Missing Reactions and Enzymes

Hi,

I'm using the package to retrieve the enzymes and their reactions but the output from the package is missing reactions and enzymes found on the website. For example in the https://www.genome.jp/kegg-bin/show_pathway?hsa00670 pathway, the MTHFD1 (1.5.1.5) protein faciliates a reaction which is missing from the reactions retrieved from the KEGGgraph. Why is this?

Thank you, Savvas

library(KEGGgraph)

tmp <- tempfile() genes_reactions <- data.frame(Gene_id = NULL, Reaction = NULL, pathway = NULL, stringsAsFactors = F) compound_reactions <- data.frame(Reaction = NULL, Substrate = NULL, Product = NULL, Direction = NULL, pathway = NULL, stringsAsFactors = F)

j<- "hsa00670" retrieveKGML(j, organism="hsa", destfile=tmp, method="auto", quiet=TRUE) testing <- KEGGgraph::parseKGML2Graph(tmp)

test_folate <- KEGGgraph::parseKGML(tmp)

for (i in 1:length(testing@nodeData@defaults[["KEGGNode"]][["nodes"]])){
    df <- data.frame(Gene_id = testing@nodeData@defaults[["KEGGNode"]][["nodes"]][[i]]@entryID,
                     Reaction = testing@nodeData@defaults[["KEGGNode"]][["nodes"]][[i]]@reaction,
                     pathway = j,
                     stringsAsFactors = FALSE)
    genes_reactions <- rbind(genes_reactions,df)

}

for (i in 1:length(test_folate@reactions)){
    df <- data.frame(Reaction = test_folate@reactions[[i]]@name,
                     Substrate = test_folate@reactions[[i]]@substrateName,
                     Product = test_folate@reactions[[i]]@productName,
                     Direction = test_folate@reactions[[i]]@type,
                     pathway = j,
                     stringsAsFactors = FALSE)
    compound_reactions <- rbind(compound_reactions,df)

}

Accio / KEGGgraph

Missing Reactions and Enzymes #4