Considering the Path-A based metabolic pathway prediction (http://nar.oxfordjournals.org/content/34/suppl_2/W714.short). It uses machine learning for pathway prediction. Suppose that the input was a protein sequence of a query organism. I do not understand what these protein sequences are? Are these the enzymes for the reactions?
The basic algorithm has two inputs: a set of protein sequences from the query organism and a set of model pathways, one for each target pathway.