diff --git a/R/rmReact.R b/R/rmReact.R
index 0efb32c1de032df7a56bbabf84caed276379fd94..c420d70941bb3161316ccfcf208bf212cbbf25f3 100644
--- a/R/rmReact.R
+++ b/R/rmReact.R
@@ -162,21 +162,9 @@ rmReact <- function(model, react, rm_met = TRUE) {
      	ag					<- ag[which(ncag != 0)]
       	allGenes(mod_out)   <- ag
       }
-      #TODO: update indices in the GPR rules accoording to the updated allGenes slot!
       
-
-      # reaction to gene mapping
-      #SrGMbin     <- rxnGeneMat(mod_out) != 0
-
-      #SrGMbindiag <- diag(crossprod(SrGMbin))
-
-      #keepGenes   <- ifelse(SrGMbindiag == 0, FALSE, TRUE)
-      keepGenes <- sapply(allGenes(model), function(x) match(x, allGenes(mod_out)))
-      keepGenes <- ifelse(is.na(keepGenes), FALSE, TRUE)
-      #print(keepGenes)
-
-      rxnGeneMat(mod_out)   <- rxnGeneMat(mod_out)[, keepGenes, drop = FALSE]
-      #print(dim(rxnGeneMat))
+      newGeneOrder <- match(allGenes(mod_out), allGenes(model))
+      rxnGeneMat(mod_out)   <- rxnGeneMat(mod_out)[, newGeneOrder, drop = FALSE]
   }
   
 
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 9f9fd1fc7e00edb4df6c915bc1bf7afc4e1e3aeb..7e44a597cad5ec973f0eb0dd4f7306af531b6521 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -8,6 +8,8 @@
 
 \section{Changes in version 2.0.1 2016-07-05}{
   \itemize{
+  	\item After \code{rmReact} the columns of \code{rxnGeneMat} and 
+  		\code{allGenes}-slot did not match.
   	\item \code{upgradeModelorg} was not working correctly, when all gprRules
   	are empty.
   }