research.md
  title: Manual research analysis of rule biological context
  findings:
  - statement: 'Rule incorrectly annotates structural ribosomal proteins with transport process'
  - statement: 'Low GO term coverage (12-28%) indicates poor specificity'
  - statement: 'High domain overlap within condition sets shows redundancy'
  - statement: 'InterPro entries IPR027312 and IPR037700 provide more appropriate coverage'
- id: file:rules/arba/ARBA00090252/ARBA00090252-analysis.yaml
  title: Quantitative domain overlap analysis
  findings:
  - statement: 'Condition set 2 domains show 90% Jaccard similarity indicating redundancy'
  - statement: 'Only 2 external InterPro mappings exist for this GO term with 100% containment'
  - statement: 'Average Jaccard similarity across all pairs is only 0.092'
supported_by: []