Fig 1.
Two branched metabolic pathways.
a) A part of the branched metabolic pathway rn00330 from L-Glutamate to L-Ornithine in KEGG. b) A part of the branched metabolic pathway rn00030 from D-Ribose 5-phosphate to beta-D-Fructose 1,6-bisphosphate in KEGG. The conserved atom groups transferred from source compound to current compound are drawn in red for pathways 1 and 2. The conserved atom groups transferred from source compound to current compound are drawn in orange and green for pathways 3 and 4 respectively. The partition circled with green dashed line in the compound L-Glutamate 5-semialdehyde is the overlapping part of the conserved atom groups of pathways 1 and 2. Note that, in this paper, the compounds and reactions are represented by their KEGG identifiers.
Table 1.
The number of found branched pathways and the average RELCCS, sensitivity, positive prediction value and accuracy for the 30 known core branched pathways tested.
Table 2.
The number of found branched pathways and the average RELCCS, sensitivity, positive prediction value and accuracy for the 20 organism-specific branched pathways tested.
Table 3.
The average RELCCS, sensitivity, positive prediction value and accuracy for the 30 known core pathways tested under different weight parameters.
Table 4.
The average RELCCS, sensitivity, positive prediction value and accuracy for the 20 known organism-specific pathways tested under different weight parameters.
Fig 2.
Branched pathway from pyruvate to L-valine.
a) The known branched pathway from pyruvate to L-valine in KEGG. cr1, cr2 are two sub-branched pathways in this known pathway. b) The found pathway of BPAT-M. c) The found pathway of BPAT-S. d) The found pathway of Retrace. e) The found pathway of BPFinder. dr1, dr2, dr3 are three sub-branched pathways in the found pathway of BPFinder. The compounds circled with dashed ellipses are the branched compounds in the pathways. In the found pathways, the reactions that appear with the same substrates and products in the known pathway are drawn in green. The conserved atom groups from pyruvate in the branched compounds are drawn in red in the dashed rectangles.
Fig 3.
Branched pathway from pregnenolone to 11beta-Hydroxyprogesterone.
a) The known branched pathway from pregnenolone to 11beta-Hydroxyprogesterone in KEGG. b) The found pathway of BPAT-M. c) The found pathway of BPAT-S. d) The found pathway of Retrace. e) The found pathway of BPFinder. The compounds circled with dashed ellipses are the branched compounds in the pathways. In the found pathways, the reactions that appear with the same substrates and products in the known pathway are drawn in green. The conserved atom groups from pregnenolone in the branched compounds are drawn in red in the dashed rectangles.
Fig 4.
Branched pathway from d-Glucose 1-phosphate to 2-Phospho-D-glycerate.
a) The known branched pathway from d-Glucose 1-phosphate to 2-Phospho-D-glycerate in KEGG. er1 and er2 are two sub-branched pathways in this known pathway. b) The found pathway of BPAT-M. c) The found pathway of BPAT-S. d) The found pathway of Retrace. e) The found pathway of BPFinder. fr1 and fr2 are two sub-branched pathways in the found pathway of BPFinder. The compounds circled with dashed ellipses are the branched compounds in the pathways. In the found pathways, the reactions that appear with the same substrates and products in the known pathway are drawn in green. In the sub-branched pathways er1 and fr1, the conserved atom groups from d-Glucose 1-phosphate in the branched compounds are drawn in blue and orange in the dashed rectangles respectively. In the sub-branched pathways er2 and fr2, the conserved atom groups from d-Glucose 1-phosphate in the branched compounds are drawn in red in the dashed rectangles.
Fig 5.
The compounds circled with ellipses are marked as CA-CK and the reactions are marked as R1-R19. The conserved atom groups are drawn in red or blue in the compounds.
Fig 6.
The atom group transferred from pyruvate to (S)-2-Acetolactate in reaction R00226.
The dotted arrows denote the mapping of atoms from pyruvate to (S)-2-Acetolactate via R00226. The partition circled with green dashed line is the atom group transferred from pyruvate to (S)-2-Acetolactate in R00226. The rectangle on the right shows the atom mapping information between the compounds pyruvate and (S)-2-Acetolactate of R00226 in the KEGG RPAIR.
Fig 7.
A linear atom group conserving pathway from pyruvate to 3-Hydroxy-3-methyl-2-oxobutanoate.
This pathway is composed of reactions R00226 and R05071. The conserved atom group transferred from pyruvate to 3-Hydroxy-3-methyl-2-oxobutanoate is marked in red.
Fig 8.
Two branched metabolic pathways obtained by using overlapping rule and non-overlapping rule respectively.
a) The branched pathway obtained by using overlapping rule. b) The branched pathway obtained by using non-overlapping rule. In the compounds bn1 and bn2, a circle represents an atom and the edges connecting atoms represent bonds. The red and blue partitions in the compounds bn1 and bn2 are the conserved atom group transferred from the source compound. The partition circled with green dashed line in the compound bn1 is the overlapping part of the conserved atom group for pathways 1 and 2.
Table 5.
Producing branched pathways.