Table 2

Grouping compounds into equivalence classes clarifies their nutrient roles
Class Element(s) Compounds
1 C alpha-D-glucose, glycerol, D-mannose, D-glucarate, and 27 others
2 C, P beta-D-glucose-6-phosphate,alpha-D-glucose-1-phosphate, 2 others
3 C, N N-acetyl-beta-D-glucosamine, L-serine, adenosine, and 7 others
4 C, N L-alanine, D-alanine, and 2 others
5 C, N glycylproline
6 C (R)-malate
7 C acetoacetate
8 C fumarate
9 C 2-oxoglutarate
10 C acetate
11 C formate
12 C (S)-lactate
13 C succinate
14 C, N ethanolamine
15 C, N L-proline
16 C, N L-glutamine
17 C, N L-glutamate
18 N ammonium
19 C, P sn-glycerol-3-phosphate
20 P phosphate
21 S sulfate

The equivalence classes of compounds generated from our original minimal nutrient sets are shown here. All the compounds in an equivalence class are interchangeable in their roles in predicted minimal nutrient sets. For example, alpha-D-glucose (class 1) can substitute for glycerol, D-mannose, and so forth. Column one shows the class’ number, column two shows the elements that we believe it provides as part of predicted minimal nutrient sets, and column three lists all or a representative part of the compounds contained within the class.

Eker et al.

Eker et al. BMC Bioinformatics 2013 14:114   doi:10.1186/1471-2105-14-114

Open Data