Fig. 2

Overview of in silico approaches to identify limitations to anaerobic respiration in P. putida. a Comparative genomics workflow. Genomes of the P. putida group and the anaerobic Pseudomonas group were systematically annotated using SAPP [24, 29], the protein domains were extracted, and both all domains or only the domains common to all anaerobic Pseudomonas species (the core domains) were selected using a 95% persistence threshold. Analysis was performed on the whole set of genomes (left) or a genome cluster of closely related strains (right). Each of these methods resulted in a list of protein domains related to an aerobic lifestyle (purple) or an anaerobic lifestyle (light green). b Transcriptome analysis. c GSM simulations. GSM iJP962 [5] and iJN1411 [35] were expanded with indicated reaction sets and tested for anaerobic growth under anaerobic conditions. Colours indicate final implementation in the design (green). Model and genome base predictions were combined to obtain a final design