General structure of ssrA genomic islands (ssrA-GIs). (A) Generalized structure of Dehalococcoides ssrA-GIs, oriented according to published Dehalococcoides complete genomes. Labels below genes in the integration module indicate the most informative homolog of the protein encoding gene. (B) Alignment of the 84 bp region surrounding the 3' end of ssrA or its direct repeat (DR) fragments (shaded black in the consensus) from 40 such positions in available Dehalococcoides genomes. Each sequence is labeled by its strain or enrichment name, underscore, and the order in which it occurs, beginning with the 3' end of ssrA. Positions in the alignment that disagree with the 75% consensus sequence are shaded in darker grey. The alignment is ordered such that sequences corresponding to Dehalococcoides ssrA ("_01") are the top 10 sequences, emphasizing a conserved position of disagreement between ssrA sequences and the direct repeat regions, position 15 in the alignment, 333 in ssrA. The two bases flanking the inferred integration site are marked with a hash. (C) To-scale genomic maps of region downstream of Dehalococcoides ssrA in (meta)genomic datasets. Orientation of genes is indicated with arrows. Key genes are shaded according to the provided legend.
McMurdie et al. BMC Genomics 2011 12:287 doi:10.1186/1471-2164-12-287