KEGG ID conversion to pathways

Question

[siu]

Dear all, I have C. reinhardtii protein sequences and I have submitted these sequences into KAAS to get the KEGG ID to the corresponding protein sequence and got:

Cre1        K07870
Cre2        K01952
Cre3        K20989
Cre4        K12667

Now, i want to convert these KEGG ids to the pathways. How can I do it? My expected out should be

Cre1        K07870       Pathway1
Cre2        K01952       Pathway2
Cre3        K20989       Pathway3
Cre4        K12667       Pathway4

Please help.

Thanks in advance.

Answer 1

[shelkmike]

You can find correspondence between KEGG ids and KEGG pathways in files that are stored on KEGG ftp. Note, however, that there can be several pathways corresponding to a single KEGG id.

[andres.firrincieli]

Unfortunately, even for academic users the ftp access require an annual subscrition fee: link

[shelkmike]

Alternatively, you can write a script that, for each Kegg Orthology (KO) id that is present in your file, will access the web page of that KO like https://www.genome.jp/dbget-bin/www_bget?ko:K07870 . Then your script can parse the page and get the list of pathways of that KO. I did a similar thing with the KEGG database using Perl and the LWP library that allows to browse web pages. If you prefer Python, there should definitely be some library for web page browsing too.

[siu]

Thanks, I will try this.

Regards