PATHsupcre8

PATHsupcre8 identifies and ranks heterologous biosynthetic pathways to optimize microbial cell factories for production of target compounds.

Key Features:

• Pathway search and ranking: Accepts a starting compound, a desired end product, and a heterologous host organism to explore potential biosynthetic routes across a wide range of organisms, including Cyanobacteria.
• Reaction thermodynamics: Evaluates energetic feasibility of candidate reactions within pathways.
• Compound toxicity assessment: Detects potentially toxic intermediates or end products that could affect host viability or yield.
• Product consumption analysis: Identifies intermediates susceptible to consumption by competing metabolic processes that may reduce target yield.
• Host-specific information: Incorporates host-relevant data such as enzyme copy number into pathway evaluation.
• Efficiency and benchmarking: Ranks functional pathways efficiently and has been reported to outperform several similar tools in pathway ranking.

Scientific Applications:

• Synthetic biology and metabolic engineering: Supports rational design of microbial systems for production of pharmaceuticals, biofuels, and specialty chemicals.
• Isoprene production: Demonstrated utility through a case study focusing on isoprene biosynthesis optimization.
• Cocaine biodegradation and bioremediation: Applied in a case study for pathway design relevant to cocaine biodegradation and environmental bioremediation.

Methodology:

Computationally explores biosynthetic routes from a specified starting compound to a target product in a chosen heterologous host (including searches across organisms such as Cyanobacteria) and ranks pathways using feature scores that consider reaction thermodynamics, compound toxicity, product consumption, and host-specific data such as enzyme copy number.