. 2021 May 18;37(20):3560–3568. doi: 10.1093/bioinformatics/btab368

Table 2.

Output of pathway search from tyrosine (C00082) to syringin (C01197)

Distance	Index	Pathway length	Intermediates	Mapping	Pathway score	Average CAR
$\frac{1}{CAR}$	1	4	C00082->C00811->C16827->C00031->C01533	A	9.06	0.51
	2	4	C00082->C00811->C04415->C00029->C01533	B	9.86	0.48
	3	4	C00082->C00811->C16827->C00029->C01533	C	9.86	0.48
	4	8	C00082->C00811->C01197->C01494->C05619->C00482->C05610->C02325->C01533	D^*	9.88	0.86
	5	8	C00082->C00811->C01197->C01494->C02666->C12204->C05610->C02325->C01533	E^*	9.90	0.85
$\sqrt[2]{\frac{1}{CAR}}$	1	4	C00082->C00811->C16827->C00031->C01533	A	5.93	0.51
	2	4	C00082->C00811->C04415->C00029->C01533	B	6.18	0.48
	3	4	C00082->C00811->C16827->C00029->C01533	C	6.18	0.48
	4	5	C00082->C00079->C00423->C04164->C00031->C01533	F	7.00	0.58
	5	5	C00082->C00811->C00423->C04164->C00031->C01533	G	7.00	0.58
$\frac{e^{\frac{1}{CAR}}}{e}$	1	8	C00082->C00811->C01197->C01494->C05619->C00482->C05610->C02325->C01533	D^*	11.09	0.86
	2	8	C00082->C00811->C01197->C01494->C02666->C12204->C12205->C02325->C01533	H^*	11.13	0.85
	3	8	C00082->C00811->C01197->C01494->C02666->C00590->C12205->C02325->C01533	I^*	11.13	0.85
	4	8	C00082->C00811->C01197->C01494->C02666->C12204->C05610->C02325->C01533	E^*	11.13	0.85
	5	9	C00082->C00811->C00223->C00323->C00406->C12203->C00411->C05610->C02325->C01533	J^*	11.79	0.90

Note: Three different CAR transformations were used to calculate the distance between pairs of reactants and products: The first one (1/CAR) is the default option in NICEpath, the second is a square root transformation that decreases the effect of atom conservation, and the third one is an exponential transformation that increases the effect of conserved atoms in reactant–product pairs. Pathways are mapped across distance transformations with letters indicated in the column labeled ‘Mapping’.

Pathways marked with an asterisk correspond to known metabolic pathways that fulfill the criteria of biologically relevant pathways.