📊

Fitness Browser

kescience_fitnessbrowser

Tenant: KE Science · Snapshot 2026-04-29T21:35:53.838483+00:00

Primary

Schema status

discovered

Curation status

curated

Source

berdl-spark-connect://metrics.berdl.kbase.us:443

Philosophy

Connect genotype to phenotype through systematic mutagenesis. Understand which genes are essential for growth, which provide advantages under specific conditions, and how genetic background affects fitness.

Data sources: RB-TnSeq experiments KEGG MetaCyc SEED

Citation & Attribution

Provider: Price Lab, LBNL

Cite as: Price MN et al. (2018) Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 557:503-509

DOI: 10.1038/s41586-018-0124-0

Website: https://fit.genomics.lbl.gov/

Scale

40+

organisms

1000+

experiments

90+

tables

Schema Browser

Tables (93)

besthitkegg besthitmetacyc besthitswissprot cofit compounds conservedcofit ecinfo experiment fitbyexp_acidovorax_3h11 fitbyexp_ana3 fitbyexp_azobra fitbyexp_bfirm fitbyexp_btheta fitbyexp_burk376 fitbyexp_caulo fitbyexp_cola fitbyexp_cup4g11 fitbyexp_dda3937 fitbyexp_ddia6719 fitbyexp_ddiame23 fitbyexp_dino fitbyexp_dvh fitbyexp_dyella79 fitbyexp_herbies fitbyexp_kang fitbyexp_keio fitbyexp_korea fitbyexp_koxy fitbyexp_magneto fitbyexp_marino fitbyexp_methanococcus_jj fitbyexp_methanococcus_s2 fitbyexp_miya fitbyexp_mr1 fitbyexp_pedo557 fitbyexp_phaeo fitbyexp_ponti fitbyexp_ps fitbyexp_pseudo13_gw456_l13 fitbyexp_pseudo1_n1b4 fitbyexp_pseudo3_n2e3 fitbyexp_pseudo5_n2c3_1 fitbyexp_pseudo6_n2e2 fitbyexp_psrch2 fitbyexp_putida fitbyexp_pv4 fitbyexp_ralstoniabsbf1503 fitbyexp_ralstoniagmi1000 fitbyexp_ralstoniapsi07 fitbyexp_ralstoniauw163 fitbyexp_sb2b fitbyexp_smeli fitbyexp_syne fitbyexp_syringaeb728a fitbyexp_syringaeb728a_mexbdelta fitbyexp_wcs417 gene genedomain genefeature genefitness keggcompound keggconf keggmap keggmember kgroupdesc kgroupec locusxref mediacomponents metacyccompound metacycpathway metacycpathwaycoverage metacycpathwayprimarycompound metacycpathwayreaction metacycpathwayreactionpredecessor metacycreaction metacycreactioncompound metacycreactionec organism ortholog publication reannotation reannotationec scaffoldseq seedannotation seedannotationtoroles seedclass seedreaction seedrolereaction seedroles specificphenotype specog straindataseek swissprotdesc

`cofit`

Column	Type	Description

Sample Queries

Get organisms in the fitness browser

SELECT *
FROM kescience_fitnessbrowser.organism
LIMIT 20

Get fitness scores for a gene

SELECT
  e.condition,
  f.fitness,
  f.t_score
FROM kescience_fitnessbrowser.fitness f
JOIN kescience_fitnessbrowser.experiment e
  ON f.experiment_id = e.experiment_id
WHERE f.gene_id = 'YOUR_GENE_ID'
ORDER BY ABS(f.fitness) DESC
LIMIT 20

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Atlas Pages

meta

Claims

Entry point for reusable evidence-backed statements that can be cited across topics, directions, hypotheses, and data products.

claim

Metal-specific genes remain core-enriched

Metal-specific genes are functionally distinct from general stress genes but remain enriched in the core genome.

claim

Lab 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.

claim

Prophage 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.

conflict

Lab fitness signals versus field ecology

Lab-derived fitness or tolerance scores can predict ecology in some settings, but metadata quality and field complexity limit broad generalization.

