identifier: traitmech:000413
label: Tab system
definition: A phage defense system in which an organism or resident prophage possesses
  a Tab virion-assembly-inhibition locus that expresses the Tab tail-assembly-blocking
  protein, blocks assembly of invading phage tails, prevents infectious virion formation,
  and protects the bacterial community from phage spread.
definition_source: DOI:10.1038/s41467-024-45892-x
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: Tab
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1038/s41467-024-45892-x
evidence:
- reference: DOI:10.1038/s41467-024-45892-x
  snippet: a type of anti-phage defence that interferes with the virion assembly pathway
    of invading phages
  notes: Patel et al. define the Tab-associated anti-phage defence as interference
    with the virion assembly pathway of invading phages.
- reference: DOI:10.1038/s41467-024-45892-x
  snippet: The protein that mediates this defence, which we call Tab
  notes: Patel et al. name the protein mediating this prophage defence Tab.
- reference: DOI:10.1038/s41467-024-45892-x
  snippet: blocks assembly of the phage tail, thus preventing formation of infectious
    virions
  notes: Patel et al. show that Tab blocks phage-tail assembly and thereby prevents
    production of infectious virions.
- reference: DOI:10.1038/s41467-024-45892-x
  snippet: there is no release of infectious phage progeny, and the bacterial community
    is thereby protected from a phage epidemic
  notes: Patel et al. connect Tab-mediated inhibition of infectious phage release
    to protection of the bacterial community from a phage epidemic.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| Tab | 10\.1038/s41467-024-45892-x | Anti-phage defence through inhibition
    of virion assembly |'
  notes: The pinned DefenseFinder article registry maps the named Tab system to the
    Patel et al. virion-assembly-inhibition paper. The pinned HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md)
    and pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv)
    do not list Tab, so this row is name-to-paper evidence rather than model-component
    evidence.
causal_graphs:
- graph_id: tab_blocks_virion_assembly
  title: Tab blocks phage virion assembly
  description: Conservative system-level sketch linking a Tab prophage-associated
    locus to inhibition of invading phage tail assembly, blocked infectious virion
    formation, and Tab system possession.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures Tab as a prophage-encoded virion-assembly-inhibition
    system without asserting the full host range, full sensitive-phage range, Tab
    counter-defence specificity, or profile-to-component DefenseFinder modeling.
  nodes:
  - node_id: tab_locus
    label: Tab prophage locus
    node_type: GENETIC_ELEMENT
    description: A prophage locus expressing Tab, a phage tail assembly blocker.
  - node_id: tab_virion_assembly_inhibition
    label: Tab-mediated virion assembly inhibition
    node_type: BIOLOGICAL_PROCESS
    description: Tab-mediated interference with the virion assembly pathway of invading
      phages.
  - node_id: phage_tail_assembly
    label: phage tail assembly
    node_type: BIOLOGICAL_PROCESS
    description: Assembly of the phage tail during productive virion morphogenesis.
  - node_id: infectious_virion_formation
    label: infectious virion formation
    node_type: BIOLOGICAL_PROCESS
    description: Formation and release of infectious phage progeny.
  - node_id: tab_system_trait
    label: Tab system
    node_type: TRAIT
    grounding: traitmech:000413
    description: Possession of a genome-encoded Tab phage-defense system.
  - node_id: phage_defense_system
    label: phage defense system
    node_type: TRAIT
    grounding: traitmech:000209
    description: Possession of one or more genome-encoded immune systems that inhibit
      bacteriophage infection.
  edges:
  - subject: tab_locus
    predicate: enables
    predicate_id: RO:0002327
    object: tab_virion_assembly_inhibition
    description: A prophage-associated tab locus expresses the Tab protein that mediates
      virion-assembly inhibition.
    evidence:
    - reference: DOI:10.1038/s41467-024-45892-x
      snippet: The protein that mediates this defence, which we call Tab
      notes: Patel et al. name Tab as the protein mediating this prophage anti-phage
        defence.
