search

ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
Other
53 stars 38 forks source link

Fructanohydrolase reaction error #34

Closed gregmedlock closed 7 years ago

gregmedlock commented 7 years ago

Hello,

The reaction rxn06945 appears as:

H2O -> Levan n

Which has obvious mass balance issues. The name associated with the reaction is 2,6-beta-D-Fructan fructanohydrolase. It looks like any of the 'M' units of Levan were stripped when transferring from KEGG (http://www.genome.jp/dbget-bin/www_bget?rn:R05624), giving the current reaction.

samseaver commented 7 years ago

Hi Greg, where are you seeing this reaction?

gregmedlock commented 7 years ago

It appears in reactions.master.tsv. I found it while checking a few gap-filled reconstructions for leaks.

samseaver commented 7 years ago

We keep unbalanced reactions in that spreadsheet, as the "master" sheet, for future reference and expansion, indeed, the "status" column holds the mass balance results; we only include reactions that are "OK" in the templates for model construction and gapfilling.

Are you saying that you got this reaction in a model as a result of gapfilling?

samseaver commented 7 years ago

I just checked, we don't have this reaction in either microbial template.