conflict

Metal 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.

conflict

Metal-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.

meta

BERDL Data Atlas

Entry point for BERDL tenants, collections, data types, derived products, join recipes, reuse patterns, and missing complementary data.

meta

Derived Data Reuse Graph

Canonical Atlas page for project-to-project reuse, derived products, output artifacts, consumers, and review routes.

data tenant

KEScience Tenant and Fitness Evidence

Fitness Browser and related KEScience resources that provide experiment-backed genotype-to-phenotype evidence.

data collection

Fitness Browser Collection

RB-TnSeq fitness evidence used to validate gene function, stress response, essentiality, cofitness, and pathway dependency.

data type

Fitness Phenotypes

Data type lens for RB-TnSeq phenotypes, condition-specific gene effects, cofitness, essentiality, and pathway dependency.

data type

Experimental Phenotypes, Traits, and Assays

Measured organism and gene behavior across laboratory conditions, including mutant fitness, growth phenotypes, utilization traits, and exometabolomic observations.

data type

Metabolism, Biochemistry, and Pathways

Biochemical reference data and predicted or measured metabolic capabilities that support pathway-level interpretation and community design.

derived product

Metal Tolerance Scores

Reusable species and gene-level metal tolerance signals derived from metal fitness projects and environmental validation work.

derived product

Dark Gene Prioritization Tables

Reusable ranked dark-gene candidates, covering sets, and experiment plans derived from fitness, pangenome, annotation, and ecology evidence.

derived product

AMR Fitness Profiles

Reusable AMR mechanism, conservation, environment, and fitness-cost signals for resistance ecology questions.

derived product

Pangenome Openness Metrics

Reusable openness and conservation metrics that connect gene-content architecture to function and ecology.

join recipe

Genome-Fitness-Pangenome Join

Reusable join pattern that connects gene families, genome conservation, and RB-TnSeq fitness phenotypes.

data gap

Rare Earth Fitness Data Gap

Rare-earth-element fitness experiments appear absent, making cross-metal inference a prediction task rather than validated biology.

meta

Research Directions

Entry point for high-value research opportunities synthesized from existing BERIL evidence, data products, and gaps.

direction

Gene targets for critical-mineral bioprocessing

Use metal-specific fitness signals, annotations, modules, and structures to prioritize genes for bioleaching and biorecovery.

direction

Metal-AMR co-selection at contaminated sites

Test whether metal contamination selects for AMR genes, mechanisms, or support networks across DOE-relevant environments.

direction

Rare-earth gene discovery via cross-metal inference

Use cross-metal response structure to rank candidates for first rare-earth-element fitness experiments.

direction

Fitness-validated community design

Design microbial communities using tolerance, metabolic capability, measured dependency, and risk annotations.

direction

Derived data product catalog

Make high-value project outputs discoverable, reusable, and reviewable as first-class Atlas data objects.

meta

Testable Hypotheses

Entry point for concrete hypotheses that can become projects, analyses, or experiments.

hypothesis

Bakta reannotation resolves novel metal families

Updated Bakta annotations explain a subset of previously novel metal-important gene families.

hypothesis

Metal contamination co-selects AMR mechanisms

Metal-contaminated environments carry higher AMR burden or different AMR mechanism composition after controlling for taxonomy and site context.

hypothesis

Metal tolerance scores predict field isolation context

Species with higher metal tolerance scores are enriched in metal-associated isolation or contaminated-site contexts.

hypothesis

Derived product reuse predicts observatory value

Derived products reused across projects are better indicators of observatory value than raw project count alone.

meta

Atlas Review Queue

Maintainer queue for deepening flagship topics, promoting reusable products, and resolving Atlas tensions.

method

New Project Integration Pattern

Procedure for integrating newly completed projects into the BERIL Atlas without turning topic pages into project-summary dumps.

opportunity

Rare-Earth RB-TnSeq Design

Design the first rare-earth fitness experiment by ranking candidate genes from cross-metal specificity, conservation, annotation, and structure evidence.

opportunity

Metal-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.

opportunity