Pangenome Collection
kbase_ke_pangenome
Tenant: KBase · Snapshot 2026-04-29T21:35:53.838483+00:00
Schema status
discoveredCuration status
curatedSource
berdl-spark-connect://metrics.berdl.kbase.us:443Philosophy
Enable comparative genomics at scale. Understand core vs accessory genome content, functional distributions, and evolutionary patterns across bacterial and archaeal species. Answer questions about what makes species unique and what they share.
Citation & Attribution
Provider: KBase, DOE
Cite as: Arkin AP et al. (2018) KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36:566-569
DOI: 10.1038/nbt.4163
Website: https://www.kbase.us/
Scale
Schema Browser
Tables (23)
alphaearth_embeddings_all_years bakta_amr bakta_annotations bakta_db_xrefs bakta_pfam_domains eggnog_mapper_annotations gapmind_pathways gene gene_cluster gene_genecluster_junction genome genome_ani gtdb_metadata gtdb_species_clade gtdb_taxonomy_r214v1 interproscan_domains interproscan_go interproscan_pathways ncbi_env pangenome phylogenetic_tree phylogenetic_tree_distance_pairs sample
bakta_db_xrefs
| Column | Type | Description |
|---|
Sample Queries
Get species with most genomes
SELECT
s.GTDB_species,
p.no_genomes,
p.no_core,
p.no_aux_genome,
s.mean_intra_species_ANI
FROM kbase_ke_pangenome.pangenome p
JOIN kbase_ke_pangenome.gtdb_species_clade s
ON p.gtdb_species_clade_id = s.gtdb_species_clade_id
ORDER BY p.no_genomes DESC
LIMIT 20
Get functional annotations for a species
SELECT
e.COG_category,
e.Description,
COUNT(*) as gene_count
FROM kbase_ke_pangenome.gene g
JOIN kbase_ke_pangenome.eggnog_mapper_annotations e
ON g.gene_id = e.gene_id
WHERE g.gtdb_species_clade_id = 's__Escherichia_coli--RS_GCF_000005845.2'
GROUP BY e.COG_category, e.Description
ORDER BY gene_count DESC
LIMIT 20
Get genomes for a species with quality metrics
SELECT
g.genome_id,
g.ncbi_biosample_id,
m.checkm_completeness,
m.checkm_contamination,
m.genome_size,
m.gc_percentage
FROM kbase_ke_pangenome.genome g
LEFT JOIN kbase_ke_pangenome.gtdb_metadata m
ON g.genome_id = m.accession
WHERE g.gtdb_species_clade_id = 's__Escherichia_coli--RS_GCF_000005845.2'
LIMIT 100
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Do metal-resistance functions in the global microbiome reflect phylogenetic constraint (conserved in lineages) or enviro...
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Self-Sufficiency, Anaerobic Toolkit, and Cultivation Bias in Clay-Confined Cultured Bacterial Genomes
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Subsurface Bacillota_B Specialization
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Gene Function Ecological Agora
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Gene-Resolution Metal Cross-Resistance Across Diverse Bacteria
Is the genetic architecture of metal cross-resistance conserved across phylogenetically diverse bacteria, or is it rewir...
Ecotype Functional Differentiation
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Metagenome-Prioritized Phage Cocktails for Crohn's Disease and IBD
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Plant Microbiome Ecotypes
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Genotype × Condition → Phenotype Prediction from ENIGMA Growth Curves
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Acinetobacter baylyi ADP1 Data Explorer
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SSO Subsurface Community Ecology — Spatial Structure, Functional Gradients, and Hydrogeological Drivers
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Carbon Source Utilization Predicts Ecology and Lifestyle in Pseudomonas
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CF Protective Microbiome Formulation Design
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PGP Gene Distribution Across Environments & Pangenomes
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Environmental Resistome at Pangenome Scale
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AMR Co-Fitness Support Networks
What genes are co-regulated with antimicrobial resistance (AMR) genes across growth conditions, and do these "support ne...
Counter Ion Effects on Metal Fitness Measurements
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Field vs Lab Gene Importance in *Desulfovibrio vulgaris* Hildenborough
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Metabolic Capability vs Metabolic Dependency
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Within-Species AMR Strain Variation
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Pan-Bacterial Metal Fitness Atlas
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The Pan-Bacterial Essential Metabolome
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ADP1 Deletion Collection Phenotype Analysis
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Pan-Bacterial AMR Gene Landscape
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Contamination Gradient vs Functional Potential in ENIGMA Communities
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Ecotype Correlation Analysis
What drives gene content similarity between bacterial genomes: environmental similarity or phylogenetic relatedness?
