Figure 10. Predictions for four organisms lacking a metabolic reconstruction.

A, The number of nutrients found to be uptaken by four organisms for which we lack a metabolic reconstruction: Rhodopseudomonas palustris (gram-negative bacterium), Listeria monocytogenes (gram-positive bacterium), Dictyostelium discoideum (eukaryote), and Thermoplasma acidophilum (archaeon). The nutrients were determined using predictions found in TransportDB (http://www.transportdb.org). B, Prediction of whether a nutrient is a source of carbon according to class. Bars in the top panel represent predictions of G nutrients, whereas bars in the bottom panel represent predictions of NG nutrients. None of the species had fatty acids listed as nutrients, but since fatty acids can be uptaken by diffusing through the cell membrane, we show here the predictions for fatty acids as well. The prediction for nutrients in the Organic compounds class are based on our logistic regression using the KEGG pathway terms. Thus some nutrients are predicted to be G while others are predicted to be NG.