n1_4mer:GRV/n1_4mer:RV = (Global Relative Variance of OU patterns) / (Local Relative Variance of OU patterns)
n0_4mer:D = Distance between local and global OU patterns
n0_4mer:PS = Distance between 2 strands of same DNA molecule
Selected loci indicated by large D, increased GRV associated with decreased RV and moderate increase in PS
NC_004432: Mycoplasma penetrans HF-2, complete genome NCBI: NC_004432 Host Lineage: Mycoplasma penetrans; Mycoplasma; Mycoplasmataceae; Mycoplasmatales; Tenericutes; Bacteria General Information: This strain has been isolated from the tracheal aspirate of a previously healthy HIV-negative patient with severe respiratory symptoms caused by this infection. Causes urogenital and respiratory disease. This genus currently comprises more than 120 obligate parasitic species found in a wide spectrum of hosts, including humans, animals, insects and plants. The primary habitats of human and animal mycoplasmas are mucous membranes of the respiratory and urogenital tracts, eyes, mammary glands and the joints. Infection that proceeds through attachment of the bacteria to the host cell via specialized surface proteins, adhesins, and subsequent invasion, results in prolonged intracellular persistence that may cause lethality. Once detected in association with their eukaryotic host tissue, most mycoplasmas can be cultivated in the absence of a host if their extremely fastidious growth requirements are met. The latter is one of the major traits that puts them in the separate taxonomic group of microorganisms, class Mollicutes. The cell membrane is rich in protein components (up to two thirds of the membrane mass) that largely consists of highly structurally adaptive lipoproteins employed in invading the host immune system, attachment to the host cells, and pathogenic invasion. Cell division proceeds via normal binary fission or via elongation of a parental cell to form multinucleated filaments and the subsequent breakup to form coccoid bodies.Mycoplasmas carry the smallest genomes of self-replicating cells (less than 500 recognizable coding regions), which is one of the reasons they were among the first microorganisms selected for the genome-sequencing projects. During their evolution, mycoplasmas appear to have lost all of the genes involved in amino acid and cofactor biosynthesis, synthesis of the cell wall and lipid metabolism, resulting in a requirement for the full spectrum of substrates and cofactors taken up from the host or from the complex artificial culture medium. They have lost a number of genes involved in cellular processes, such as cell division, heat shock response, regulatory genes, the two-component signal transduction systems, histidine protein kinases or their target response regulators, and most transcription factors. The majority of mycoplasmas are deficient in genes coding for components of intermediary and energy metabolism and thus are dependent mostly on glycolysis as an ATP-generating pathway. This organism infects humans in the urogenital and respiratory tracts though invasion of tissues. The disease is mainly associated with HIV-1 infection, particularly in the homosexual population, and is very persistent and believed to contribute to the deterioration of the immune system during HIV. Mycoplasma penetrans infection has also been suggested to be a primary cause of some forms of human urethritis and respiratory disease in non-HIV individuals.
Islands with an asterisk (*) contain ribosomal proteins or RNA related elements and may indicate a False Positive Prediction!