AbiD system

traitmech:000318 · CLASS · PROPOSED

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.

Trait evidence (8)

PMID:7646042
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

McLandsborough et al. cloned the pBF61-derived fragment from Lactococcus lactis subsp. lactis KR5 and showed that it conferred an Abi phenotype.
PMID:7646042
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

McLandsborough et al. measured reduced plating efficiency, plaque size, and c2 phage burst size from the pBF61 AbiD determinant.
PMID:7646042
Phage adsorption was not significantly reduced

McLandsborough et al. distinguished AbiD activity from a phage-adsorption block.
PMID:7646042
An open reading frame of 1,098 bp was sequenced and designated abiD

McLandsborough et al. named the abiD open reading frame within the pBF61 determinant.
PMID:7646042
Tn5 mutagenesis confirmed that abiD was required for the Abi+ phenotype

McLandsborough et al. verified that the abiD open reading frame is required for the abortive-infection phenotype.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiD | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

The DefenseFinder article registry maps the named AbiD model namespace to a lactococcal abortive-infection review.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiD AbiD 1 1 AbiD__AbiD

The DefenseFinder rules table models AbiD as a one-component system requiring the AbiD__AbiD profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiD__AbiD | AbiD__AbiD | AbiD | Custom | 90 |

The DefenseFinder HMM inventory records AbiD__AbiD under the AbiD model namespace.

AbiD activity restricts lactococcal phages

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.

NONMECHANISTIC · 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.

Edge evidence

abiD locus contributes to AbiD antiphage activity RO:0002326
The abiD-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiD as a one-profile system.
- PMID:7646042 Tn5 mutagenesis confirmed that abiD was required for the Abi+ phenotype McLandsborough et al. show that the abiD open reading frame is required for the Abi phenotype.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiD AbiD 1 1 AbiD__AbiD The DefenseFinder rules table models AbiD as a one-component system requiring the AbiD__AbiD profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiD__AbiD | AbiD__AbiD | AbiD | Custom | 90 | The DefenseFinder HMM inventory records AbiD__AbiD under the AbiD model namespace.
AbiD antiphage activity contributes to restricted phage propagation RO:0002326
AbiD activity restricts tested small isometric- and prolate-headed lactococcal phages.
- PMID:7646042 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 McLandsborough et al. connect the AbiD determinant to reduced sk1 and c2 plating or plaque size and reduced c2 burst size.
restricted phage propagation confers AbiD system METPO:2007700
Restriction of lactococcal phage propagation realizes the AbiD abortive-infection trait.
- PMID:7646042 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 McLandsborough et al. classify the pBF61 AbiD determinant phenotype as abortive phage infection.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiD | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiD model namespace to a lactococcal abortive-infection review.
AbiD system is a abortive infection system rdfs:subClassOf
AbiD system possession is an abortive-infection-system trait.
- PMID:7646042 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 McLandsborough et al. place AbiD in the abortive-infection class of phage defense.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1128/aem.61.5.2023-2026.1995

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (1)

AbiD RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Lactococcus lactis NCBITaxon:1358 DOI:10.1128/aem.61.5.2023-2026.1995 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.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve the AbiD phage trigger, molecular activity, and direct arrest target before minting narrower AbiD mechanism children.

KNOWLEDGE GAP OPEN abid-trigger-and-effector-gap · raised by codex · 2026-09-20

Attached to causal_graphs#abid_locus_reduces_lactococcal_phage_burst

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.

Curation history

2026-09-20T20:30:20Z · MINTED_TRAITMECH_ID · codex
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.