identifier: traitmech:000318 label: AbiD system definition: An abortive infection system in which an organism possesses an abiD-family locus represented by the DefenseFinder AbiD__AbiD profile and exemplified by the Lactococcus lactis subsp. lactis KR5 pBF61 determinant whose abiD open reading frame confers an abortive phage infection phenotype with reduced plating efficiency, plaque size, and c2 phage burst size. definition_source: DOI:10.1128/aem.61.5.2023-2026.1995 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiD synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: PMID:7646042 snippet: A 6.3-kb fragment from pBF61 in Lactococcus lactis subsp. lactis KR5 was cloned and found to confer an abortive phage infection (Abi+) phenotype notes: McLandsborough et al. cloned the pBF61-derived fragment from Lactococcus lactis subsp. lactis KR5 and showed that it conferred an Abi phenotype. - reference: PMID:7646042 snippet: exhibiting a reduction in efficiency of plating and plaque size for small isometric- and prolate-headed bacteriophages sk1 and c2, respectively, and to produce a 10-fold decrease in c2 phage burst size notes: McLandsborough et al. measured reduced plating efficiency, plaque size, and c2 phage burst size from the pBF61 AbiD determinant. - reference: PMID:7646042 snippet: Phage adsorption was not significantly reduced notes: McLandsborough et al. distinguished AbiD activity from a phage-adsorption block. - reference: PMID:7646042 snippet: An open reading frame of 1,098 bp was sequenced and designated abiD notes: McLandsborough et al. named the abiD open reading frame within the pBF61 determinant. - reference: PMID:7646042 snippet: Tn5 mutagenesis confirmed that abiD was required for the Abi+ phenotype notes: McLandsborough et al. verified that the abiD open reading frame is required for the abortive-infection phenotype. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiD | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiD model namespace to a lactococcal abortive-infection review. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiD\tAbiD\t1\t1\tAbiD__AbiD" notes: The DefenseFinder rules table models AbiD as a one-component system requiring the AbiD__AbiD profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiD__AbiD | AbiD__AbiD | AbiD | Custom | 90 |' notes: The DefenseFinder HMM inventory records AbiD__AbiD under the AbiD model namespace. canonical_examples: - taxon_id: NCBITaxon:1358 taxon_label: Lactococcus lactis note: McLandsborough et al. cloned the pBF61 AbiD determinant from Lactococcus lactis subsp. lactis KR5 and showed that the abiD open reading frame is required for abortive-infection phage resistance. reference: DOI:10.1128/aem.61.5.2023-2026.1995 causal_graphs: - graph_id: abid_locus_reduces_lactococcal_phage_burst title: AbiD activity restricts lactococcal phages description: Conservative system-level sketch linking an abiD-family locus to AbiD antiphage activity, reduced lactococcal phage propagation, and abortive-infection system possession without asserting the unresolved molecular target. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiD as a named DefenseFinder single-profile abortive-infection system whose pBF61 prototype restricts sk1 and c2 phages. It leaves the direct phage trigger, AbiD molecular function, cell-death or growth-arrest route, natural locus breadth, and phage escape routes unresolved. nodes: - node_id: abid_locus label: abiD locus node_type: GENETIC_ELEMENT description: An abiD-family abortive-infection locus represented by the DefenseFinder AbiD__AbiD profile. - node_id: abid_antiphage_activity label: AbiD antiphage activity node_type: BIOLOGICAL_PROCESS description: Abortive-infection phage resistance mediated by the AbiD system. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced completion of lactococcal phage propagation in an AbiD-containing infected host cell. - node_id: abid_system_trait label: AbiD system node_type: TRAIT grounding: traitmech:000318 description: Possession of a genome-encoded AbiD abortive-infection phage-defense system. - node_id: abortive_infection_system_trait label: abortive infection system node_type: TRAIT grounding: traitmech:000214 description: Possession of a genome-encoded abortive-infection phage-defense system. edges: - subject: abid_locus predicate: contributes to predicate_id: RO:0002326 object: abid_antiphage_activity description: The abiD-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiD as a one-profile system. evidence: - reference: PMID:7646042 snippet: Tn5 mutagenesis confirmed that abiD was required for the Abi+ phenotype notes: McLandsborough et al. show that the abiD open reading frame is required for the Abi phenotype. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiD\tAbiD\t1\t1\tAbiD__AbiD" notes: The DefenseFinder rules table models AbiD as a one-component system requiring the AbiD__AbiD profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiD__AbiD | AbiD__AbiD | AbiD | Custom | 90 |' notes: The DefenseFinder HMM inventory records AbiD__AbiD under the AbiD model namespace. - subject: abid_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: AbiD activity restricts tested small isometric- and prolate-headed lactococcal phages. evidence: - reference: PMID:7646042 snippet: exhibiting a reduction in efficiency of plating and plaque size for small isometric- and prolate-headed bacteriophages sk1 and c2, respectively, and to produce a 10-fold decrease in c2 phage burst size notes: McLandsborough et al. connect the AbiD determinant to reduced sk1 and c2 plating or plaque size and reduced c2 burst size. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abid_system_trait description: Restriction of lactococcal phage propagation realizes the AbiD abortive-infection trait. evidence: - reference: PMID:7646042 snippet: A 6.3-kb fragment from pBF61 in Lactococcus lactis subsp. lactis KR5 was cloned and found to confer an abortive phage infection (Abi+) phenotype notes: McLandsborough et al. classify the pBF61 AbiD determinant phenotype as abortive phage infection. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiD | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiD model namespace to a lactococcal abortive-infection review. - subject: abid_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiD system possession is an abortive-infection-system trait. evidence: - reference: PMID:7646042 snippet: A 6.3-kb fragment from pBF61 in Lactococcus lactis subsp. lactis KR5 was cloned and found to confer an abortive phage infection (Abi+) phenotype notes: McLandsborough et al. place AbiD in the abortive-infection class of phage defense. discussions: - discussion_id: abid-trigger-and-effector-gap prompt: Resolve the AbiD phage trigger, molecular activity, and direct arrest target before minting narrower AbiD mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: McLandsborough et al. support AbiD as a named lactococcal abortive-infection determinant whose cloned pBF61 fragment reduces sk1 plating efficiency and c2 burst size, whose abiD open reading frame is required for the Abi phenotype, and whose activity does not primarily block phage adsorption. DefenseFinder represents AbiD with a one-profile rule, but this first system-level record leaves the phage trigger, AbiD molecular function, direct host or phage target, growth-arrest or cell-death route, and phage escape routes unresolved. attaches_to: - causal_graphs#abid_locus_reduces_lactococcal_phage_burst posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T20:30:20Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiD system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v195. llm_assisted: true