FMM

FMM reconstructs metabolic pathways between specified metabolites across species using KEGG and other integrated biological databases to support comparative pathway analysis, gene selection, and metabolic engineering.

Key Features:

• Pathway Reconstruction: Reconstructs metabolic routes from one metabolite to another across species based on curated pathway data.
• Database Integration: Leverages the Kyoto Encyclopedia of Genes and Genomes (KEGG) along with additional integrated biological databases for pathway information.
• KEGG Map Connectivity and Visualization: Connects different KEGG maps and provides both local and global graphical views of metabolic networks.
• Synthetic Biology and Metabolic Engineering Support: Assists design and analysis of bio-orthogonal systems and reconstruction of pathways to produce target metabolites or secondary metabolites in microorganisms such as bacteria and yeast.
• Gene Elucidation for Cloning: Identifies candidate genes from various species for cloning into target organisms via comparative pathway analysis.
• Support for Pharmaceutical and Biofuel Production: Elucidates pathways relevant to the biosynthesis of drugs and biofuels to inform engineering strategies.

Scientific Applications:

• Synthetic Biology Design: Enables identification and assembly of heterologous pathways for novel biosynthetic functions.
• Metabolic Engineering: Informs pathway selection and modification to produce desired metabolites in microbial hosts.
• Comparative Pathway Analysis: Compares metabolic routes across species to find conserved or alternative enzymatic conversions.
• Heterologous Gene Selection: Supports selection of candidate genes from donor species for cloning into production strains.
• Bioprocess Development for Pharmaceuticals and Biofuels: Guides pathway-based strategies for synthesis of pharmaceutical compounds and biofuels.

Methodology:

Analyzes KEGG and other integrated biological databases to reconstruct pathways, connects KEGG maps, and provides local and global graphical visualizations of the resulting metabolic networks.