Fig. 2: Genomic organization of eleven of the prophages in this study. | The ISME Journal

Fig. 2: Genomic organization of eleven of the prophages in this study.

From: Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

Fig. 2: Genomic organization of eleven of the prophages in this study.

Numbers correspond to the host genomes, as displayed in Fig. 3. The number in parenthesis identifies the prophage in the genome. All prophages are classified as “intact” except #63 (1) (“questionable”). Genome boundaries correspond to attL/R sites. Arrows represent predicted ORFs and are oriented according to transcriptional direction. Colors indicate assigned functional categories, tRNAs are represented as red lines and the sequences are oriented based on the putative integrase localization. Local blastn alignments (option dc-megablast) are displayed between pairs of related prophages, colored according to the percentage of identity. The Viral Quotient (VQ) from pVOG is displayed below or on top of each ORF, with gray meaning that there was no match in the pVOG profiles database and thus no associated VQ value. Prophages #62 (2) and #54(1) have inserted the core gene icd, and the boundaries correspond to icd on the right and the most distal att site found, which is likely to be a remnant prophage border. The most proximal att site is also annotated (vertical black line). This figure was generated using the R package GenoPlotR v0.8.9 [103].

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