ARBA00089395

id: ARBA00089395
description: 'Predicts spermine transmembrane transport function for proteins containing CATH FunFam 1.20.1250.20:FF:000011 domain in Taphrinomycotina fungi'
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00089395
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 1.20.1250.20:FF:000011
      curie: CATH.FunFam:1.20.1250.20:FF:000011
      label: ''
      negated: false
    - condition_type: TAXON
      value: Taphrinomycotina
      curie: NCBITaxon:451866
      label: Taphrinomycotina
      negated: false
    notes: ''
  go_annotations: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: ''
  modified_date: ''
  entries:
  - id: 1.20.1250.20:FF:000011
    type: FUNFAM
    appears_in_condition_sets:
    - 1
review_summary: 'This rule presents significant concerns due to its novel annotation status, extremely narrow taxonomic scope, and zero protein coverage. The combination of a specific CATH FunFam domain with spermine transport function in Taphrinomycotina lacks clear experimental validation. The rule appears to be speculative and may represent over-annotation without sufficient biological evidence.'
action: DEPRECATE
action_rationale: 'Recommended for deprecation due to: 1) Zero protein coverage indicating potential issues with rule conditions, 2) Novel GO annotation not supported by InterPro2GO mappings, 3) Extremely narrow taxonomic restriction without clear biological justification, 4) Lack of accessible evidence linking the specific CATH FunFam domain to spermine transport function, 5) High risk of false positive annotations without experimental validation of the domain-function relationship.'
suggested_modifications: []
parsimony:
  assessment: PARSIMONIOUS
  notes: 'Rule contains only a single condition set with one domain condition plus taxonomic restriction, representing minimal complexity. However, parsimony alone does not validate biological accuracy.'
literature_support:
  assessment: WEAK
  notes: 'Limited literature support found. GO term definition references PMID:15637075 but specific evidence linking the CATH FunFam domain to spermine transport in Taphrinomycotina is lacking.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00089395/ARBA00089395-deep-research-manual.md
    supporting_text: 'Evidence Gaps - No access to specific domain architecture or functional annotation - Limited literature support beyond the GO term definition - No specific experimental evidence for this domain-function relationship in Taphrinomycotina'
condition_overlap:
  assessment: NONE
  notes: 'No domain overlap analysis possible as rule contains only a single domain condition. No redundancy concerns from domain overlap perspective.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00089395/ARBA00089395-analysis.yaml
    supporting_text: 'Summary: Only 1 domain condition(s) in entire rule'
go_specificity:
  assessment: APPROPRIATE
  notes: 'GO:1903710 "spermine transmembrane transport" is appropriately specific for the claimed function. The term is well-defined and not overly broad or narrow.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00089395/ARBA00089395-deep-research-manual.md
    supporting_text: 'The GO term GO:1903710 "spermine transmembrane transport" was defined based on GO_REF:0000069 and PMID:15637075, indicating this is a well-established biological process.'
taxonomic_scope:
  assessment: TOO_NARROW
  notes: 'Restriction to Taphrinomycotina appears unjustifiably narrow. Spermine transport is a fundamental cellular process present across diverse organisms. No clear biological rationale for restricting this function to this specific fungal subphylum.'
  supported_by:
  - reference_id: file:rules/arba/ARBA00089395/ARBA00089395-deep-research-manual.md
    supporting_text: 'The restriction to Taphrinomycotina seems quite narrow. Is there evidence that spermine transport mechanisms are unique to this fungal subphylum?'
confidence: 0.1
references:
- id: file:rules/arba/ARBA00089395/ARBA00089395-deep-research-manual.md
  title: Manual deep research analysis
  findings:
  - statement: 'Rule covers zero proteins indicating potential issues with conditions'
  - statement: 'GO:1903710 represents novel annotation not in InterPro2GO mappings'
  - statement: 'Taxonomic restriction to Taphrinomycotina lacks clear biological justification'
  - statement: 'No accessible evidence linking CATH FunFam domain to spermine transport function'
supported_by:
- reference_id: file:rules/arba/ARBA00089395/ARBA00089395-analysis.yaml
  supporting_text: 'No redundant annotations. 1 novel annotation(s) not in ipr2go. Novel annotations: - GO:1903710'
- reference_id: file:rules/arba/ARBA00089395/ARBA00089395.enriched.json
  supporting_text: 'reviewedProteinCount: 0, unreviewedProteinCount: 0'