HUMAnN3 - mapping between UniRef90 to EC-enzymes

Microbial community profiling HUMAnN
1

Dear developers and users,

In HUMAnN3 in utility_mapping accessory files, there is file called map_level4ec_uniref90.txt.gz which maps EC-enzymes (4-numbers) to UniRef90 protein ids.

I was wondering how/from where I can generate such a mapping table myself? If for example I’d like to use the latest UniRef90 (which is updated ~8 weeks) database, and want to map them the ECs annotation.

I know this topic is not directly related to HUAMnN3, but still I’d appreciate any help!

Thanks
VadumDu

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We build these files by parsing the big “DAT” file that comes with each UniProt release. It is the file that looks like a concatenation of all these per-protein details:

https://rest.uniprot.org/uniprotkb/P06493.txt

Most EC annotations come from the lines starting with DE, but they can occasionally be found in comment lines (CC) and via the cross-references to the BRENDA database (DR BRENDA).

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Many thanks you for the answer @franzosa !

I can’t access the parent directory of this link though. It was just an example for a single record yes?

Do you refer to this huge file that come with each UniProtKB release: uniprot_trembl.dat.gz ?
There is also a much smaller uniprot_sprot.dat.gz - but it only covers the Swiss-Prot and I guess it will result in only a partial mapping?

Thanks again
VadimD

4

Correct, that was just an example of the formatting. You will want to consider both the full SwissProt and TrEMBL files. Note that if HUMAnN reports a gene family like UniRef90_XYZ, then XYZ will be an accession number in one of those files (unless the sequence has been retired).

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