Fig. 1

Overview of in silico approaches to identify limitations to anaerobic growth in P. putida. a Summary of genome-scale GSM predictions using iJP962 [7] given an aerobic environment (left) and expansions with indicated reaction sets given an anaerobic environment (right). The colours indicate no growth (orange), poor growth (purple) and growth (green). b Comparative genomics workflow. Genomes of the P. putida group and the anaerobic Pseudomonas group were systematically annotated using SAPP [22, 23], the protein domains were extracted, and the domains common to all anaerobic Pseudomonas species (the core domains) were selected. Predictions from both methods were combined to obtain a final design