Missing Reactions and Enzymes

[Skourtis]

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)
    
}

[EulleSA]

I have the same problem