KEGG mapper

KEGG is a database resource for understanding high level functions and utilities in biological systems.

You can use this databse to identify pathway maps, biochemical reactions in a cell.

Starting file

The protein sequnces “Bacteria workshop bin20.feature_protein.fasta” from PATRIC.

This was the last step in PATRIC tutorial

Goto GhostKoala
Click on choose file, select “Bacteria workshop bin20.feature_protein.fasta”
- Select the option “genus_prokaryotes”
- add your email address
- Select “request email confirmation”
Once the form is submitted, there will be an email sent to the email address provided
Check for email from “noreply@scl.kyoto-u.ac.jp via kegg.jp”, and clik on the link to submit the job
- There will be two links provided, first one is to submit the commannd and the second to delete the command
Wait…. Depending on how busy the cluster is on their end, this may take a while
Once the command is done running, they send you an email with the results. So check email
- Email from “noreply@scl.kyoto-u.ac.jp via kegg.jp” with a link to the results
- the results are only provided for 7 days so make sure to download them

The results link takes you to a new page with the annotations identified in the MAG
Click on preview 100, next to Annotation data
- The KO IDs are saved in this file
Back on the main results page
- Click on “Reconstrt Pathway”
- This takes you to the list of the pathways in KEGG
  - Can select for a specific pathway and have the genes found highlighted