Pathways in Result But Not in MetaCyc Database

Microbial community profiling HUMAnN
1

Looking through the results, almost all pathways have names. For example PWY-6163 is chorismate biosynthesis from 3-dehydroquinate 0.999 But, when I look at PWY-4242, it is blank.

PWY-4242        0.9999527979
PWY-4242|g__Fusobacterium.s__Fusobacterium_nucleatum    0.0384455671
PWY-4242|g__Fusobacterium.s__Fusobacterium_periodonticum        0.3948018469
PWY-4242|g__Porphyromonas.s__Porphyromonas_endodontalis 0.1519649698
PWY-4242|unclassified   0.0002206948
PWY-4242|g__Fusobacterium.s__Fusobacterium_sp_oral_taxon_370    0.0302844385
PWY-4242|g__Campylobacter.s__Campylobacter_rectus       0.0572872704
PWY-4242|g__Aggregatibacter.s__Aggregatibacter_segnis   0.1268270103
PWY-4242|g__Dialister.s__Dialister_invisus      0.1279188885

Checking MetaCyc website, it is not found unlike PWY-6163. Perhaps it has been removed for some special reason. How can I interpret this situation?

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2

The newest HUMAnN (3.0.0) provided a big update to the MetaCyc pathway definitions; if you upgrade you will probably find them in better agreement with the modern MetaCyc website. Note that you don’t have to reprofile your samples from raw reads to update the pathways - you can rerun HUMAnN 3 starting from your genefamilies file as an input.

3

I should have mentioned that I used HUMAnN version 3.0.0 and this seemingly deprecated pathway was in the result.