More specifically, after I get the KO numbers for each gene, how do I make the actual assignment of each gene to a specific pathway? I suppose I will have to download a database and parse it somehow, but since there are quite a few of them I'm a bit confused!
Do you have any other method to suggest (except KEGG)?
You can do this mapping using custom scripts by downloading the flat file of KO list here. You can use that list to get pathway associated with each KO numbers. If you want the pathway mapping you can check the mapping file here.
If you want to perform enrichment analysis, you may take a look at SubPathwayMiner
Just for your info... I asked the KEGG curators as you told me Khader and they told me that this is normal; the "ko.list" file contains only KOs that are assigned to a certain pathway. Hence, if a KO doesn't appear in "ko.list" then this is because it wasn't possible for it to be assigned to a pathway (poor characterization).
You should check the KEGG API through SOAP, also because the access to the KEGG ftp is now restricted without a licence.
This API contains various commands that may help you in mapping a KO ID to a pathway, like the command "get_pathways_by_kos"
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version 2.3.6
You know that you can also download species-specific pathways?
No, I didn't know that! Nevertheless, I want to find pathways in a metagenome that doesn't exist in KEGG so I have to do it from the beginning.