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 In some cases, they have been replaced by an alternative form of the pathway.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 PoplarCyc 2.0
- 2-O-alpha-mannosyl-D-glycerate degradation [ MetaCyc: PWY0-1300]
- arginine biosynthesis I [ MetaCyc: ARGSYN-PWY]
- 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.
- ornithine biosynthesis [ MetaCyc: GLUTORN-PWY]
- Comment: There is no evidence that this pathway exists in poplar.
- trans-lycopene biosynthesis I (bacteria) [ MetaCyc:PWY-5942]
- Replaced by plant variant trans-lycopene biosynthesis II (plants)
- superpathway of allantoin degradation in plants [ MetaCyc: URDEGR-PWY]
- Comment: There is no evidence in poplar to support the existence of one or more of the subpathways that are part of this superpathway.
- 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.
- superpathway of phosphatidylcholine biosynthesis [ MetaCyc: PWY4FS-5]
- Comment: There is no evidence in poplar to support the existence of one or more of the subpathways that are part of this superpathway.
- superpathway of purines degradation in plants [ MetaCyc: P165-PWY]
* 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.
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