Our method. Finally, we discuss finding pathways for synthesizing inosine 5'-monophosphate (IMP) from glucose.^ where

Our method. Finally, we discuss finding pathways for synthesizing inosine 5′-monophosphate (IMP) from glucose.^ where r is the highest-scoring reaction associis a constant.ated with the edge andTherefore, a reaction having a high score causes atom graph edges corresponding to the reaction to receive a low weight, increasing chances that shortest paths visit its edges, and finally, that the reaction appears in result pathways. Reaction scores provide a mechanism to easily incorporate measurement data to guide pathway search. In section Results, we discuss the application of ReTrace in reconstructing biosynthesis pathways on basis of genomic evidence.Figure from ReTrace result page Excerpt 7 Excerpt from ReTrace result page. Excerpt from a html result page showing the first pathway found for the query from erythrose 4-phosphate (E4P) and phosphoenolpyruvate (PEP) to phenylalanine (Phe). Green circles in molecule structures indicate atoms in sources that the pathway transfers to target atoms. Additionally, the ZO score (Z) and the composite map of this pathway are shown.Page 12 of2009, :http://www.biomedcentral.com/1752-0509/3/Figure 8 Result pathway diagram Result pathway diagram. Diagram of a result pathway for a query from erythrose 4-phosphate (E4P) and phosphoenolpyruvate (PEP) to phenylalanine (Phe). Source and target metabolites are drawn in green and yellow, respectively. For clarity, pathway has been split into two parts, with 5-O-(1-Carboxyvinyl)-3-phosphoshikimate repeated in both parts.Atom graph construction from KEGG RPAIR We constructed an atom graph corresponding to 7781 reactions in the March 2009 version of KEGG LIGAND [2]. The atom graph was constructed by considering the 11265 entries in the KEGG RPAIR subdatabase. Each RPAIR entry specifies an atom mapping for a reactant pair, or substrate and product, in one or more reactions. For instance, RPAIR entry RP00001 describes the mapping ofatoms between NADPH and NADP+ in those 815 reactions, where the mapping for this reactant pair is identical. A total of 140 RPAIR entries where two or more entries were found to refer to the same atom number by different type (e.g., carbon vs nitrogen) were discarded from further analysis. Unfortunately, the RPAIR data fails to map many reactions with non-1-0-stoichiometries correctly, mapping usually only one instance of reactants and leavingPage 13 of2009, :http://www.biomedcentral.com/1752-0509/3/1e+Carbon Nitrogen Phosphorus1e+Carbon Nitrogen Phosphorus1000 Number of components1e+1e+06 Frequency1 1 10 100 1000 Component size 100001 0 20 40 60 Distance 80 100Figure 9 Component sizes and numbers in PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28914615 atom graph Component sizes and numbers in atom graph. Component size vs. the number of components in the atom graph induced by 7781 KEGG reactions. Components of carbon, nitrogen and phosphorus atoms shown separately. Both Xand Y-axes are shown in log-scale.Figure shortest distances in atom graph Pairwise10 Pairwise shortest distances in atom graph. Pairwise distances in three SC144 solubility subgraphs corresponding to the carbon, nitrogen and phosphorus specific mappings in the atom graph. Y-axis shown in log-scale.others unmapped. Confronted with such cases, ReTrace fails to find pathways utilizing the unmapped portions of the reactions. The atom graph contained 90219 nodes corresponding to 80688 carbon, 7408 nitrogen and 2123 phosphorus atoms. In particular, it consisted of a large number of components, i.e., disconnected subgraphs. Figure 9 shows the di.