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Table 1 F1 scores of the closest pathway found by the HPAT meta-algorithm (uses precomputed subpaths) and LPAT algorithm (does not use precomputed subpaths) compared to known pathways, where an F1 score of one indicates that the HPAT search found the exact known pathway

From: Improving the organization and interactivity of metabolic pathfinding with precomputed pathways

  F 1 Score, LPATF 1 Score, LPAT
Known pathwayF 1 Score, HPAT(Top 20 Paths)(All Paths)
Pyruvate → Lysine I1.000.700.70
Pyruvate → Lysine II1.000.700.70
Pyruvate → Lysine III1.001.001.00
Pyruvate → Lysine IV1.000.780.78
Pyruvate → Lysine V1.0000
Glutamate → Proline1.001.001.00
UDP-Galactose → Stachyose1.001.001.00
alpha-D-glucose → Phenylpyruvate0.71 +0.710.71
alpha-D-glucose → Dopamine0.59 0.420.76
*Pyruvate → 3-HP, I1.001.001.00
*Pyruvate → 3-HP, II0.50 0.330.33
*Pyruvate → 3-HP, III0.60 0.380.78
*Pyruvate → 3-HP, IV0.42 0.710.71
*Pyruvate → 3-HP, V0.36 0.400.40
*Pyruvate → 3-HP, VI0.36 #0.360.36
*Pyruvate → 3-HP, VII0.53 #0.360.50
Glucose → Glucaric acid1.001.001.00
alpha-D-glucose → 1,3-propanediol1.000.671.00
Tryptophan → Melatonin1.001.001.00
  1. The closer the F1 score is to one, the more similar the found pathway’s reactions are to that of the known pathway. The first column of F1 scores for LPAT is calculated based on the closest pathway within the top twenty pathways found by LPAT, while the second column of F1 scores for LPAT is calculated based on the closest pathway for all LPAT pathway results
  2. *Pathway is experimentally validated; does not exist naturally in organisms
  3. #Requires an engineered, non-natural 2,3-alanine aminomutase
  4. +Known pathway conserves less than two carbons
  5. Hub in canonical pathway closest to start/target not among closest hubs