Metabolic pathway reconstruction has been used to generate the first legume pathway database for Medicago truncatula (MedicCyc) and currently features more than 240 pathways with related genes, enzymes, and metabolites. MedicCyc was assembled based on over 225,000 Medicago truncatula ESTs and available genomic sequences (for more information see Introduction). The initial compilation was manually annotated to remove non plant pathways, and several Medicago-specific pathways including isoflavonoid, lignin, and saponin biosyntheses were modified or added based on available literature. Predicted pathways and annotations in MedicCyc were then verified through comparison with AraCyc and RiceCyc database. MedicCyc can be used as a reference for the study of primary and secondary metabolism of Medicago truncatula as well as for other legume species.

Introduction - all the information you need concerning the creation of MedicCyc and the current status of its content.

Contents of MedicCyc - summary of current version Medicago truncatula database. Information about numbers of transcripts used for pathways reconstructions, number reconstructed pathways, including number of enzymatic reactions and compounds.

Search MedicCyc - a link, which allows you to search or browse the information (Pathways, Compounds, Enzymes...) contained in the MedicCyc database.

Release note

Omics viewer - map your microrray expression, metabolomics and other datasets on Pathway overview diagrams.

Current pathway holes of medicago truncatula - list of the reactions for which no corresponding enzymes have been identified in Medicago truncatula annotated part of genome, which were used for current version of MedicCyc.

Useful external links

• Center for Medicago Genomics Research • Medicago truncatula sequencing resources • Medicago truncatula Gene Index (MtGI) at TIGR • AraCyc • RiceCyc • MetaCyc • Pathway Tools software • KEGG pathway • IUBMB Enzyme nomenclature • BRENDA enzyme database