PathPred

[…] Rhodococcus aetherivorans BCP1 genome analysis was performed to detect the possible genes involved in NA degradation. Using Pathpred software and in silico comparative analyses, we identified genes encoding cyclohexanone monooxygenases and genes possibly encoding enzymes involved in oxidative degradation processes (Supplem […]

[…] ding the names of the enzymes catalyzing the reactions.The next step in pathway annotation was to determine the synthesis pathway from fragments to drug compound. To accomplish this task, we used the Pathpred webserver (http://www.genome.jp/tools/pathpred), which predicts the synthesis pathway given the substrates and the final product. The Pathpred webserver is linked to the KEGG database and the […]

[…] e genes was also performed as above by GO function enrichment analysis. Possible enzyme-catalyzed metabolic pathways for multi-step reactions involved in naphthenic acid degradation were predicted by PathPred [], which was based on the local RDM pattern (KEGG atom type changes at the reaction center (R), the difference region (D), and the matched region (M) for each reactant pair.) match and the g […]

[…] romo-4-nitrophenol. For the prediction, users may enter a compound into the system by either drawing the structure and generating SMILES or entering SMILES directly.Another pathway prediction system, PathPred (http://www.genome.jp/tools/pathpred/), is a knowledge based prediction system that uses data derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) in the form of the KEGG REACTION […]