Web of Microbes Data Explorer
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Ecotype Reanalysis: Environmental-Only Samples
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Condition-Specific Respiratory Chain Wiring in ADP1
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Temporal Core Genome Dynamics
How does core genome composition change over sampling time, and do genes transition in and out of core status?
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COG Functional Category Analysis
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The 5,526 Costly + Dispensable Genes
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AlphaEarth Embeddings, Geography & Environment Explorer
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Aromatic Catabolism Support Network in ADP1
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Metabolic Capability vs Dependency
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Co-fitness Predicts Co-inheritance in Bacterial Pangenomes
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BacDive Isolation Environment × Metal Tolerance Prediction
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Pangenome Openness Analysis
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Fitness Cost of Antimicrobial Resistance Genes
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Atlas Pages
Claims
Entry point for reusable evidence-backed statements that can be cited across topics, directions, hypotheses, and data products.
claimMetal-specific genes remain core-enriched
Metal-specific genes are functionally distinct from general stress genes but remain enriched in the core genome.
claimLab fitness can predict field ecology
Several projects suggest that lab-measured fitness signals can align with environmental abundance or isolation context when validation data are available.
claimAMR mechanism composition is environment-structured
AMR mechanisms differ by environment, making resistance ecology a field and context problem rather than only a clinical annotation problem.
claimEcotype analyses need rigor gates before translation
Ecotype-derived target lists can collapse under leakage, confound, and independent-evidence checks, so translation requires explicit gates.
claimLanthanide-dependent methylotrophy is widespread and soil-linked
XoxF markers are far more common than canonical MxaF markers across the BERDL pangenome, with strong soil/sediment enrichment and important marker-calibration caveats.
claimPangenome openness shapes functional opportunity
Pangenome openness and gene-content class affect which functions are stable, variable, mobile, or available for niche adaptation.
claimProphage density predicts AMR repertoire breadth
Pangenome-scale prophage marker density is a strong species-level predictor of AMR breadth, while gene-level AMR-prophage proximity is weaker and threshold-sensitive.
claimMetal type diversity predicts ecological niche breadth
Genus-level metal resistance type diversity predicts broader ecological niche breadth after phylogenetic control, while total AMR burden is less informative.
conflictEcotype labels versus translational leakage
Ecotype labels are reusable stratification products, but translational target lists can collapse when labels and outcomes share leaked or confounded features.
conflictMetal specificity versus general stress
Metal fitness hits include both specific metal biology and broad stress response, so engineering targets need specificity filters and counter-ion controls.
conflictMetal-AMR co-selection readiness
BERIL has the pieces to test metal-AMR co-selection, but the current evidence is a strong opportunity rather than a resolved result.
metaBERDL Data Atlas
Entry point for BERDL tenants, collections, data types, derived products, join recipes, reuse patterns, and missing complementary data.
metaDerived Data Reuse Graph
Canonical Atlas page for project-to-project reuse, derived products, output artifacts, consumers, and review routes.
data tenantKBase Tenant and Foundational Genome Data
KBase-provided genome, pangenome, phenotype, and ModelSEED resources that form the core comparative-genomics substrate.
data tenantKEScience Tenant and Fitness Evidence
Fitness Browser and related KEScience resources that provide experiment-backed genotype-to-phenotype evidence.
data tenantENIGMA Tenant and Contaminated-Site Context
ENIGMA CORAL and related contaminated-site data that connect microbial genomics and communities to DOE field environments.
data collectionPangenome Collection
Genome and pangenome tables for comparative genomics, conservation, openness, annotation, and cross-project derived products.
data collectionFitness Browser Collection
RB-TnSeq fitness evidence used to validate gene function, stress response, essentiality, cofitness, and pathway dependency.
data typeGenomes and Pangenomes
Data type lens for genome metadata, pangenome structure, annotations, and species-level comparative genomics.
data typeFitness Phenotypes
Data type lens for RB-TnSeq phenotypes, condition-specific gene effects, cofitness, essentiality, and pathway dependency.
