Table 1 Node names and descriptions for Bayes classifier.
From: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
node | description |
|---|---|
has-function | true if the protein has the function required to fill the pathway hole, false if it does not |
Shotgun-score | the number of query sequences whose BLAST output included the candidate sequence |
best-E-value | negative log of the E-value for the best alignment of the candidate with a query sequence |
average-rank | the average rank of the candidate sequence in the BLAST output lists (e.g., if a candidate is the best hit in each search, the average rank for the candidate is 1) |
average-fraction-aligned | the average of each alignment length normalized by the length of the query sequence |
pathway-directon | true if the hit is in the same directon as another gene in the same pathway; a directon is a contiguous series of genes transcribed in the same direction |
adjacent-rxns | true if the hit is adjacent to one of the genes coding the enzyme for an adjacent reaction in the pathway |