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EcoCyc E. coli Database
EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.New to EcoCyc? Take the guided tour of the EcoCyc.org Web site, watch our free online instructional videos, or read our article in EcoSal (updated November 2018): "The EcoCyc Database".
EcoCyc User Guide >>
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Crystal structure of E. coli Cascade. Image from the RCSB PDB (www.rcsb.org) of PDB ID 1VY8 (R.N. Jackson et al. (2014) Science 345:1473-9).
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Except for top right (CC By 2.5) all images public domain.
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Metabolic Model for E. coli K-12
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Schematic diagram of the Bam complex, Fig. 1a in Kim et al.. Used under creative commons license.
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SmartTable display generated by Pathway Tools.
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BioCyc iOS App for iPhone/iPad
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Multi-organism Genome Browser image generated by Pathway Tools.
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Cellular Overview Omics Viewer image generated by Pathway Tools.
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EcoCyc Tools
EcoCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:
- Genome browser and regulatory network browser
- Display of individual metabolic pathways, and of full metabolic maps
- Multiple omics data analysis methods for user-supplied omics and multi-omics datasets including the Omics Dashboard, painting onto pathway diagrams and metabolic maps, and tables of perturbed pathways
- Store groups of genes, metabolites, etc. in your account as SmartTables; share, analyze, transform those groups
- Metabolic route search tools
- Run metabolic models
- Comparative analysis tools
Related Sites
The E. coli Student Portal is a microbiology education site.
How to Cite EcoCyc
Please cite EcoCyc as Keseler et al. (2017), "EcoCyc: reflecting new knowledge about Escherichia coli K-12", Nucleic Acids Research 45:D543-50.
Funding Sources
The development of EcoCyc is funded by NIH grant GM077678 from the NIH National Institute of General Medical Sciences.
Video Tutorials
The BioCyc webinar series introduces users to the basic and advanced features of the BioCyc website and the Pathway Tools software. A complete list of videos in additional download formats are available on the Video and Podcast page.
This video introduces the BioCyc.org site and the BioCyc collection of hundreds of Pathway/Genome Databases and covers:
- BioCyc site contents, including EcoCyc, MetaCyc, and our extensive database collection
- How to search, browse, and find what you need in the BioCyc collection
- How we represent metabolism, transcription, and all their parts
