SynPAL identifies metabolic pathway genes conserved as co-directional chromosomal clusters across prokaryotes and ranks pathways by readiness for cluster-based heterologous reconstruction.
Gene order is scored per pathway by co-directional clustering (same replicon, same strand, intergenic distance ≤ 2 kb) across55 prokaryotic genomes derived from BioCyc.
method v2 co-directional · max gap 2,000 bp · real genomic coordinates
- Metabolic pathways
- 887
- BioCyc-derived, analyzable
- Prokaryotic genomes
- 55
- 52 Bacteria · 3 Archaea
- MEDIUM + HIGH
- 32.7%
- medium-to-high clustering
- Design-ready
- 307
- T1 + T2 of 887
Analysis pipeline
The pipeline maps pathway genes to chromosomal coordinates, detects co-directional clusters, scores cross-species conservation, and exports assembly-oriented constructs. The same four steps run across all 887 analyzable pathways.
Map
Each pathway's enzymes are anchored to 55 genomes using real genomic coordinates — not pathway-table column order.
Cluster
Co-directional genes on the same replicon within2,000 bp are grouped into candidate operon-like clusters.
Score
Cluster, order, and strand conservation are scored against a randomized null to separate real synteny from chance proximity.
Design
The best-scoring arrangement is exported as an assembly-oriented cassette — order, parts, and primers — ranked by design-readiness tier.
Resource overview
All data are static and downloadable — no accounts, no API keys.