Geb system

traitmech:000287 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Geb locus that can protect bacteria from bacteriophage infection.

Trait evidence (5)

DOI:10.1101/2025.01.08.631966
Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).

Mordret et al. directly name Geb among six Streptomyces systems that increased resistance to at least one phage.
DOI:10.1101/2025.01.08.631966
The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted

Mordret et al. motivate a conservative system-level record that does not assert a resolved Geb trigger, effector output, or universal pathway.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses

The DefenseFinder model registry maps the named Geb system to the Mordret et al. antiphage-system discovery preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Geb__GebA1 | | Geb

The DefenseFinder HMM inventory records GebA1 in the Geb model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Geb__GebA2 | | Geb

The DefenseFinder HMM inventory records GebA2 in the Geb model namespace.

Geb loci confer bacterial phage defense

Conservative system-level sketch linking possession of a Geb locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.

NONMECHANISTIC · The graph captures Geb as a named anti-phage system with GebA1 and GebA2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.

Edge evidence

Geb locus contributes to restricted phage propagation RO:0002326
DefenseFinder maps Geb to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs GebA1 and GebA2 HMM profile entries in the Geb model namespace.
- DOI:10.1101/2025.01.08.631966 Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). Mordret et al. directly name Geb among six Streptomyces systems that restricted at least one phage.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses The DefenseFinder registry maps Geb itself to the Mordret et al. bacterial antiphage-system discovery preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Geb__GebA1 | | Geb The DefenseFinder HMM inventory records GebA1 in the Geb model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Geb__GebA2 | | Geb The DefenseFinder HMM inventory records GebA2 in the Geb model namespace.
restricted phage propagation confers Geb system METPO:2007700
Geb-mediated phage restriction realizes the Geb system trait.
- DOI:10.1101/2025.01.08.631966 Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). Mordret et al. directly name Geb among six systems that increased resistance to at least one phage.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses DefenseFinder records Geb as a named system from the Mordret et al. antiphage discovery preprint.
Geb system is a phage defense system rdfs:subClassOf
Geb system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses | DefenseFinder associates Geb with the Mordret et al. bacterial antiphage-system discovery preprint.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1101/2025.01.08.631966

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

Geb EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
GebA1 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
GebA2 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 Geb phage triggers and effector outputs before minting narrower Geb mechanism children.

KNOWLEDGE GAP OPEN geb-mechanism-gap · raised by codex · 2026-09-19

Attached to causal_graphs#geb_locus_restricts_phage

Mordret et al. and DefenseFinder support Geb as a named anti-phage system with GebA1 and GebA2 HMM profile entries, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.

Curation history

2026-09-19T17:00:41Z · MINTED_TRAITMECH_ID · codex
Minted Geb system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v164.
2026-09-19T17:39:40Z · ADDRESSED_PR_REVIEW · codex
Resolved PR #1073 review issues #1074 and #1075 by making the Geb subclass evidence snippet self-supporting and replacing unsupported GebA1-or-GebA2 profile-choice wording with wording limited to the DefenseFinder HMM inventory.
2026-09-19T18:00:25Z · ADDRESSED_PR_REVIEW · codex
Resolved PR #1073 review issue #1076 by replacing abstract-only Geb validation support with Mordret full-text snippets that directly name Geb among the six phage-restricting systems.