Pangenome Collection
kbase_ke_pangenome
Philosophy
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)
genome 293,059 gtdb_species_clade 27,690 pangenome 27,702 gtdb_metadata 293,059 gtdb_taxonomy_r214v1 293,059 gene 1,011,650,903 gene_cluster 132,531,501 gene_genecluster_junction 1,011,650,762 eggnog_mapper_annotations 93,558,330 genome_ani 421,218,641 sample 293,059 ncbi_env 4,124,801 alphaearth_embeddings_all_years 83,287 gapmind_pathways 305,471,280 phylogenetic_tree 330 bakta_annotations 132,538,155 bakta_db_xrefs 572,376,477 bakta_pfam_domains 18,807,208 bakta_amr 83,008 interproscan_domains 833,303,130 interproscan_go 266,317,724 interproscan_pathways 287,228,475 phylogenetic_tree_distance_pairs 22,570,755
genome
293,059 rows
Central genome table linking to species clades and taxonomy.
| Column | Type | Description |
|---|---|---|
genome_id |
string | **Primary Key**. Format: `RS_GCF_XXXXXXXXX.X` or `GB_GCA_XXXXXXXXX.X` |
gtdb_species_clade_id |
string | FK → `gtdb_species_clade` |
gtdb_taxonomy_id |
string | FK → `gtdb_taxonomy_r214v1` |
ncbi_biosample_id |
string | NCBI BioSample accession |
fna_file_path_nersc |
string | Path to nucleotide FASTA at NERSC |
faa_file_path_nersc |
string | Path to protein FASTA at NERSC |
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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