Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Jan 4;45(D1):D543-D550.
doi: 10.1093/nar/gkw1003. Epub 2016 Nov 28.

The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12

Free PMC article

The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12

Ingrid M Keseler et al. Nucleic Acids Res. .
Free PMC article


EcoCyc ( is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.


Figure 1.
Figure 1.
Transporter classes in EcoCyc.
Figure 2.
Figure 2.
Sulfoquinovose degradation pathway.
Figure 3.
Figure 3.
Zoom levels of the genome browser, with the previously available ‘genes’ and ‘sites’ levels compared to the new ‘sequence’ level.
Figure 4.
Figure 4.
Running metabolic models on the EcoCyc web site.

Similar articles

  • EcoCyc: a comprehensive database of Escherichia coli biology.
    Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD. Keseler IM, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. Nucleic Acids Res. 2011. PMID: 21097882 Free PMC article.
  • EcoCyc: a comprehensive database resource for Escherichia coli.
    Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD. Keseler IM, et al. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D334-7. doi: 10.1093/nar/gki108. Nucleic Acids Res. 2005. PMID: 15608210 Free PMC article.
  • EcoCyc: fusing model organism databases with systems biology.
    Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD. Keseler IM, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D605-12. doi: 10.1093/nar/gks1027. Epub 2012 Nov 9. Nucleic Acids Res. 2013. PMID: 23143106 Free PMC article.
  • The EcoCyc Database.
    Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I. Karp PD, et al. EcoSal Plus. 2018 Nov;8(1):10.1128/ecosalplus.ESP-0006-2018. doi: 10.1128/ecosalplus.ESP-0006-2018. EcoSal Plus. 2018. PMID: 30406744 Free PMC article. Review.
  • Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.
    McCloskey D, Palsson BØ, Feist AM. McCloskey D, et al. Mol Syst Biol. 2013;9:661. doi: 10.1038/msb.2013.18. Mol Syst Biol. 2013. PMID: 23632383 Free PMC article. Review.
See all similar articles

Cited by 102 articles

See all "Cited by" articles


    1. McClung D.J., Calixto A., Mosera M.N., Kumar R., Neidle E.L., Elliott K.T. Novel heterologous bacterial system reveals enhanced susceptibility to DNA damage mediated by yqgF, a nearly ubiquitous and often essential gene. Microbiology. 2016;162:1808–1821. - PubMed
    1. Keseler I.M., Mackie A., Peralta-Gil M., Santos-Zavaleta A., Gama-Castro S., Bonavides-Martinez C., Fulcher C., Huerta A.M., Kothari A., Krummenacker M., et al. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 2013;41:D605–D612. - PMC - PubMed
    1. Karp P.D., Weaver D., Paley S., Fulcher C., Kubo A., Kothari A., Krummenacker M., Subhraveti P., Weerasinghe D., Gama-Castro S., et al. The EcoCyc database. EcoSal Plus. 2014;2014 - PMC - PubMed
    1. Weaver D.S., Keseler I.M., Mackie A., Paulsen I.T., Karp P.D. A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Syst. Biol. 2014;8:79. - PMC - PubMed
    1. Karp P.D., Latendresse M., Paley S.M., Krummenacker M., Ong Q.D., Billington R., Kothari A., Weaver D., Lee T., Subhraveti P., et al. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform. 2015;17:877–890. - PMC - PubMed

Publication types

MeSH terms