Fig. 2

Global pairwise sequence alignment of distinct tfs4 ICE modular subtypes. The ‘vir’ gene labelled tfs4 ICE gene cluster (top) is representative of the tfs4 ICE from strain G27 (L1C1R1, including genes 0959–0986) used as a reference scaffold sequence for each ICE alignment and closely approximates the position of genes in the alignment graphs. L1, C1 and R1 module gene complements are coloured blue, whereas orthologous genes characteristic of L2, C2, R2 modules are shown coloured red in the schematic of the L2C2R2 ICE type from strain R036d (bottom). Sequence conserved genes common to all tfs4 ICEs are coloured cyan. Global pairwise sequence alignments of different tfs4 ICEs was performed using the Shuffle-LAGAN alignment program in mVISTA. Individual mVISTA graphs depict sequence similarity of tfs4 ICEs from strains Shi470 (L1C1R1, genes 4480–4640), R036d (L2C2R2, genes 0976–1010), P12 (L2C1R2, genes 0437–0473), NQ4053 (L2C1R1, genes 1511–1596), P-25 (L2C1R1f, genes 1401–1438), A-8 (L1C1R1f, genes 0913–0945), A-11 (LmC1R1, genes 0721–0756), PeCan4 (LmC1R2, genes 7670–7835) and SouthAfrica7 (LmC2R2, genes 7540–7710) relative to the G27 tfs4 ICE using a 50 bp calculation window and 70% sequence identity cut-off. The midline in individual alignment graphs corresponds to 50% sequence identity to the G27 reference tfs4 ICE sequence and regions with sequence identity ≥ 70% are indicated by blue (coding sequence) or red (non-coding intergenic sequence) shading