Comments (1)
Calvin2077
commented on June 16, 2024
From my experiences a potential answer to your first question is due to your pathways within your species missing key enzymes or having vague reactions (see below)
A potential answer to your second is 'vague reactions' are "Number of reactions without available sequences" (obtained from GapSeq tutorial pages) More specifically, "In cases in which no sequence data is available for specific reactions, the status of the reactions is set to ‘vague’ and these reactions do not count as missing if they account for less than vagueCutoff of the total reactions of a pathway or subsystem. We used a value of 1/3 for this threshold." (GapSeq publication article)
These are just my (a big user of GapSeq) understanding of the results I am not a developer of this application but I totally wish I was
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