About EcoCyc

Information

Services

EcoCyc Overview

EcoCyc 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. [project overview]

New to EcoCyc? Take the guided tour of the EcoCyc.org Web site, watch our free online instructional videos, or read our 2011 article: "EcoCyc: a comprehensive database of Escherichia coli biology."

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EcoCyc News

Highlighted publication from version 16.5:


Selkrig et al. have reported the characterization of a novel ‘translocation and assembly module’ that spans the inner and outer membranes of E. coli K-12 and is responsible for the efficient secretion of adhesin protein. This newly described complex comprises the inner membrane protein TamB (YtfO) and the outer membrane protein TamA (YtfM).

Highlighted publication from version 16.5:


The release of solutes through mechanosensitive ion channels functions to protect bacterial cells against hypo-osmotic shock. Edwards et al. have recently reported experimental characterization of two mechanosensitive channels encoded by the genes ynaI and ybiO. This latest report brings the total number of known mechanosensitive channels in E. coli K-12 to seven, experimental evidence from Edwards et al. suggests that this represents the full complement.

Highlighted publication from version 16.5:


With the discovery of RlmJ as the enzyme responsible for methylation of A2030 in 23S ribosomal RNA by Golovina et al., the set of methyltransferases that modify E. coli ribosomal RNAs is now complete.

Highlighted publication from version 16.5:


The mechanism of ribosomal silencing has been an active area of research. A recent addition to the set of proteins that regulate the assembly or activity of the ribosome is RsfS. Häuser et al. discovered that RsfS is able to inhibit the assembly of a functional 70S ribosome during stationary phase.

Current Article of Interest


A recent publication by Spira et al. in BMC Microbiology highlights the genetic heterogeneity, particularly in the rpoS gene, that can result from storage and transfer of E. coli strains between laboratories.

EcoliHouse relational database available


EcoliHouse is a publicly queryable relational database of EcoCyc and other Escherichia coli K-12 datasets. It provides an environment for large-scale data mining using SQL statements issued to a MySQL database via the Internet.

Run EcoCyc and 13 E. coli and Shigella genomes on your computer:


You can install this new suite of E. coli and Shigella genomes on your computer (Mac, PC, Linux) for faster and more powerful operation than the Web site. [download info]

BioCyc now contains 130 E. coli genomes.


To access a genome of interest, click on "change organism database" under the quick search box at the top right of most EcoCyc and BioCyc Web pages.

Search the text of 37,000 E. coli articles, including EcoSal articles, using Textpresso [Textpresso Search]

Download the EcoCyc iPhone app from the iTunes store.

The first E. coli publication


The oldest E. coli paper we've found indexed in PubMed is The Importance to the Surgeon of Familiarity with the Bacillus Coli Communis by Roswell Park. The oldest paper around is the original by Escherich. It's not indexed in PubMed, but you can click the following link to read Die Darmbakterien des Neugeborenen und Säuglings.

The full EcoCyc release history is available here. You can read past highlights pieces by clicking here.

PortEco

EcoCyc's sister site PortEco now hosts E. coli omics data and powerful analysis tools.

EcoCyc Project Leaders

Peter D. Karp | Julio Collado-Vides | Ian Paulsen | Rob Gunsalus

See our credits page for more details on EcoCyc contributors and their roles.

Acknowledgements

The development of EcoCyc is funded by NIH grant GM077678 from the NIH National Institute of General Medical Sciences and National Center for Research Resources.