AbiL system

traitmech:000340 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a two-component AbiL-family locus represented by DefenseFinder as mandatory AbiL__AbiLi and AbiL__AbiLii profiles.

Trait evidence (7)

DOI:10.1016/S0168-1656(98)00175-8
Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis

Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI.
DOI:10.1093/femsre/fuag009
13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu

The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems.
DOI:10.1093/femsre/fuag009
AbiL has been included among systems such as PARIS, which feature an ABC ATPase and a TOPRIM nuclease

The FEMS review places AbiL among predicted ATPase-plus-TOPRIM systems but does not resolve the AbiLi and AbiLii molecular activities.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiL | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

The DefenseFinder article registry maps the named AbiL model namespace to the Chopin et al. lactococcal abortive-infection review.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiL AbiL 2 2 AbiL__AbiLi, AbiL__AbiLii

The DefenseFinder rules table models AbiL as a two-component system requiring the AbiL__AbiLi and AbiL__AbiLii profiles.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiL__AbiLi | AbiL__AbiLi | AbiL | Custom | 20 |

The DefenseFinder HMM inventory records AbiL__AbiLi under the AbiL model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiL__AbiLii | AbiL__AbiLii | AbiL | Custom | 20 |

The DefenseFinder HMM inventory records AbiL__AbiLii under the AbiL model namespace.

AbiL loci confer abortive-infection phage defense

Conservative system-level sketch linking possession of a DefenseFinder AbiL locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, AbiLi or AbiLii molecular activity, or AbiL-to-PARIS mechanistic correspondence.

NONMECHANISTIC · The graph captures AbiL as a named lactococcal abortive-infection system with DefenseFinder AbiL__AbiLi and AbiL__AbiLii HMM profiles while leaving its direct phage trigger, the exact AbiLi and AbiLii activities, the relationship between the mandatory and suffixed HMM rows, and the similarity of its route to PARIS unresolved.

Edge evidence

AbiL locus contributes to restricted phage propagation RO:0002326
The DefenseFinder AbiL namespace is modeled as a two-profile AbiL__AbiLi plus AbiL__AbiLii system, and AbiL is a confirmed lactococcal Abi-like system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiL AbiL 2 2 AbiL__AbiLi, AbiL__AbiLii The DefenseFinder rules table models AbiL as a two-component system requiring the AbiL__AbiLi and AbiL__AbiLii profiles.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiL__AbiLi | AbiL__AbiLi | AbiL | Custom | 20 | The DefenseFinder HMM inventory records AbiL__AbiLi under the AbiL model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiL__AbiLii | AbiL__AbiLii | AbiL | Custom | 20 | The DefenseFinder HMM inventory records AbiL__AbiLii under the AbiL model namespace.
- DOI:10.1093/femsre/fuag009 13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems.
restricted phage propagation confers AbiL system METPO:2007700
Restriction of phage propagation realizes the AbiL abortive-infection system possession trait.
- DOI:10.1016/S0168-1656(98)00175-8 Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI.
- DOI:10.1093/femsre/fuag009 13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems.
AbiL system is a abortive infection system rdfs:subClassOf
AbiL system possession is an abortive-infection-system trait.
- DOI:10.1016/S0168-1656(98)00175-8 Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiL | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiL model namespace to the Chopin et al. lactococcal abortive-infection review.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/S0168-1656(98)00175-8

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (3)

AbiL RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiL__AbiLi RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
AbiL__AbiLii RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

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

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 AbiL phage trigger, AbiLi and AbiLii activities, AbiLi2 and AbiLii2 HMM row relationships, and ATPase-plus-TOPRIM mechanism before minting narrower AbiL mechanism children.

KNOWLEDGE GAP OPEN abil-trigger-and-effector-gap · raised by codex · 2026-09-21

Attached to causal_graphs#abil_locus_restricts_lactococcal_phage

Deng et al. support AbiL as a lactococcal phage abortive infection system, the FEMS review lists AbiL among confirmed two-component lactococcal Abi-like systems, and DefenseFinder represents AbiL with mandatory AbiL__AbiLi and AbiL__AbiLii profiles. The same pinned HMM inventory also contains AbiL__AbiLi2 and AbiL__AbiLii2 rows that are not in the pinned two-profile rule, and the FEMS review summarizes unresolved ATPase and TOPRIM predictions. This first system-level record therefore leaves the direct phage trigger, exact AbiLi and AbiLii molecular activities, accessory-model interpretation, AbiL-to-PARIS similarity, growth-arrest or cell-death route, and phage escape routes unresolved.

Evidence

https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiL__AbiLi2 | AbiL__AbiLi2 | AbiL | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiL__AbiLii2 | AbiL__AbiLii2 | AbiL | Custom | 20 |
DOI:10.1093/femsre/fuag009
AbiL has been included among systems such as PARIS, which feature an ABC ATPase and a TOPRIM nuclease
DOI:10.1093/femsre/fuag009
No significant sequence similarity was found between the second components of AbiL and PARIS

Curation history

2026-09-21T17:17:22Z · MINTED_TRAITMECH_ID · codex
Minted AbiL 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_v217.