ARBA00090252 ribosomal large subunit export from nucleus (GO:0000055)

View original ARBA rule on UniProt

Type: ARBA
Status: IN_PROGRESS
Action: UNDECIDED

Description

Assigns GO:0000055 (ribosomal large subunit export from nucleus) to two groups of budding-yeast ribosomal proteins: ubiquitin-ribosomal protein eL40 fusions in Saccharomycotina, and ribosomal protein uL1 (L10a) in Saccharomycetes. Each condition set requires two CATH FunFams and a taxon.

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

No domain overlap table is shown: the cached overlap analysis for this version of the review is not available. Run just analyze-rule ARBA00090252 and re-render to add it.

Review Summary

Both live condition sets were examined. Set 2 (uL1) is supported: Saccharomyces cerevisiae RPL1A and RPL1B carry GO:0000055 with IMP evidence from SGD. Set 1 (eL40) has no manual support: its two reviewed matches, RPL40A and RPL40B, carry the term only through this rule. Nothing checked shows the eL40 annotation to be wrong, so the rule is left undecided on that set.

Action Rationale

Set 2 rests on a curated experimental annotation of the yeast protein. Set 1 rests on no manual annotation that could be found, and no published result was checked that either supports or excludes a role for eL40 in export. A decision on set 1 needs the yeast eL40 literature to be read.

GO Annotations

GO:0000055 - ribosomal large subunit export from nucleus
Aspect: BP

Annotation Assessments

UNDECIDED GO_TERM GO:0000055 - ribosomal large subunit export from nucleus
Matched proteins: ; incorrect:
Correct examples: P0CX43, P0CX44

Set 2: P0CX43 (RPL1A) and P0CX44 (RPL1B), GO:0000055 IMP, PMID:31439809, assigned by SGD. Set 1: P0CH08 (RPL40A) and P0CH09 (RPL40B) carry GO:0000055 only as IEA GO_REF:0000117 with ARBA00090252 as source. Source: QuickGO annotation search, retrieved 2026-11-09.

Rule Definition

Condition Sets

Condition Set 1

3 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0000055, 0 of those by a manual-evidence GO annotation. 83 unreviewed entries match.

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)
Notes:

UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0000055, 2 of those by a manual-evidence GO annotation. 61 unreviewed entries match.

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

References (1)

Raw YAML

View Source YAML 
id: ARBA00090252
description: >-
  Assigns GO:0000055 (ribosomal large subunit export from nucleus) to two groups of budding-yeast
  ribosomal proteins: ubiquitin-ribosomal protein eL40 fusions in Saccharomycotina, and ribosomal
  protein uL1 (L10a) in Saccharomycetes. Each condition set requires two CATH FunFams and a taxon.
status: IN_PROGRESS
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: Saccharomycotina
      curie: NCBITaxon:147537
      label: Saccharomycotina
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0000055, 0
      of those by a manual-evidence GO annotation. 83 unreviewed entries match.
    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: Saccharomycetes
      curie: NCBITaxon:4891
      label: Saccharomycetes
      negated: false
    notes: >-
      UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0000055, 2
      of those by a manual-evidence GO annotation. 61 unreviewed entries match.
    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:
  - go_id: GO:0000055
    go_label: ribosomal large subunit export from nucleus
    aspect: BP
  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: 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: 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: 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: PREDICTS
      target_id: GO:0000055
      containment: 0.15
      jaccard_similarity: 0.04
      intersection_count: 6
      exclusive_count: 34
  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: 2
review_summary: >-
  Both live condition sets were examined. Set 2 (uL1) is supported: Saccharomyces cerevisiae RPL1A
  and RPL1B carry GO:0000055 with IMP evidence from SGD. Set 1 (eL40) has no manual support: its two
  reviewed matches, RPL40A and RPL40B, carry the term only through this rule. Nothing checked shows
  the eL40 annotation to be wrong, so the rule is left undecided on that set.
action: UNDECIDED
action_rationale: >-
  Set 2 rests on a curated experimental annotation of the yeast protein. Set 1 rests on no manual
  annotation that could be found, and no published result was checked that either supports or excludes
  a role for eL40 in export. A decision on set 1 needs the yeast eL40 literature to be read.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0000055
  label: ribosomal large subunit export from nucleus
  assessment: UNDECIDED
  correct_examples:
  - P0CX43
  - P0CX44
  notes: >-
    Set 2: P0CX43 (RPL1A) and P0CX44 (RPL1B), GO:0000055 IMP, PMID:31439809, assigned by SGD. Set
    1: P0CH08 (RPL40A) and P0CH09 (RPL40B) carry GO:0000055 only as IEA GO_REF:0000117 with ARBA00090252
    as source. Source: QuickGO annotation search, retrieved 2026-11-09.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    Ribosomal proteins are cargo, not export factors, so annotating them with large-subunit export
    is a biological misconception, and the literature contradicts the rule.
  correction: >-
    For uL1 a curated experimental annotation says otherwise: SGD annotates RPL1A and RPL1B to GO:0000055
    by IMP. The only source given for the claim was the review's own research note.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - >-
    QuickGO: UniProtKB:P0CX43 (RPL1A) and UniProtKB:P0CX44 (RPL1B), GO:0000055, IMP, PMID:31439809,
    assigned by SGD.
  - >-
    PMID:31439809, title: The L1 stalk is required for efficient export of nascent large ribosomal
    subunits in yeast.
- date: '2026-11-10'
  withdrawn_claim: Only 12-28% of the targeted proteins carry the GO term, so the rule has poor specificity.
  correction: >-
    Those percentages were computed for each FunFam on its own across all of Swiss-Prot. The rule
    requires two FunFams together with a taxon; the reviewed proteins that satisfy a whole condition
    set all carry the term.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    UniProtKB release 2026_04: set 1 (both eL40 FunFams AND Saccharomycotina) matches 2 reviewed entries,
    set 2 (both uL1 FunFams AND Saccharomycetes) matches 4; all 6 carry GO:0000055.
- date: '2026-11-10'
  withdrawn_claim: >-
    InterPro entries IPR027312 and IPR037700 already cover this GO term more appropriately, so the
    rule is unnecessary.
  correction: >-
    Those entries are different protein families (Sda1 and nucleoporin NUP88/NUP82) and share no proteins
    with the rule's FunFams, so they cannot stand in for it.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'InterPro API: IPR027312 name Sda1; IPR037700 name Nucleoporin NUP88/NUP82.'
  - >-
    The old file's own overlap table recorded intersection 0 between each of these entries and each
    FunFam of the rule.
- date: '2026-11-10'
  withdrawn_claim: The two conditions inside a condition set overlap by 64-90%, so the rule is redundant.
  correction: >-
    Conditions within a set are combined with AND. Overlap between them is expected and does not make
    the set redundant.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    UniProt ARBA API, ARBA00090252: each condition set lists two FunFam conditions and one taxon condition,
    all required.
- date: '2026-11-10'
  withdrawn_claim: The rule is restricted to Fungi (set 1) and Dikarya (set 2).
  correction: The live rule restricts set 1 to Saccharomycotina and set 2 to Saccharomycetes.
  error_type: STALE_RULE_VERSION
  evidence:
  - >-
    UniProt ARBA API, ARBA00090252, modified 2026-07-18: taxon conditions Saccharomycotina (NCBITaxon:147537)
    and Saccharomycetes (NCBITaxon:4891).
references:
- id: PMID:31439809
  title: The L1 stalk is required for efficient export of nascent large ribosomal subunits in yeast
  findings:
  - statement: Reference for the SGD IMP annotation of GO:0000055 on RPL1A and RPL1B.