meaning that EcoCyc is one of 37 resources whose long term funding and sustainability is
critical to life science and biomedical research worldwide.
More than just K-12 MG1655
More than 500 E. coli strain databases are available via the "Change Current Database" button above. They are less curated than EcoCyc but work with all our website tools, from Omics Dashboard to metabolic route search.
Hazards of the Gut Habitat: Bile
Bile acids are secreted into the intestine, where they promote digestion and absorption of dietary fats. Bile salts are able to diffuse across the inner membrane of E. coli and are cytotoxic. The MdtM antiporter contributes significantly to E. coli's resistance to bile salts, which may represent the natural substrate of this inner membrane transporter.
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.
A quantitative metabolic model for E. coli K-12 derived from EcoCyc is available.
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.
Comparative Genome Analysis
Multiple comparative analysis tools are available in this website.
Gene Expression Data Analysis
Multiple tools are available in this website for analysis of gene expression data.
EcoCyc E. coli DatabaseEcoCyc 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.
EcoCyc is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click "Change Current Database" above to explore the available databases.
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: "The EcoCyc Database".
What people are saying
"BsubCyc is a tool of the utmost value."
Prof. of Biochemistry
& Molecular Biology
"My lab uses these resources on a daily basis."
Professor and Chair,
Dep't. of Biomolecular Chemistry
"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."
Assoc. Prof. Biochemistry
"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."
William Cannon, Team Lead
"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."
"BioCyc is a tremendous resource for pathway analysis in metabolomics."
Art Edison, Dept of Genetics
"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."
Timothy J. Donohue, Director
"I have not found another database that has a better interface than BioCyc."
Gary B. Huffnagle, Professor
Microbiology and Immunology
Webinar #1: Introduction to BioCyc
- BioCyc Overview Part 1 (14:04) [mp4 video] or [YouTube]
- Searching in BioCyc (17:00) [mp4 video] or [YouTube]
- Genome Browsing, Searching, and Alignment (15:38) [mp4 video] or [YouTube]
- Pathways (13:19) [mp4 video] or [YouTube]
- Reactions (3:37) [mp4 video] or [YouTube]
- Compounds (6:42) [mp4 video] or [YouTube]
Webinar #2: Introduction to SmartTables
- Part 1: SmartTables Overview (4:30) [mp4 video] or [YouTube]
- Part 2: SmartTables Basics (12:43) [QuickTime Video]
- Part 3: SmartTables Transformations (8:08) [QuickTime Video]
- Part 4: SmartTables Import and Export (9:00) [QuickTime Video]
- Part 5: SmartTables Gene Expression Analysis (7:40) [QuickTime Video]
- Part 6: Metabolomics Analysis with SmartTables (6:45) [QuickTime Video]
Webinar #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
- Part 1: The Cellular Overview: Navigating metabolic networks (17:15) [mp4 video] or [QuickTime Video] or [YouTube]
- Part 2: Comparative Genomics (21:06) [Windows Media Video] or [QuickTime Video]
- Part 3: Ortholog Viewing (10:02) [Windows Media Video] or [QuickTime Video]
- Part 4: The Regulatory Overview -- exploring transcriptional regulatory networks (15:21) [mp4 video] or [YouTube]
Webinar #4: Omics Data Analysis
- Transcriptomics Analysis Tools [brief tour (2:40) mp4 video or YouTube] [detailed tutorial (21:36) mp4 video or YouTube]
- Metabolomics Analysis Tools [brief tour (3:26) mp4 video or YouTube] [detailed tutorial (24:09) mp4 video or YouTube]
- Omics Dashboard Part 1 (16:35) [mp4 video], or [YouTube]
- Omics Dashboard Part 2 (24:29) [mp4 video], or [YouTube]
Webinar #5: Pathway Collages
Webinar #6: Creating a Pathway/Genome Database
- Part 1A: Introduction to Database Building and Pathologic (14:04) [MP4 Video] or [YouTube]
- Part 1B: Building a Database: Detailed Pathologic Example (23:53) [MP4 Video] or [YouTube]
- Part 2A: General Editing Strategies (8:00) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2B: Creating and Editing Reactions and Compounds (17:32) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2D: Making and Editing Pathways (9:42) [Windows Media Video] or [QuickTime Video] or [YouTube]