Reconstructor

Reconstructor generates SBML-compliant genome-scale metabolic reconstructions (GENREs) from annotated protein .fasta sequences, BLASTp output, or existing SBML models and applies parsimony-based gap-filling to produce COBRApy-compatible models for microbial metabolic analysis.

Key Features:

• COBRApy Compatibility: Produces models compatible with COBRApy to enable downstream network analysis.
• High-Quality Draft Reconstructions: Generates high-quality GENREs with consistent reaction and metabolite naming.
• Gap-Filling Technique: Incorporates a parsimony-based gap-filling method that adds the minimal set of reactions required to close network gaps.
• Flexible Input Options: Accepts annotated protein .fasta sequences (Type 1), BLASTp output (Type 2), and existing SBML GENREs for further refinement (Type 3).
• Bacterial Reconstructions: Demonstrated to generate bacterial reconstructions that capture functional metabolic differences across strains, species, and higher taxonomic levels.

Scientific Applications:

• Microbial metabolism reconstruction: Produces detailed metabolic models that reflect genetic and phenotypic diversity in microbes.
• Comparative metabolic analysis: Enables comparison of metabolic capabilities across strains, species, and higher taxonomic ranks.
• Growth phenotype prediction: Supports prediction of growth conditions and metabolic capabilities from reconstructed models.
• Target identification for biotechnology and drug development: Facilitates identification of metabolic targets for biotechnological engineering or drug discovery.

Methodology:

Generates SBML-compliant GENREs from input data (annotated protein .fasta, BLASTp output, or SBML GENREs) and applies a parsimony-based gap-filling method to add the minimal reactions needed; output models are compatible with COBRApy.