Question: KEGG and metacyc database downloads
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gravatar for allerdrengen55
11 months ago by
allerdrengen5520 wrote:

Hi!

I have a file with a lot of eC_numbers. I would like to convert these numbers, so they represent KEGG and metacyc IDs instead. I need file where I can see what eC_numbers represent which KEGG/metacyc IDs. I also need a database of what the KEGG/metacyc IDs represent, enzyme-wise.

I can't find a proper file on their websites. Can anyone help me out?

download kegg metacyc • 458 views
ADD COMMENTlink modified 11 months ago by Mark800 • written 11 months ago by allerdrengen5520

EC and ko's are not 1:1 mapping

ADD REPLYlink written 11 months ago by Asaf8.4k

So there's no point in trying to convert EC to other IDs ?

ADD REPLYlink written 11 months ago by allerdrengen5520

No. You can try eggNOG-mapper to get KOs. Also what's the organism?

ADD REPLYlink written 11 months ago by Asaf8.4k

It's a metagenomic sample.

ADD REPLYlink written 11 months ago by allerdrengen5520
0
gravatar for Mark
11 months ago by
Mark800
Mark800 wrote:

Use Uniprot. It collates all the info you need. But it's organism dependant. So hopefully your org of interest is in the db (it usually is). For metacyc, this falls under biocyc. For example I work on Hi:

https://www.uniprot.org/uniprot/?query=haemophilus+influenzae&sort=score

ADD COMMENTlink written 11 months ago by Mark800

Thanks, I'll give it a shot. Though, I'm working with metagenomic data, so I have thousands of different organisms in my sample, and can't really filter any out.

ADD REPLYlink written 11 months ago by allerdrengen5520

I believe they have an API you could access. Or possibly you could download an instance of the db: https://www.uniprot.org/downloads

IMO this might be the best way forward.

ADD REPLYlink written 11 months ago by Mark800
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