XTMS

XTMS explores and evaluates metabolic pathways to identify and prioritize heterologous routes for producing value-added chemicals in chassis organisms such as Escherichia coli.

Key Features:

• Extended Metabolic Space (XMS) framework: Provides a modeling framework to enumerate potential pathways that can be integrated into a chassis organism.
• Molecular signature–derived reaction rules: Uses molecular signatures as a coding system to derive reaction rules for metabolic reactions.
• Substrate and product enumeration: Enumerates all corresponding substrates and products implied by the derived reaction rules.
• In vivo biochemical transformation identification: Identifies biochemical transformations capable of being processed in vivo.
• Pathway evaluation metrics: Evaluates pathways by metabolite exchange capabilities, maximum allowable pathway yield, toxicity considerations, and enzyme efficiency.
• Non-natural metabolite processing and enzyme discovery: Expands the scope to process non-natural metabolites and discover novel enzymatic transformations.

Scientific Applications:

• Metabolic pathway exploration in industrial organisms: Explores and proposes heterologous pathways for organisms such as Escherichia coli.
• Metabolic engineering design and rationalization: Prioritizes pathway designs based on yield, exchange, toxicity, and enzyme efficiency considerations.
• Production of value-added chemicals: Supports identification of routes for sustainable production of diverse chemicals in engineered organisms.
• Discovery of novel biochemistry: Enables processing of non-natural metabolites and discovery of novel enzymatic transformations.

Methodology:

Uses the Extended Metabolic Space modeling framework and molecular signatures to derive reaction rules, enumerate substrates and products, identify biochemical transformations capable of being processed in vivo, and evaluate pathways on metabolite exchange, yield, toxicity, and enzyme efficiency.