  - subject: tab_virion_assembly_inhibition
    predicate: mitigates
    predicate_id: METPO:2007407
    object: phage_tail_assembly
    description: Tab-mediated virion assembly inhibition blocks assembly of invading
      phage tails.
    evidence:
    - reference: DOI:10.1038/s41467-024-45892-x
      snippet: blocks assembly of the phage tail, thus preventing formation of infectious
        virions
      notes: Patel et al. connect Tab to blockade of phage-tail assembly.
  - subject: tab_virion_assembly_inhibition
    predicate: mitigates
    predicate_id: METPO:2007407
    object: infectious_virion_formation
    description: By blocking tail assembly, Tab-mediated defence prevents formation
      and release of infectious phage progeny.
    evidence:
    - reference: DOI:10.1038/s41467-024-45892-x
      snippet: there is no release of infectious phage progeny, and the bacterial
        community is thereby protected from a phage epidemic
      notes: Patel et al. report no infectious phage progeny release under Tab-mediated
        defence.
  - subject: tab_virion_assembly_inhibition
    predicate: confers
    predicate_id: METPO:2007700
    object: tab_system_trait
    description: Virion assembly inhibition realizes the Tab system trait.
    evidence:
    - reference: DOI:10.1038/s41467-024-45892-x
      snippet: Tab-mediated inhibition of virion assembly provides a new type of anti-phage
        defence
      notes: Patel et al. frame Tab-mediated virion assembly inhibition as a new anti-phage
        defence type.
  - subject: tab_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Tab system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1038/s41467-024-45892-x
      snippet: a type of anti-phage defence that interferes with the virion assembly
        pathway of invading phages
      notes: Patel et al. place Tab in anti-phage defence by virion assembly pathway
        interference.
discussions:
- discussion_id: tab-defensefinder-model-gap
  prompt: Resolve Tab host breadth, sensitive-phage breadth, counter-defence specificity,
    and DefenseFinder HMM/rules coverage before minting narrower Tab mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Patel et al. support Tab as a prophage-encoded anti-phage defence protein
    that blocks invading phage-tail assembly and prevents release of infectious phage
    progeny, while the pinned DefenseFinder article registry names a Tab system. The
    pinned DefenseFinder HMM inventory and rules table have no Tab rows, and the evidence
    does not yet resolve host breadth, target-phage breadth, counter-defence specificity,
    or profile-to-activity modeling.
  evidence:
  - reference: DOI:10.1038/s41467-024-45892-x
    snippet: blocks assembly of the phage tail, thus preventing formation of infectious
      virions
    notes: Patel et al. support Tab blockade of phage-tail assembly.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| Tab | 10\.1038/s41467-024-45892-x | Anti-phage defence through inhibition
      of virion assembly |'
    notes: The pinned DefenseFinder article registry maps the named Tab system to
      the Patel et al. virion-assembly-inhibition paper. The pinned HMM inventory
      (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md)
      and pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv)
      do not list Tab, so this row is name-to-paper evidence rather than model-component
      evidence.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    notes: The pinned DefenseFinder HMM inventory does not list Tab, leaving profile-level
      components unresolved.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list Tab, leaving rule-level
      detection criteria unresolved.
  attaches_to:
  - causal_graphs#tab_blocks_virion_assembly
  posed_by: codex
  posed_date: '2026-09-27'
curation_history:
- timestamp: '2026-09-27T17:41:07Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted Tab system as a DOI-backed GENOMICS TraitRecord under phage defense
    system after an ignored-and-hidden duplicate review found no exact live TraitMech,
    METPO, history, or prior proposal record; kept the graph at prophage-locus and
    virion-assembly-inhibition level because the pinned DefenseFinder article row
    is not backed by pinned HMM or rules rows; the replacement placeholder is reserved
    in proposals/metpo_traitmech_v290.
  llm_assisted: true