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Fig. 1 | BMC Biotechnology

Fig. 1

From: Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri

Fig. 1

The L. reuteri ATCC PTA 6475 genome-scale metabolic reconstruction. (a) Template-based modeling pipeline. The iNF517 was employed as the primary template model and extracted ortholog genes and reactions based on bidirectional best hits (BBH) to generate the draft models. After comparing with LbReuteri, iML1515 and iBT721, the exchange and transport reactions were added from the templates according to the transporter annotations and corresponding medium composition. The gap-filling was performed with COBRApy on the primary template model and used the MetaCyc database as a backup to improve the model performance. The GEM was also manually curated during the simulation and validation. (b) The COG functional distribution of genes in GEM. J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; D, cell cycle control, cell division, chromosome partitioning; V, defense mechanisms; T, signal transduction mechanisms; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification, protein turnover, chaperones; C, energy production and conversion; G, carbohydrate transport and metabolism; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; *, no COG categories. (c) The venn diagram of common and unique reactions in the four lactic acid bacterium models. iHL622 is the GEM of L. reuteri ATCC PTA 6475 in this study, iNF517, LbReuteri and iBT721 are the GEMs of L. lactis MG1363, L. reuteri JCM 1112 and L. plantarum WCFS1 separately

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