Clarification on KEGG orthologs, why don't all have KEGG modules?
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4 months ago
O.rka ▴ 390

I ran KOFAMSCAN and everything looks good. Trying to go from KEGG orthologs to KEGG modules. Now I'm seeing that certain orthologs just don't have any modules and I'm trying to figure out how KEGG is structured. For example, there is this KEGG ortholog: K16148

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I see there are 2 KEGG pathways but why isn't this enzyme associated with any KEGG modules?

When I click on one of the pathways ko00500, I see there are 3 modules in this pathway M00854, M00855, and M00565 but why don't they have K16148?

I just need a way to group KEGG orthologs into higher level categories that's consistent.

I made a venn diagram of the following:

  1. The JSON file from here https://www.genome.jp/kegg-bin/get_htext?ko00001.keg (Accessed 2021.06.22)
  2. The KEGG ortholog hits I got from KOFAMSCAN using the most recent database
  3. The BioPython implementation of this: How to get a mapping between KEGG module and KEGG orthologs? (Accessed 2021.06.22)

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ortholog database kegg • 252 views
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see there are 2 KEGG pathways but why isn't this enzyme associated with any KEGG modules?

The simplest explanation is that K16148 is not involved in M00854 (Glycogen biosynthesis), M00855 (Glycogen degradation), M00565 (Trehalose biosynthesis). From KEGG:

The most unique data object in KEGG is the molecular networks -- molecular interaction, reaction and relation networks representing systemic functions of the cell and the organism. Experimental knowledge on such systemic functions is captured from literature and organized in the following forms:

  1. Pathway map - in KEGG PATHWAY (see: Pathway maps)
  2. Brite hierarchy and table - in KEGG BRITE (see: Brite hierarchies)
  3. Membership (logical expression) - in KEGG MODULE
  4. Membership (simple list) - in KEGG DISEASE
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