data typeGenes, Proteins, and Annotations
Gene and protein identifiers, functional annotation, literature coverage, orthology, and controlled vocabulary layers used to connect raw genomes to interpretable biology.
data typeMetabolism, Biochemistry, and Pathways
Biochemical reference data and predicted or measured metabolic capabilities that support pathway-level interpretation and community design.
data typeEnvironment, Geochemistry, and Ecology
Environmental samples, coordinates, geochemistry, sample metadata, and ecology-facing observations used to validate laboratory predictions in the field.
data typeMulti-Omics, Embeddings, and Molecular Profiles
Metabolomics, proteomics, trait profiles, embeddings, and other matrix-style summaries that create reusable sample or organism representations.
data typePhage, Mobile Elements, and Defense
Host-specific phage browsers, pathogen genome views, and mobile-element signals used to reason about host range, defense, resistance, and engineered interventions.
derived productMetal Tolerance Scores
Reusable species and gene-level metal tolerance signals derived from metal fitness projects and environmental validation work.
derived productEcotype Assignments
Reusable within-species or community ecotype labels that support environmental validation, microbiome stratification, and downstream hypothesis tests.
derived productEnvironment Harmonization Labels
Reusable environment category and coordinate-quality labels that make cross-collection ecology joins safer.
derived productDark Gene Prioritization Tables
Reusable ranked dark-gene candidates, covering sets, and experiment plans derived from fitness, pangenome, annotation, and ecology evidence.
derived productFunctional Innovation KO Atlas
Reusable clade-level functional innovation and acquisition-depth outputs from the ecological agora project.
derived productAMR Fitness Profiles
Reusable AMR mechanism, conservation, environment, and fitness-cost signals for resistance ecology questions.
derived productPangenome Openness Metrics
Reusable openness and conservation metrics that connect gene-content architecture to function and ecology.
join recipeGenome-Fitness-Pangenome Join
Reusable join pattern that connects gene families, genome conservation, and RB-TnSeq fitness phenotypes.
derived productCF Formulation Scores
Reusable formulation scoring outputs for CF airway community design and Pseudomonas competition analysis.
data gapRare Earth Fitness Data Gap
Rare-earth-element fitness experiments appear absent, making cross-metal inference a prediction task rather than validated biology.
metaResearch Directions
Entry point for high-value research opportunities synthesized from existing BERIL evidence, data products, and gaps.
directionGene targets for critical-mineral bioprocessing
Use metal-specific fitness signals, annotations, modules, and structures to prioritize genes for bioleaching and biorecovery.
directionMetal-AMR co-selection at contaminated sites
Test whether metal contamination selects for AMR genes, mechanisms, or support networks across DOE-relevant environments.
directionRare-earth gene discovery via cross-metal inference
Use cross-metal response structure to rank candidates for first rare-earth-element fitness experiments.
directionFitness-validated community design
Design microbial communities using tolerance, metabolic capability, measured dependency, and risk annotations.
directionDerived data product catalog
Make high-value project outputs discoverable, reusable, and reviewable as first-class Atlas data objects.
metaTestable Hypotheses
Entry point for concrete hypotheses that can become projects, analyses, or experiments.
hypothesisBakta reannotation resolves novel metal families
Updated Bakta annotations explain a subset of previously novel metal-important gene families.
hypothesisStructures support metal-binding or transport roles
Top metal-specific candidates have predicted structures or topology consistent with metal binding, transport, or regulation.
hypothesisMetal contamination co-selects AMR mechanisms
Metal-contaminated environments carry higher AMR burden or different AMR mechanism composition after controlling for taxonomy and site context.
hypothesisMetal tolerance scores predict field isolation context
Species with higher metal tolerance scores are enriched in metal-associated isolation or contaminated-site contexts.
hypothesisOpen pangenomes carry broader pathway diversity
Species with more open pangenomes have broader metabolic pathway repertoires after controlling for genome count and taxonomy.
hypothesisDerived product reuse predicts observatory value
Derived products reused across projects are better indicators of observatory value than raw project count alone.
metaAtlas Review Queue
Maintainer queue for deepening flagship topics, promoting reusable products, and resolving Atlas tensions.
methodNew Project Integration Pattern
Procedure for integrating newly completed projects into the BERIL Atlas without turning topic pages into project-summary dumps.
