EcoCyc E. coli DatabaseEcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire 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 2013 article: "EcoCyc: fusing model organism databases with systems biology"
EcoCyc User Guide >>
New version of the E. coli K-12 MG1655 sequence. The current release of EcoCyc uses the version of the E. coli genome sequence from GenBank record U00096.2. We plan to upgrade to version U00096.3 in our next release in April 2016. The nucleotide coordinates of genes and other features differ between U00096.2 and U00096.3. We will be offering a coordinate mapping service as part of the new release.
Cascade to the Rescue!
From protecting E. coli against phage infection to the promise of gene therapy: How does Cascade do it? Recent crystal structures of the enzyme are improving our understanding of this enzyme.Learn More
Search BioCyc by Locus ID
You can now enter locus IDs into the EcoCyc quick search box. There is no need to first select the correct BioCyc organism database - if the organism is part of BioCyc, the unique locus ID will automatically find it. Some example locus IDs look like this: MSM_0046, MXAN_1061.
A quantitative metabolic model for E. coli K-12 derived from EcoCyc is available.Learn More
Maintaining the Outer Membrane
The 5-subunit Bam complex is responsible for the assembly and insertion of beta-barrel proteins into the OM of E. coli. Although a full understanding of its function in beta-barrel folding remains elusive, recent work has yielded many insights into subunit interaction and activity.
Metabolomics Data Analysis
Multiple tools are available in this website for metabolomics data analysis.Learn More
EcoCyc App is now BioCyc App
Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse EcoCyc on the go! The NEW BioCyc app comes preloaded w/ EcoCyc.Download Here
Comparative Genome Analysis
Multiple comparative analysis tools are available in this website.Learn More
Gene Expression Data Analysis
Multiple tools are available in this website for analysis of gene expression data.Learn More
BioCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:
- Genome browser
- Display of individual metabolic pathways, and of full metabolic maps
- Multiple analysis methods for user-supplied omics and multi-omics datasets including painting onto metabolic maps, regulatory maps, and genome maps
- Store groups of genes and pathways in your account as Smart Tables; share, analyze, transform those groups
- Comparative analysis tools
|PortEco hosts E. coli omics data and analysis tools; the E. coli Student Portal is a microbiology education site.|
How to Cite EcoCyc
Please cite EcoCyc as Keseler et al. (2013), "EcoCyc: fusing model organism databases with systems biology", Nucleic Acids Research 41: D605-12.
The development of EcoCyc is funded by NIH grant GM077678 from the NIH National Institute of General Medical Sciences.
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