Background

Some biochemical reactions involve a large number of steps, and describing them all in a pathway diagram while maintaining an easy-to-read pathway can be difficult. To save space and maintain clarity, multi-step processes can be depicted as a dashed line indicating an indirect path. The enzymes involved in the multiple steps are then drawn as a group of enzymes.

Your Mission

Complete the multi-step conversion of lanosterin to lathosterol by a group of enzymes. The complete reaction corresponds to the highlighted area in this figure:



  • Download the starter pathway here: met-1-indirect-start.gpml.
  • Launch PathVisio and open the dowloaded file via File > Open.

    • Add the metabolite

  • Select Metabolite 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.
  • Search for “lathosterol”; Choose any of the entries that just say “lathosterol” (in order of priority ChEBI, LIPIDMAPS, PubChem, CAS); Click OK to select the identifier, and then click OK again to close the node properties window.

    • Add and connect the conversion arrow

  • Select the mim-conversion arrow from the MIM interactions palette in the Objects tab.
  • Drag and drop anywhere on the canvas to create the interaction.
  • Select the conversion arrow, and in the Properties tab in the right side panel, change the Line Style to “dashed”:
  • Drag the plain end (start) of the interaction over a target area on the starting metabolite node (lanosterin).
  • Drag the arrow end (end) of the interaction over a target area on the ending metabolite node (lathosterol).
  • Right-click on the conversion interaction and select Add anchor, or select the conversion interaction and then use the keyboard shortcut Ctrl+R (Command+R on Mac), to add the anchor.

    • Add the enzymes

  • Select GeneProduct from the Data Node palette in the Objects tab.
  • Click on canvas to place the node.
  • Double-click on the node to open its properties.
  • Search for “CYP51A1”; Choose any of the entries that just say “CYP51A1”; Click OK to select the identifier, and then click OK again to close the node properties window.
  • Repeat the last 4 steps for two more enzymes: MSMO1 and NSDHL.
  • Select all three enzyme nodes by click-and-drag. With all three nodes selected, right-click and select Group.

    • Add and connect the catalysis arrow

  • Select the mim-catalysis arrow from the MIM interactions palette in the Objects tab.
  • Drag and drop anywhere on the canvas to create the interaction.
  • Drag the plain end (start) of the interaction over a target area on the enzyme group.
  • Drag the catalysis end (end) of the interaction over the anchor on the conversion line.
  • (Optional) Align nodes using toolbar actions.
  • 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.