opportunityRare-Earth RB-TnSeq Design
Design the first rare-earth fitness experiment by ranking candidate genes from cross-metal specificity, conservation, annotation, and structure evidence.
opportunityMetal-AMR Site Co-Selection Analysis
Test whether metal contamination at BER-relevant sites co-selects antibiotic resistance mechanisms using metal fitness, AMR profiles, and environmental metadata.
opportunityEcotype Label Validation Benchmark
Build a benchmark that tests whether ecotype labels survive stricter metadata, batch, and holdout validation.
opportunityFunctional Innovation KO Atlas Reuse Test
Test whether the Functional Innovation KO Atlas helps explain pangenome, pathway, or plant-microbiome signals beyond generic annotation summaries.
opportunityDark Gene Structure Prioritization
Prioritize dark gene families for mechanistic review by joining fitness, cofitness, annotation novelty, and AlphaFold structure signals.
opportunityPangenome Openness Confounder Audit
Audit whether openness-function relationships remain after controlling for taxonomy, genome quality, sampling density, and annotation completeness.
opportunityPhage Host-Range Reuse Map
Map where phage and mobile-element project outputs can become reusable host-range, defense, or genome-plasticity products.
opportunityPlant Microbiome Function Validation
Validate whether plant microbiome functional signals persist across ecotype labels, pangenome context, and environmental metadata.
opportunityDerived Product Readiness Burn-Down
Review candidate and promoted derived products to close missing consumers, artifacts, caveats, and review routes before they become default inputs.
personExpertise Map
Topic-to-reviewer routing scaffold based on project ownership and source provenance.
atlasBERIL Atlas
Entry point for the BERIL Atlas over projects, data, claims, directions, hypotheses, methods, and contributor provenance.
metaTopic Landscape
Entry point for broad science and application syntheses that connect BERIL projects to claims, directions, hypotheses, and data.
topicCritical Minerals and Metal Biology
Progressive synthesis of metal fitness, tolerance, validation, and critical-mineral research opportunities.
topicAMR, Resistance Ecology, and Co-selection
Synthesis of AMR gene distribution, fitness cost, cofitness support networks, environment structure, and metal co-selection opportunities.
topicPangenome Architecture and Gene-Content Evolution
Cross-project synthesis of pangenome openness, core/accessory structure, functional composition, conservation, and gene-content tradeoffs.
topicFitness-Validated Gene Function
Synthesis of essential genes, metabolic dependency, ICA modules, dark genes, and functional annotation repair through fitness evidence.
topicMicrobial Ecotypes, Environment, and Field Validation
Synthesis of species-level ecotypes, environmental embeddings, lab-field validation, ENIGMA ecology, and metadata limitations.
topicHost Microbiome Translation
Synthesis of IBD phage targeting, formulation design, metabolomics caveats, patient stratification, and intervention cost accounting.
topicPlant Microbiome Function and Agriculture
Synthesis of plant-associated microbial function, beneficial/pathogenic duality, compartment structure, PGP markers, and pangenome ecology.
topicMobile Elements, Phage, and Genome Plasticity
Synthesis of phage ecology, prophage signals, defense systems, mobile-element gene flow, and intervention relevance.
topicMetabolic Capability, Dependency, and Community Design
Synthesis of GapMind capability, fitness dependency, metabolic models, community ecology, and design-ready derived data.
Atlas Reuse
Metal Tolerance Scores
promoted · 3 downstream projects
label_setEcotype Assignments
promoted · 2 downstream projects
label_setEnvironment Harmonization Labels
promoted · 2 downstream projects
metric_tablePangenome Openness Metrics
candidate · 1 downstream projects
profile_tableAMR Fitness Profiles
promoted · 1 downstream projects
candidate_listDark Gene Prioritization Tables
promoted · 1 downstream projects
rankingCF Formulation Scores
candidate · 0 downstream projects
atlas_tableFunctional Innovation KO Atlas
candidate · 0 downstream projects
partially resolvedEcotype labels versus translational leakage
Ecotype labels are reusable stratification products, but translational target lists can collapse when labels and outcomes share leaked or confounded features.
partially resolvedMetal specificity versus general stress
Metal fitness hits include both specific metal biology and broad stress response, so engineering targets need specificity filters and counter-ion controls.
unresolvedMetal-AMR co-selection readiness
BERIL has the pieces to test metal-AMR co-selection, but the current evidence is a strong opportunity rather than a resolved result.