BioCyc Guided Tour

This page provides a tour 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.

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 promoter arrow to display:
   • Transcription-unit page for Transcription unit tyrB

3. On the "Site 1" line, click on "TyrR-Tyrosine DNA-binding transcriptional repressor" to display:
   • Transcription-factor page for TyrR-tyrosine repressor

4. Back in the gene page for tyrB
   • Click on the "View in Genome Browser" button to view: Genome browser focused on tyrB

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

6. Back in the gene page for tyrB, click on the pathway name "leucine biosynthesis" to display
   • Pathway page for L-leucine Biosynthesis

7. Within that pathway display click on the arrow for the last reaction to display
   • Reaction page for EC 2.6.1.42

8. 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

9. Click on one of the transport reactions near the end of the page to show
   • Transport-reaction page for leucine transport reaction

10. Click on "leucine ABC transporter" to display
    • Transporter page for leucine ABC transporter

11. From the "Metabolism" menu at the top of the page, click on "Cellular Overview" to display the Cellular Overview (metabolic map diagram) for E. coli. This diagram can be magnified using the ladder on the left, or by scrolling with the mouse. Drag the diagram with the mouse to move it around. Search for enzymes or metabolites using the right-sidebar menu.

12. Click on Genome → Regulatory Overview  to display a regulatory network diagram for E. coli. This diagram can also be magnified.

13. For a guide to painting transcriptomics or metabolomics data onto the diagram, see sample data files and animations.

14. Analysis → Comparative Analysis  will allow you to compare genome and pathway information.

15. Let's now look at information for another organism, Aquifex aeolicus. You can switch the current organism that BioCyc queries by:
    • Clicking on the blue "change organism database" link in the upper-right corner of every page

16. After switching the current organism to Aquifex aeolicus, click on Analysis Menu →  Summary Statistics to see how and when the database for this organism was created.

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