Thanks, I had completely forgotten that METABOLIC works with protein sequences. That will work :)
I was just trying to figure out how people handle Prokka annotations.
I also tried kofam_scan — it gave me multiple definitions for one sequence. It was one enzyme but appearing in a couple of systems, so here I think I need to choose the best e-value or score. However, eggnog-mapper gave me just one name of the system. Therefore, I was looking for a tool to work with this data further.
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shevch2009 •
Prokka is just an annotation pipeline and relies on/amalgamates predictions generated by a number of other tools - it doesn't do any more than decent annotation.
You can use tools like
CD-HITand evenroaryto cluster genes together into othologue groups, on which you can then do various gene ontology-type analyses.I'm personally a bit out of touch with the metagenome space to know what the best tools are these days but what you describe sounds like a clustering and annotation refinement kind of task.
If you're only interested in metabolic pathways, then you're probably already on the right track looking at what is commonly used in the literature at the moment.
I am still confused how to put all predicted genes into metabolic pathways, I used eggnog-mapper for the prokka output, and can't find a tool which just put those KO into KEGG pathways, I don't want to use KEGG-mapper because It's web tool, I need something for the cluster and that will give me a simple table with all full pathways in my MAGs...
In some articles people just create thier own piplines and custom things or say they used KEGG db. I have found - MinPath, but It's a minimal ammount of pathways, Also, KEGGDecoder, but it needs kofamscan outputs as input, Just looking for something like METABOLIC, but for prokka-eggnog output files!
I would appreciate any help. Thanks