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ModelSEED Biochemistry

kbase_msd_biochemistry

Primary

Philosophy

Enable metabolic modeling and pathway analysis. Map genes to reactions, understand metabolic capabilities, and support flux balance analysis.

Data sources: ModelSEED KEGG MetaCyc

Citation & Attribution

Provider: ModelSEED / Henry Lab

Website: https://modelseed.org/

Scale

4
tables

Schema Browser

Tables (5)

reaction 56,012 molecule 45,708 reagent 262,517 structure 97,490 reaction_similarity

molecule 45,708 rows

Column Type Description
id string **Primary Key**. ModelSEED compound ID (e.g., `seed.compound:cpd00001`)
name string Compound name
abbreviation string Short name
formula string Molecular formula
charge int Net charge
mass float Molecular mass
deltag float Gibbs free energy of formation
deltagerr float Uncertainty in deltaG
smiles string SMILES structure
inchikey string InChIKey identifier
pka string Acid dissociation constants
pkb string Base dissociation constants
source string Data source

Sample Queries

Get reactions

SELECT *
FROM kbase_msd_biochemistry.reaction
LIMIT 20

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