GAPS4 system

traitmech:000379 · CLASS · PROPOSED

A phage defense system in which an organism possesses a GMT-encoded GAPS4 locus represented by DefenseFinder as a two-profile model, GAPS4__GAPS4a and GAPS4__GAPS4b, and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed in E. coli.

Trait evidence (11)

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 four anti-phage defense systems in Gamma-Mobile-Trio islands.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded Anti-Phage System.

The DefenseFinder wiki describes GAPS4 as a two-gene GMT-encoded anti-phage system.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.

The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.

The DefenseFinder wiki summarizes evidence for PDDEXK-domain GAPS4a, dual-gene requirement, and lambda-vir-associated host DNA degradation.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
The GAPS4 system in *Hafnia alvei* (GCF_902387815.1, NZ_LR699008) is composed of 2 proteins GAPS4a (WP_111329122.1) GAPS4b (WP_111329123.1)

The DefenseFinder wiki illustrates a predicted two-protein GAPS4 locus in RefSeq assembly GCF_902387815.1 on NZ_LR699008.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir

The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
subgraph Title4[Protects against] T7 T4 P1-vir Lambda-vir

The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir, and Lambda-vir in the GAPS4 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
GAPS4 | 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 GAPS4 system to the Mahata et al. preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS4 GAPS4 2 2 GAPS4__GAPS4a, GAPS4__GAPS4b

The DefenseFinder rules table models GAPS4 as a two-profile system requiring GAPS4__GAPS4a and GAPS4__GAPS4b.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS4__GAPS4a | GAPS4__GAPS4a | GAPS4 | Custom | 20 |

The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4 system namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS4__GAPS4b | GAPS4__GAPS4b | GAPS4 | Custom | 20 |

The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4 system namespace.

GAPS4 loci protect against T7, T4, P1-vir, and lambda-vir

Conservative system-level sketch linking GAPS4 locus possession to protection against T7, T4, P1-vir, and lambda-vir.

NONMECHANISTIC · The graph captures GAPS4 as a named two-profile DefenseFinder phage-defense system while leaving natural host breadth, the lambda-vir trigger of host DNA degradation, the abortive-infection mechanism, and exact GAPS4a/GAPS4b profile-to-protein correspondence unresolved.

Edge evidence

GAPS4 locus contributes to T7, T4, P1-vir, and lambda-vir protection RO:0002326
The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS4 locus from Mahata et al. to protection against T7, T4, P1-vir, and lambda-vir, and DefenseFinder models GAPS4 through GAPS4a and GAPS4b profiles.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded Anti-Phage System. The DefenseFinder wiki describes GAPS4 as a two-gene GMT-encoded anti-phage system.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}. The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md subgraph Title4[Protects against] T7 T4 P1-vir Lambda-vir The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir, and Lambda-vir in the GAPS4 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv GAPS4 GAPS4 2 2 GAPS4__GAPS4a, GAPS4__GAPS4b The DefenseFinder rules table models GAPS4 as a two-profile system requiring GAPS4__GAPS4a and GAPS4__GAPS4b.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | GAPS4__GAPS4a | GAPS4__GAPS4a | GAPS4 | Custom | 20 | The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4 system namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | GAPS4__GAPS4b | GAPS4__GAPS4b | GAPS4 | Custom | 20 | The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4 system namespace.
T7, T4, P1-vir, and lambda-vir protection confers GAPS4 system METPO:2007700
Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS4 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}. The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md subgraph Title4[Protects against] T7 T4 P1-vir Lambda-vir The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir, and Lambda-vir in the GAPS4 protects-against subgraph.
GAPS4 system is a phage defense system rdfs:subClassOf
GAPS4 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 four anti-phage defense systems in Gamma-Mobile-Trio islands.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md GAPS4 | 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 GAPS4 system to the Mahata et al. preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv GAPS4 GAPS4 2 2 GAPS4__GAPS4a, GAPS4__GAPS4b The DefenseFinder rules table models GAPS4 as a two-profile system requiring GAPS4__GAPS4a and GAPS4__GAPS4b.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

GAPS4 EXACT_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
GAPS4__GAPS4a RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
GAPS4__GAPS4b 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 GAPS4 natural host breadth, lambda-vir host-DNA-degradation triggers, abortive-infection mechanism, and exact GAPS4a/GAPS4b profile-to-protein correspondence before minting narrower GAPS4 mechanism traits.

KNOWLEDGE GAP OPEN gaps4-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#gaps4_locus_restricts_phages

Mahata et al. support GAPS4 as a GMT-encoded anti-phage defense system that protects E. coli against T7, T4, P1-vir, and lambda-vir when expressed from a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS4 as a two-profile system. Natural host breadth, the lambda-vir-specific trigger of host DNA degradation, the abortive-infection mechanism, and exact profile-to-protein correspondence remain unresolved.

Evidence

https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS4 GAPS4 2 2 GAPS4__GAPS4a, GAPS4__GAPS4b
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS4__GAPS4a | GAPS4__GAPS4a | GAPS4 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS4__GAPS4b | GAPS4__GAPS4b | GAPS4 | Custom | 20 |

Curation history

2026-09-26T10:47:13Z · MINTED_TRAITMECH_ID · codex
Minted GAPS4 system as a DOI- and DefenseFinder-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_v256.
2026-09-26T10:47:14Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed GAPS4 system canonical_examples and left them empty because the current sources support a Vibrio parahaemolyticus accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Hafnia alvei example, but not a direct native microbial isolate exemplar with experimentally verified endogenous GAPS4 activity. No paid research was used.