Gao-Upx system

traitmech:000358 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Gao_Upx locus represented by DefenseFinder as a single-profile model requiring Gao_Upx__UpxA.

Trait evidence (4)

PMID:32855333
By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.

Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Gao_Upx | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes

The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Gao_Upx Gao_Upx 1 1 Gao_Upx__UpxA

The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Gao_Upx__UpxA | Gao_Upx__UpxA | Gao_Upx | Custom | 250 |

The DefenseFinder HMM inventory records Gao_Upx__UpxA under Gao_Upx.

Gao-Upx loci confer bacterial phage defense

Conservative system-level sketch linking possession of a Gao_Upx locus to Gao et al. antiviral cassette defense without asserting the unresolved UpxA component activity.

NONMECHANISTIC · The graph captures Gao-Upx as a named DefenseFinder single-profile Gao-family system while leaving natural hosts, UpxA protein function, phage triggers, and direct effector activity unresolved.

Edge evidence

Gao_Upx locus contributes to Gao 2020 antiviral cassette defense RO:0002326
DefenseFinder maps Gao_Upx to the Gao et al. systematic antiphage-system discovery paper and models it as a single-profile system requiring UpxA.
- PMID:32855333 By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. Gao et al. support bacteriophage protection by widespread antiviral gene cassettes.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Gao_Upx | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Gao_Upx Gao_Upx 1 1 Gao_Upx__UpxA The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Gao_Upx__UpxA | Gao_Upx__UpxA | Gao_Upx | Custom | 250 | The DefenseFinder HMM inventory records Gao_Upx__UpxA under Gao_Upx.
Gao 2020 antiviral cassette defense confers Gao-Upx system METPO:2007700
Gao_Upx-associated antiviral cassette defense realizes the Gao-Upx system trait.
- PMID:32855333 By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. Gao et al. support bacteriophage protection by widespread antiviral gene cassettes.
Gao-Upx system is a phage defense system rdfs:subClassOf
Gao-Upx system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Gao_Upx | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Gao_Upx Gao_Upx 1 1 Gao_Upx__UpxA The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1126/science.aba0372

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

Gao_Upx RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Gao_Upx__UpxA 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 Gao_Upx natural hosts, UpxA component function, phage triggers, and effector activity before minting narrower Gao_Upx mechanism children.

KNOWLEDGE GAP OPEN gao-upx-mechanism-gap · raised by codex · 2026-09-22

Attached to causal_graphs#gao_upx_locus_restricts_phage

Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Upx as a single-profile system. The exact natural host breadth, UpxA component identity, phage trigger, and profile-to-activity mapping remain unresolved.

Curation history

2026-09-22T07:33:14Z · MINTED_TRAITMECH_ID · codex
Minted Gao-Upx 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_v235.