Accessing the Comparative Pathway KEGG Map on the PATRIC Website
This tool is accessible via the “KEGG Map” Tab, which is accessed by clicking on any Pathway Name in the initial search results page generated within our Comparative pathway Tool. For information on how to use the Comparative pathway Tool please see Comparative Pathway Tool FAQs.
All pathways at PATRIC come from the Kyoto Encyclopedia of Genes and Genomes, commonly known as KEGG.
KEGG Map Numbers
The numbers in the boxes are Enzyme Commission, or EC numbers. These numbers are part of a numerical classification schema that has been developed for enzymes and the chemical reactions they catalyze.
The box containing the EC number will be one of three colors. Note the colors are specific to your chosen annotation source, which is PATRIC by default. If you change annotation sources, the colors may change as well.
- A bright green color indicates that a protein with this EC number has been annotated in all the genomes chosen in your original Comparative Pathway Tool search.
- A muted green color indicates that a protein with this EC number has been annotated in at least one, but not all, genomes chosen in your original Comparative Pathway Tool search by that specific annotation source.
- White indicates that the annotation source did not identify a protein with that EC number.
Names Associated with EC numbers
Scrolling over the box that contains the EC number will tell you the name of the EC number. You may also chose to show the “Description” column (hidden by default), within the EC Table by clicking the arrow in the top of any column, scrolling down to Columns, and checking the box next to Description.
Generally, an individual KEGG pathway will show different associated pathways that specific enzymes play a part in. These pathways are named and are found on the KEGG Map in boxes with rounded corners. Clicking the link that appears when scrolling over one of these boxes will take you to that pathway. Alternatively, you could begin a new Comparative Pathway Tool Search using the pathway name as a keyword in the initial search criteria.
This table, located to the left of the KEGG Map, allows you to easily compare EC numbers at a glance.
EC Table Features and Functionality
- The columns may be shown and/or sorted as described in Feature Table FAQs.
- From here you may also select Annotation Source. To learn more about annotation sources, see Annotation FAQs.
- Select any cell within the column and the associated EC number will be highlighted in red within the KEGG Map.
- Click on any Feature Count number within the table to access a new Comparative Pathways Table, containing all of the data for all of the genomes associated with that particular EC number.