The EcoCyc Database in 2021

Front Microbiol. 2021 Jul 28:12:711077. doi: 10.3389/fmicb.2021.711077. eCollection 2021.


The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

Keywords: EcoCyc; Escherichia coli; drug efflux transporters; gene regulation; metabolism; model-organism database.