Basic Search | Intermediate Search | Advanced SQL Search | Gene Image Map| Home

Genomic Island Table for Treponema pallidum

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.

Gen. Island ID Start Stop %GC GC Skew Genome Signature Skew Codon Bias
Skew Codon Bias (Ribosomal) Skew Description
1 550459 563497 45.19 1.72 89 -0.51 346 -0.16 424 0.14 recombination, repair, and virulence factor protein containing gene cluster
2 752824 759952 36.19 1.77 86 -0.21 316 0.07 340 0.02 mccF immunity-like protein containing island
3 1123127 1128443 62.77 2.31 157 0.68 525 1.18 609 1.51 uncharacterized genomic island
4 953660 962475 43.28 2.16 92 -0.46 361 -0.05 399 -0.03 ABC transporter containing island

Total Records: 4

Los Alamos National Laboratory     
Operated by the University of California for the National Nuclear Security Administration,
of the US Department of Energy.     Copyright © 2001 UC | Disclaimer/Privacy