Background
In this task, you will complete the first two reactions in the published figure. These include the conversion from glucose to glucose-6-phosphate, and the interaction from glucose-6-phosphate to the Pentose Phosphate Pathway.
Your Mission
Draw the conversion reactions highlighted in the below figure.
- Launch PathVisio and start a new pathway under File > New.
- Add metabolite nodes for glucose and glucose-6-phosphate.
- To add the pathway node, select PATH from the Data Node palette in the Objects tab.
- Click on the canvas to place the node.
- Double-click on the node to open its properties.
- Instead of searching for an ID, enter the id “WP134” in the Identifier field, and enter “WikiPathways” in the Database field.
- Type in “Pentose Phosphate Pathway” as the Text label. Click OK.
- A pathway node is by default of Shape Type "None". Update the Shape Type to "RoundedRectangle" for the “Pentose Phosphate Pathway” node. This ensures that the pathway node is clickabile in WikiPathways.
- Draw the mim-conversion arrows between the glucose and glucose-6-phosphate nodes, and add an anchor to it.
- For the interaction between glucose-6-phosphate node and the pentose phosphate pathway node, add the default arrow interaction.
- Add the gene products that catalyze the conversion between glucose and glucose-6-phosphate, HK1. For the interaction between glucose-6-phosphate and the pentose phosphate pathway, we will not add the catalyzing enzyme node (G6PD), since this interaction is generic and does not end with a specific metabolite.
- Add the two mim-catalysis arrows for HK1.
- To add the glycolysis label, select Label from the Graphical elements palette in the Objects tab.
- Double-click the label to open its properties.
- Type in “Glycolysis“ and click OK.
- With the label still selected, in the Properties tab, check the Bold checkbox to make the label bold.
- Done!
- Save your work as a GPML file under File > Save As.
- Drag-and-drop the GPML file below to check if it is correct.
