The PMN 9.0 release completely rebuilt databases for twelve phylogenetically diverse species including moss, Selaginella, barley, Brachypodium, grape, cassava, Chinese cabbage, papaya, poplar, setaria, sorghum and switchgrass. We have significantly revised and updated AraCyc, CornCyc, ChlamyCyc, OryzaCyc and SoyCyc.
Our computational predictions of enzyme functions in PMN 9.0 are based on an enhanced Ensemble Enzyme Prediction Pipeline (E2P2 v2.1) that can cover a significantly greater reaction space and reduce false positive enzyme predictions. Our final database construction relies upon a pathway-level Semi-Automated Validation and Integration (SAVI v3.02) refinement process.
PlantCyc 9.0 currently houses over 180,000 proteins and over 1000 metabolic pathways.
All of the PMN databases can now be explored using the updated 17.5 version of the Pathway Tools software.
We hope that these enhanced resources will be useful to researchers, educators, and students who want to learn more about plant metabolism!