Fig 4.

Nucleotide alignments of Dehalococcoides ethenogenes strain 195 genome segments with the tceA- and prophage-containing Dehalococcoides contig from the KB-1 metagenome. In both alignments, tceA and tceB are highlighted in red, annotated phage genes are highlighted in blue, and genes associated with transposable elements are highlighted in purple. Letters A to F correspond to genes examined using PCR (Fig. 5). (Upper alignment) Alignment of two noncontiguous segments of the DET195 genome with the first ∼70 kbp of the Dehalococcoides KB-1 contig. Numbers correspond to the nucleotide positions on the KB-1 Dehalococcoides contig and the DET195 genome coordinates (32). The origin and terminus of the predicted phage genome are marked with blue boundaries. There was no homologous region in the DET195 genome to align to the prophage portion of the KB-1 contig. The bar graph above the alignment depicts identity between the aligned sequences, where a green bar indicates 100% identity and yellow indicates disagreement and where the height of a yellow bar gives the percent identity across a 50-bp window. (Lower alignment) Zoomed-in view of the first 15 kbp of the upper alignment (dashed box), depicting the highly conserved transposable element containing the tceA and tceB genes. Alignments were created using the Geneious alignment algorithm (9), and annotations for the KB-1 contig were determined by the RAST server (2).