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

The EcoCyc Database in 2021

Ingrid M Keseler  1 , Socorro Gama-Castro  2 , Amanda Mackie  3 , Richard Billington  1 , César Bonavides-Martínez  2 , Ron Caspi  1 , Anamika Kothari  1 , Markus Krummenacker  1 , Peter E Midford  1 , Luis Muñiz-Rascado  2 , Wai Kit Ong  1 , Suzanne Paley  1 , Alberto Santos-Zavaleta  2   4 , Pallavi Subhraveti  1 , Víctor H Tierrafría  2 , Alan J Wolfe  5 , Julio Collado-Vides  2   6 , Ian T Paulsen  3 , Peter D Karp  1
Affiliations

The EcoCyc Database in 2021

Ingrid M Keseler et al. Front Microbiol. .

Abstract

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.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Curation of Gdx in EcoCyc. (A) The guanidinium:proton antiport reaction mediated by Gdx. (B) Gdx regulation by a guanidine II riboswitch.
Figure 2
Figure 2
Reactions assigned to recently characterized DNA repair proteins in EcoCyc. (A) Genome maintenance protein YedK. (B) Interstrand DNA crosslink repair glycosylase YcaQ.
Figure 3
Figure 3
Example display of the Metabolic Network Explorer to explore Escherichia coli metabolism starting from the metabolite D-glyceraldehyde 3-phosphate.
Figure 4
Figure 4
An example Circular Genome Viewer display, with tracks that showcase a variety of feature types, filtering and highlighting options, listed in order from the outermost circle inwards.
Figure 5
Figure 5
The Genome Overview diagram captures an entire genome with each arrow representing a single gene; neighboring genes that are part of the same operon are displayed in the same color. Arrow sizes are not to scale.
Figure 6
Figure 6
The Regulatory Overview diagram captures user-specified portions of a regulatory network. The user has specified the display of regulation by FliA (red) and RhyB (yellow).
See this image and copyright information in PMC

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