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Fig. 5 | BMC Bioinformatics

Fig. 5

From: Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

Fig. 5

Proteins in the periplasm involved in the assembly of fimbriae are enriched in antioxidative properties. a PCA of antioxidative properties for periplasmic fimbriae assembly proteins, in relation to their simulated ROStype and annotated pathotype. PC1 separates the observed ExPEC/AIEC/APEC strains well, confirmed by DBSCAN clustering (Table 1, Table 2). The location of two asymptomatic strains (83972) is specified as they have been found to outcompete UPEC strains in adhesion of the bladder wall [51]. b Specific antioxidative properties contributing to PC1. The 2D and 3D columns indicate if the protein subsequences were determined by predictions from sequence (2D) or calculations from structure (3D). c Selected examples from the proteins involved in fimbriae assembly that show enrichment of antioxidative properties. YehB, YehD, and YfcS are relatively unknown components of operons similar to the fim operon [52]. Up to 3000 copies of FimA form the structural pilus of the fimbriae [53]. Highlighted residues indicate mutations which are seen in the cluster with the most ExPEC/AIEC/APEC pathotypes. The size of the highlighted residue corresponds to the number of strains that mutation appears in. Note that all mutations do not co-occur together in all strains. The structures shown here are from a collection of homology models from the SWISS-MODEL and I-TASSER modeling pipelines [48, 54]

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