GAPS1 system

traitmech:000371 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Gamma-Mobile-Trio island-associated GAPS1 locus that can be triggered by a phage capsid protein to induce cell dormancy.

Trait evidence (6)

DOI:10.1038/s41564-024-01840-5
GMT islands' cargoes contain various anti-phage defence systems

Mahata et al. identify GMT islands as carriers of anti-phage defense-system cargo.
DOI:10.1038/s41564-024-01840-5
We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy

Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy.
DOI:10.1101/2023.03.28.534373
Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools

The bioRxiv version of Mahata et al. is the DOI cited in DefenseFinder's GAPS1 article-registry row.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
GAPS1 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools

The DefenseFinder article registry maps the named GAPS1 system to the Mahata et al. preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS1 GAPS1 1 1 GAPS1__GAPS1

The DefenseFinder rules table models GAPS1 as a single-profile system requiring GAPS1__GAPS1.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS1__GAPS1 | GAPS1__GAPS1 | GAPS1 | Custom | 100 |

The DefenseFinder HMM inventory records GAPS1__GAPS1 under the GAPS1 model namespace.

GAPS1 loci induce cell dormancy during phage defense

Conservative system-level sketch connecting the named GAPS1 locus model and the phage-capsid-protein-triggered dormancy phenotype to the GAPS1 system trait.

NONMECHANISTIC · The graph captures GAPS1 as a named GMT-island anti-phage defense system represented in DefenseFinder by a single GAPS1__GAPS1 profile while leaving its universal host range, the molecular activity of the GAPS1 component, and the exact capsid-protein trigger unresolved.

Edge evidence

GAPS1 locus contributes to GAPS1 system RO:0002326
DefenseFinder records GAPS1 as a named system and models it as a single-profile GAPS1__GAPS1 rule.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md GAPS1 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools The DefenseFinder article registry maps the named GAPS1 system to the Mahata et al. preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv GAPS1 GAPS1 1 1 GAPS1__GAPS1 The DefenseFinder rules table models GAPS1 as a single-profile system requiring GAPS1__GAPS1.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | GAPS1__GAPS1 | GAPS1__GAPS1 | GAPS1 | Custom | 100 | The DefenseFinder HMM inventory records GAPS1__GAPS1 under the GAPS1 model namespace.
GAPS1-induced cell dormancy confers GAPS1 system METPO:2007700
Phage-capsid-protein-triggered cell dormancy is the characterized output that realizes the GAPS1 system trait.
- DOI:10.1038/s41564-024-01840-5 We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy.
GAPS1 system is a phage defense system rdfs:subClassOf
GAPS1 system possession is a phage-defense-system trait.
- DOI:10.1038/s41564-024-01840-5 We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md GAPS1 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools The DefenseFinder article registry maps the named GAPS1 system to the Mahata et al. preprint.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/s41564-024-01840-5

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

GAPS1 EXACT_SYNONYM · DOI:10.1038/s41564-024-01840-5
GAPS1__GAPS1 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 GAPS1 component activity and natural-host exemplars before minting narrower GAPS traits.

KNOWLEDGE GAP OPEN gaps1-trigger-sibling-gap · raised by codex · 2026-09-24

Attached to causal_graphs#gaps1_capsid_triggered_dormancy

Mahata et al. support GAPS1 as one GMT-island anti-phage defense system triggered by a phage capsid protein to induce cell dormancy, and DefenseFinder represents GAPS1 as one GAPS1__GAPS1 profile. This first system-level record does not assert the GAPS1 component's molecular activity, the capsid trigger identity, or a universal GAPS1 host range.

Evidence

DOI:10.1038/s41564-024-01840-5
We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS1 GAPS1 1 1 GAPS1__GAPS1

Curation history

2026-09-25T04:19:09Z · MINTED_TRAITMECH_ID · codex
Minted GAPS1 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; the replacement placeholder is reserved in proposals/metpo_traitmech_v248.
2026-09-26T11:02:35Z · UPDATED_DISCUSSION · codex
Resolved GitHub issue #1274 by narrowing stale GAPS1 sibling-boundary references to GAPS2/GAPS6 after GAPS4 was split into its own TraitRecord.
2026-09-26T11:26:43Z · UPDATED_DISCUSSION · codex
Narrowed stale GAPS1 sibling-boundary references to GAPS6 after GAPS2 was split into its own TraitRecord.
2026-09-26T11:58:15Z · UPDATED_DISCUSSION · codex
Resolved the remaining stale GAPS1 sibling-boundary reference after GAPS6 was split into its own TraitRecord.