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EcoCyc specifications


Unique identifier OMICS_01645
Name EcoCyc
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • Bacteria
    • Escherichia coli



  • person_outline Ingrid M. Keseler
  • person_outline Peter D Karp

Publications for EcoCyc


The EcoCyc Database.

2014 EcoSal Plus
PMCID: 4243172
PMID: 26442933
DOI: 10.1128/ecosalplus.ESP-0009-2013

The EcoCyc Database.

2002 Nucleic Acids Res
PMCID: 99147
PMID: 11752253

EcoCyc citations


SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

PMCID: 5946812
PMID: 29762652
DOI: 10.1093/database/bay035

[…] e de-facto standard in species-specific database curation, and Pathway Tools generated and manually curated PGDBs have been created across the domains of life, including bacteria [Escherichia coli in EcoCyc ()], fungi (Saccharomyces cerevisiae in YeastCyc, mammals [Bos taurus in CattleCyc ()] and plants such as Arabidopsis thaliana in AraCyc (, ), Medicago truncatula in M […]


Synergistic Killing of Polymyxin B in Combination With the Antineoplastic Drug Mitotane Against Polymyxin Susceptible and Resistant Acinetobacter baumannii: A Metabolomic Study

Front Pharmacol
PMCID: 5911485
PMID: 29713282
DOI: 10.3389/fphar.2018.00359

[…] ds) using exact mass and predicted retention time based on the Kyoto Encyclopedia of Genes and Genomes (KEGG), MetaCyc, and LIPIDMAPS databases, using preference to bacterial metabolites annotated in EcoCyc. Raw peak intensity was used to quantify each metabolite. The free online tool MetaboAnalyst 3.0 was used for the statistical analysis. Briefly, putative metabolites with median RSD ≤ 0.2 (20%) […]


Evaluation of reaction gap filling accuracy by randomization

BMC Bioinformatics
PMCID: 5813426
PMID: 29444634
DOI: 10.1186/s12859-018-2050-4

[…] ons of GenDev based on three techniques, A, B and C; using two solvers, SCIP and CPLEX; and using two methods for MILP formulation, called Big M and indicators. We randomly removed reactions from the EcoCyc-20.0-GEM metabolic model, ran each of the 13 gap-filler variations on the resulting reaction network, and assessed how closely the resulting set of reactions matched the removed set of reaction […]


PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli

Sci Rep
PMCID: 5772556
PMID: 29343727
DOI: 10.1038/s41598-017-18648-5

[…] the 23 putative CRP-binding sites have high probability to be CRP-binding sites according to the consensus sequence criterion, we further proved the 23 sites as CRP-binding sites by referring to the EcoCyc database (see Supporting Information). The 23 predicted CRP-regulated interactions are given in Figure , which were validated by qPCR experiments. […]


A review of computational tools for design and reconstruction of metabolic pathways

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] vely, the Chemical Translation Service and UniChem provide a simple web application that can interconvert metabolite IDs across different databases. Organism-specific GSMs or knowledge-bases (e.g., EcoCyc , AraCyc , and HumanCyc ) are often constructed or extracted from the larger databases, to ensure the design or identification of alternative pathways within an organism's native network. While […]


Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor G Mutants in Escherichia coli

PMCID: 5714492
PMID: 29046437
DOI: 10.1534/g3.117.300284

[…] y rate in multiple testing). Genes and their fold-changes can be found in File S1.Gene ontology (GO) analysis was carried out using the R package topGO (). E. coli gene annotations were obtained from Ecocyc ( p. 2014) and GO terms were obtained from the GO Consortium (). In topGO, the Fisher test was used to assess significance of enriched gene sets and terms with P values <0.01 were considered si […]


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EcoCyc institution(s)
SRI International, Menlo Park, CA, USA; Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia; Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
EcoCyc funding source(s)
Supported by National Institute of General Medical Sciences of the National Institutes of Health under Award Numbers U24GM077678 to P.D.K. and R01GM110597.

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