A number of pathways have been deleted* from the database since the previous release. In some cases, they have been replaced by an alternative form of the pathway.
Pathways deleted in PlantCyc 4.0
- 2-O-alpha-mannosyl-D-glycerate degradation [ MetaCyc: PWY0-1300]
- GDP-glucose biosynthesis [ MetaCyc: PWY-5661]
- Comment: The pathway was initially computationally predicted for PoplarCyc. After re-examination of the validation results this pathway has been removed from both PoplarCyc and PlantCyc.
- trans-lycopene biosynthesis I (bacteria) [ MetaCyc:PWY-5942]
- Replaced by plant variant trans-lycopene biosynthesis II (plants)
- superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle [ MetaCyc: PWY-5464]
- superpathway of gluconate degradation [ MetaCyc: GLUCONSUPER-PWY]
- Comment: The pathway was initially computationally predicted for PoplarCyc. After re-examination of the validation results this pathway has been removed from both PoplarCyc and PlantCyc.
- superpathway of histidine, purine, and pyrimidine biosynthesis [ MetaCyc: PRPP-PWY]
- Comment: This superpathway has a bacterial variant subpathway. A new superpathway composed solely of subpathways that exist in plants should be created for the future.
* Please note that we have a separate list of pathways where the database ID for the pathway has changed, but the series of reactions, compounds, etc., present in the pathway remain the same.
You can also see a list of all the pathways that have been removed from PlantCyc after the PlantCyc 1.0 release.
Return to the PlantCyc Release Notes page
Return to the PMN Release Notes page
