What this entity is
Canonical name: SEED. 1
Known aliases: No additional aliases are specified in the source reports. 1,2
Stable external identifier: No stable external identifier is specified in the source reports. 1,2
SEED is a functional annotation resource used alongside KEGG, TIGRFam, and PFam to derive enrichment-based function predictions from fitness modules. 1 In the metabolic-capability study, SEED subsystem annotations served as a proxy for pathway membership when matching GapMind pathway predictions to gene-fitness data, which refines SEED’s role from functional interpretation to pathway-level integration. 2
Key facts
The analysis used SEED-derived enrichment as one evidence source for interpreting independent component analysis (ICA) fitness modules across 32 organisms. 1
The study generated 6,691 function predictions for hypothetical proteins, including predictions based on enrichment from SEED together with KEGG, TIGRFam, and PFam. 1
The 6,691 predictions comprised 2,455 family-backed predictions, representing 37%, and 4,236 module-only predictions. 1
These predictions were interpreted as evidence for biological-process involvement rather than proof of a specific gene-level molecular function or KEGG KO assignment. 1
SEED therefore contributes functional-context evidence to the study’s cofitness-network-architecture analysis, while the held-out benchmark found that ortholog transfer was substantially stronger than module-based approaches for specific gene-level function prediction. 1
The results connect SEED-supported module interpretation with cross-organism conservation across 1.15M bidirectional-best-hit pairs, 13,402 ortholog groups, and 156 module families spanning at least 2 organisms. 1
For pathway-dependency analysis, SEED-proxy mapping enabled classification of complete pathways as active, intermediate, or latent, but the report cautions that related subsystem annotations can create false-positive pathway-membership assignments; direct GapMind per-step gene assignments would improve precision. This qualifies the earlier use of SEED as functional-context evidence rather than contradicting it. 2
Two GapMind pathways, deoxyribonate and myoinositol, lacked matching SEED subsystem role descriptions and were excluded from all analyses; full-name phenylalanine and tyrosine were recovered through phe and tyr abbreviation matching, while alanine was excluded because fewer than 3 SEED-annotated genes met the minimum coverage threshold. 2
See the full source summaries: Pan-bacterial Fitness Modules via Independent Component Analysis and Metabolic Capability vs Metabolic Dependency. 1,2
Related topics include gene-essentiality, pangenome-integration, and cofitness-network-architecture. 1