This list includes all the pathways that have been deleted from PoplarCyc since the release of PlantCyc 1.0. In some cases, they have been replaced by an alternative form of the pathway.
- adenosylmethionine biosynthesis [PWY-802]
- Comment: This single-reaction pathway is contained within other larger pathways in PlantCyc.
- 2-O-alpha-mannosyl-D-glycerate degradation [ MetaCyc: PWY0-1300]
- 4-aminobutyrate degradation [4AMINOBUTMETAB-PWY-ARA]
- arginine biosynthesis III [MetaCyc:ARGININE-SYN4-PWY]
- carbon tetrachloride degradation II [MetaCyc:PWY-5372]
- Comment: An alternative pathway for carbon tetracholride degradation exists in plants, but it has not been curated in PlantCyc yet.
- geranylgeranyldiphosphate biosynthesis II (plastidic) [PWY-5121]
- 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.
- D-gluconate degradation [ MetaCyc: GLUCONSUPER-PWY]
- glycine degradation [GLYCCAT-PWY]
- Comment:This pathway has been removed from MetaCyc
- thiamine biosynthesis [THISYN-PWY]
- Replaced with: THISYNARA-PWY
- Comment: A bacterial pathway has been replaced with a plant pathway.
- trans-lycopene biosynthesis I (bacteria) [ MetaCyc:PWY-5942]
- Replaced by plant variant trans-lycopene biosynthesis II (plants)
- tryptophan degradation (via tryptamine) [MetaCyc:PWY-3181]
- ubiquinone-9 biosynthesis [PWYQT-4448]
- Replaced with: PWY-5871
- Comment: A hypothetical pathway based on bacteria has been replaced with a pathway found in 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.
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