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Genomic islands (GI) are formerly mobile genetic elements that have been integrated into an organism's genome. They encode a variety of different functions that depend largely on the environment of the organism, and can be involved in symbiosis or pathogenesis. Often, they confer on an organism fitness to occupy a particular ecological niche. (Hentschel et al., Microbes Infect. 2001 Jun;3(7):545-8.). A single mobile element can be found in many distantly related species. The lateral gene transfer of mobile elements occurs between different organisms and strains in a variety of ways: Transformation, Conjugation, and Transduction. Base Composition Analysis (G+C content, genome signature, codon usage) can be used to identify laterally transferred genes. Base composition analyses methods established by Samuel Karlin (Trends Microbiol. 2001 Jul;9(7):335-43.) were used to find atypical genes. BLAST taxonomy data was also used to find genes with hits to viral or plasmid genes which indicates a possible lateral gene transfer.
The following table contains records of GIs that have been identified in Treponema pallidum using base composition analyses and BLAST taxonomy data. The genome coordinates, the value of each parameter and a measure of its deviation is provided for each island. The skew is the number of standard deviations from the genome mean value of the quantity measured. The Genomic Island ID is hyperlinked to a annotated GI record that contains more detailed information.
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