Comparison of the Salmonella enterica subsp. LT۲ metabolic model in biochemical databases

Metabolic models include the description of all biochemical reactions, metabolites, and metabolism genesfor a particular organism, biochemical, genetic, and genomic knowledge. We analyzed five biochemicaldatabases (Bigg, KEGG, SEED, PATRIC, and BIOCYC) commonly used for metabolic modeling andperformed pairwise comparisons to examine compatibility, incompatibility, and ambiguity of reactions,metabolites, and genes between databases. Salmonella enterica subsp. LT۲ that there's a metabolic model forit in the Bigg database. (ID BIGG: STM_v۱_۰) The SEED model is also the primary source of genomicscalemetabolic models based on microbial or plant annotation genomes. We created the metabolic model ofour reference genome using the Model SEED web server and reconstructed it in the PATRIC metabolicdatabase. (PATRIC Database ID: ۹۹۲۸۷.۱) We compared the Bigg and Seed metabolic models for the numberof reactions, metabolites, and genes. The Seed model had ۱۶۴۶ reactions, ۱۷۲۶ metabolites, and ۹۵۸ genes,and the Bigg model had ۲۵۴۵ reactions, ۱۸۰۲ metabolites, and ۱۲۷۱ genes. There were ۱۹۳۵ reactions and۱۵۴۷ metabolites in the Seed model that were not presented in the Bigg model, and conversely, there were۱۰۷۳ reactions and ۹۵۱ metabolites in the Bigg model that were not presented in the Seed model. In theSEED database, our organism had ۵۶۶ subsystems and in the PATRIC database, it had ۳۴۴ subsystems. Tofind functional proteins that are in the metabolic pathway but are not in the PATRIC database, we searchedfor organisms in the KEGG database.Conclusion: Each database uses its own naming space; when different tools are used, the same metabolitesand reactions may have different naming conventions. It is now recommended to use unique identifiers,independent of the specific databases used or referred to different namespaces. Also, manual verification ofmaps is a useful solution to eliminate inconsistencies while combining the models.

Keywords:

databases , incompatibility , name ambiguity , chemical nomenclature