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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, LPAT F 1 Score, LPAT
Known pathway F 1 Score, HPAT (Top 20 Paths) (All Paths)
Pyruvate → Lysine I 1.00 0.70 0.70
Pyruvate → Lysine II 1.00 0.70 0.70
Pyruvate → Lysine III 1.00 1.00 1.00
Pyruvate → Lysine IV 1.00 0.78 0.78
Pyruvate → Lysine V 1.00 0 0
Glutamate → Proline 1.00 1.00 1.00
UDP-Galactose → Stachyose 1.00 1.00 1.00
alpha-D-glucose → Phenylpyruvate 0.71 + 0.71 0.71
alpha-D-glucose → Dopamine 0.59 0.42 0.76
*Pyruvate → 3-HP, I 1.00 1.00 1.00
*Pyruvate → 3-HP, II 0.50 0.33 0.33
*Pyruvate → 3-HP, III 0.60 0.38 0.78
*Pyruvate → 3-HP, IV 0.42 0.71 0.71
*Pyruvate → 3-HP, V 0.36 0.40 0.40
*Pyruvate → 3-HP, VI 0.36 # 0.36 0.36
*Pyruvate → 3-HP, VII 0.53 # 0.36 0.50
Glucose → Glucaric acid 1.00 1.00 1.00
alpha-D-glucose → 1,3-propanediol 1.00 0.67 1.00
Tryptophan → Melatonin 1.00 1.00 1.00
  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