ARBA00087037 laminin-121 trimer (GO:0005608)

id: ARBA00087037
description: >-
  Assigns GO:0005608 (laminin-121 trimer) through two condition sets, each a conjunction of three CATH
  FunFams with fungi excluded. Set 1 matches laminin subunit beta-2 and set 2 matches laminin subunit
  gamma-1.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00087037
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 2.10.25.10:FF:000011
      curie: CATH.FunFam:2.10.25.10:FF:000011
      label: Cadherin EGF LAG seven-pass G-type receptor
      negated: false
    - condition_type: FUNFAM
      value: 2.10.25.10:FF:000209
      curie: CATH.FunFam:2.10.25.10:FF:000209
      label: Laminin subunit alpha 5
      negated: false
    - condition_type: FUNFAM
      value: 2.170.300.10:FF:000004
      curie: CATH.FunFam:2.170.300.10:FF:000004
      label: Laminin subunit beta 1
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      875. Swiss-Prot matches: P55268 (LAMB2), P15800 (Lamb2), Q61292 (Lamb2). Experimental annotation
      to GO:0005608 laminin-121 trimer or an is_a/part_of descendant (QuickGO): P55268 LAMB2 GO:0005608
      laminin-121 trimer IPI PMID:10964500 (UniProt); Q61292 Lamb2 GO:0005608 laminin-121 trimer IDA PMID:20566382
      (MGI).
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 2.10.25.10:FF:000067
      curie: CATH.FunFam:2.10.25.10:FF:000067
      label: Laminin subunit gamma 1
      negated: false
    - condition_type: FUNFAM
      value: 2.10.25.10:FF:000105
      curie: CATH.FunFam:2.10.25.10:FF:000105
      label: laminin subunit gamma-1
      negated: false
    - condition_type: FUNFAM
      value: 2.10.25.10:FF:000415
      curie: CATH.FunFam:2.10.25.10:FF:000415
      label: Laminin subunit gamma 1
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: true
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      180. Swiss-Prot matches: P11047 (LAMC1), P02468 (Lamc1). No experimental annotation; curated non-experimental
      annotation (QuickGO): P02468 Lamc1 GO:0005608 laminin-121 trimer TAS PMID:21421915 (GO_Central);
      P11047 LAMC1 GO:0005608 laminin-121 trimer TAS PMID:21421915 (GO_Central).
  go_annotations:
  - go_id: GO:0005608
    go_label: laminin-121 trimer
    aspect: CC
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2025-03-21'
  modified_date: '2026-07-18'
  source_condition_set_count: 2
  retrieved_date: '2026-11-09'
review_summary: >-
  Both live condition sets were examined. Set 1 matches three Swiss-Prot entries, all laminin subunit
  beta-2 (human P55268, rat P15800, mouse Q61292); human and mouse LAMB2 are experimentally annotated
  to laminin-121 trimer. Set 2 matches two Swiss-Prot entries, laminin subunit gamma-1 of human (P11047)
  and mouse (P02468), both annotated to the term by TAS. GO defines laminin-121 as the alpha1, beta2,
  gamma1 complex, so both families are subunits of it. Gamma-1 is also a subunit of other laminin trimers;
  the rule records only this one.
action: ACCEPT
action_rationale: >-
  Each condition set identifies one chain of the laminin-121 trimer and the reviewed matches are curated
  to the exact term. Confidence is limited by the small number of reviewed matches (three and two) against
  875 and 180 unreviewed matches, and by set 2 resting on TAS rather than experimental evidence.
go_specificity:
  assessment: APPROPRIATE
  notes: >-
    The reviewed matches of both sets are curated to GO:0005608 itself: P55268 IPI PMID:10964500, Q61292
    IDA PMID:20566382, P11047 and P02468 TAS PMID:21421915.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0005608
  label: laminin-121 trimer
  assessment: CORRECT
  correct_examples:
  - P55268
  - Q61292
  - P11047
  - P02468
  notes: >-
    P55268 LAMB2 GO:0005608 IPI PMID:10964500 (UniProt); Q61292 Lamb2 GO:0005608 IDA PMID:20566382 (MGI);
    P15800 Lamb2 GO:0005608 ISO GO_REF:0000121 (RGD); P11047 LAMC1 and P02468 Lamc1 GO:0005608 TAS PMID:21421915
    (GO_Central). GO:0005608 definition (QuickGO): a laminin complex composed of alpha1, beta2 and gamma1
    polypeptide chains.
confidence: 0.7
references:
- id: PMID:10964500
  title: >-
    Posttranslational modifications and beta/gamma chain associations of human laminin alpha1 and laminin
    alpha5 chains: purification of laminin-3 from placenta.
- id: PMID:21421915
  title: 'Basement membranes: cell scaffoldings and signaling platforms.'
- id: PMID:15979864
  title: A simplified laminin nomenclature.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule requires cadherin, laminin beta and netrin domains, which cannot co-occur in a laminin chain.
  correction: >-
    The conditions are FunFams of the CATH laminin EGF-like superfamily 2.10.25.10; a FunFam name is the
    name of one member, not a statement that the matched protein is a cadherin or a netrin. The live conjunctions
    match laminin chains.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - >-
    Live set 1 (2.10.25.10:FF:000011 AND 2.10.25.10:FF:000209 AND 2.170.300.10:FF:000004, NOT Fungi):
    Swiss-Prot matches P55268, P15800, Q61292, all LAMB2
  - >-
    Live set 2 (2.10.25.10:FF:000067 AND 2.10.25.10:FF:000105 AND 2.10.25.10:FF:000415, NOT Fungi): Swiss-Prot
    matches P11047, P02468, both LAMC1
- date: '2026-11-10'
  withdrawn_claim: The three conditions were assessed as separate, unrelated domain families.
  correction: >-
    The conditions of a set are a conjunction; what matters is the set of proteins that match all of them.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    Swiss-Prot query on the full conjunction of live set 1 returns 3 entries, of live set 2 returns 2
    entries (UniProtKB, 2026-11-10)
- date: '2026-11-10'
  withdrawn_claim: The rule predicts 0 proteins, so the target architecture may not exist.
  correction: >-
    The UniProt ARBA API reports zero protein counts for this rule although its sets match reviewed and
    unreviewed entries; the zero is not a count of matches.
  error_type: UNEXAMINED_RULE
  evidence:
  - >-
    Live set 1: 3 Swiss-Prot and 875 unreviewed matches; live set 2: 2 Swiss-Prot and 180 unreviewed matches
    (UniProtKB, 2026-11-10)
- date: '2026-11-10'
  withdrawn_claim: Literature contradicts the rule.
  correction: The curated annotations of the matched proteins support it.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - UniProtKB:P55268 GO:0005608 IPI PMID:10964500
  - UniProtKB:Q61292 GO:0005608 IDA PMID:20566382
  - UniProtKB:P11047 GO:0005608 TAS PMID:21421915
- date: '2026-11-10'
  withdrawn_claim: >-
    The condition set recorded was 2.10.25.10:FF:000011 AND 2.10.25.10:FF:000065 AND 2.10.25.10:FF:000333,
    with no taxon condition.
  correction: The live rule has two different three-FunFam sets, each with NOT Fungi.
  error_type: STALE_RULE_VERSION
  evidence:
  - >-
    https://rest.uniprot.org/arba/ARBA00087037 retrieved 2026-11-09, modifiedDate 2026-07-18, two condition
    sets