BioCyc Guided Tour

This page provides a tour of some of the information pages available through the EcoCyc/BioCyc website.

A convenient way to take the guided tour is to keep this page visible in one tab in your Web browser, while viewing the other pages listed in a separate browser tab.

Use Case: Find Genome Information

  1. Begin the tour at:
    • EcoCyc gene/protein page for tyrB / tyrosine aminotransferase
    • Click on the different tabs about four inches down the page, such as "Protein Features"
    • Click on the "Operons" tab

  2. In the resulting operon diagram, click on the "Show Details" button to display:

  3. On the "Site 1" line, click on "TyrR-Tyrosine DNA-binding transcriptional repressor" to display:

  4. Back in the gene page for tyrB
    • Click on the "View in Genome Browser" button to view: Genome browser focused on tyrB
      • Hover the mouse over a gene for more information
      • Use the zoom controls in the upper left to zoom in/out or move left/right

  5. Back in the gene page for tyrB, click on the "Align in Multi-Genome Browser" in the right-sidebar menu on the far right. Select a set of organisms in the next page and click Submit near the bottom of the page. The resulting page will align the tyrB gene across all the selected organisms, when present. Example:
    • Comparative genome browser focused on tyrB

Use Case: Find Pathway and Metabolite Information

  1. Enter the words "leucine biosynthesis" in the search field near the top of most pages, then click on the pathway name "L-leucine biosynthesis" in the search-result page to see:

  2. Within that pathway display click on the arrow for the last reaction to display

  3. Click on the chemical structure of leucine in the reaction page to display
    • Compound page for leucine
    • Click on several of the tabs, such as "Regulation", to see additional information
    • Click on the "Reactions" tab and scroll to the bottom of the page

Use Case: Navigate Metabolic and Regulatory Networks

Use Case: Search Other Organism Databases

Use Case: Comparative Analysis

  • "Tools → Analysis → Comparative Analysis" will compare information across organism databases. For example, this result compares overall database statistics plus metabolic pathways for six enteric bacteria.

    Learn More

    See the Guide to BioCyc or watch the BioCyc Webinars.