Pre_GI Island

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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_010729: Porphyromonas gingivalis ATCC 33277, complete genome

NCBI: NC_010729

Host Lineage: Porphyromonas gingivalis; Porphyromonas; Porphyromonadaceae; Bacteroidales; Bacteroidetes; Bacteria

General Information: This strain was isolated from human gingiva. This organism is associated with severe and chronic periodontal (tissues surrounding and supporting the tooth) diseases. Progression of the disease is caused by colonization by this organism in an anaerobic environment in host tissues and severe progression results in loss of the tissues supporting the tooth and eventually loss of the tooth itself. The black pigmentation characteristic of this bacterium comes from iron acquisition that does not use the typical siderophore system of other bacteria but accumulates hemin. Peptides appear to be the predominant carbon and energy source of this organism, perhaps in keeping with its ability to destroy host tissue. Oxygen tolerance systems play a part in establishment of the organism in the oral cavity, including a superoxide dismutase. Pathogenic factors include extracellular adhesins that mediate interactions with other bacteria as well as the extracellular matrix, and a host of degradative enzymes that are responsible for tissue degradation and spread of the organism including the gingipains, which are trypsin-like cysteine proteases.

Islands with an asterisk (*) contain ribosomal proteins or RNA related elements and may indicate a False Positive Prediction!

#StartEndLengthIsland TextGRV_RVDPSNeighboursClusterSub ClusterBLASTNKey Word ConfirmationOther DB ConfirmationDownload Island
1225616*24523819623Island text1.5168133.440148.7581Neighbours312BLASTN+IslandViewer 225616.gbk
2265791*29310327313Island text1.6738737.992130.2035Neighbours355BLASTN+265791.gbk
3619664*65510835445Island text2.6943535.272325.1912Neighbours21BLASTN+IslandViewer 619664.gbk
41014957103460619650Island text1.5131530.040130.8137Neighbours21BLASTN+IslandViewer 1014957.gbk
51179008*120985230845Island text2.4397234.870115.1062Neighbours21BLASTN+IslandViewer 1179008.gbk
61344903*136284917947Island text2.0548428.672238.9877Neighbours312BLASTN+1344903.gbk
71385217140844823232Island text1.6428626.404438.9268Neighbours312BLASTN1385217.gbk
81462135148658524451Island text1.6940129.231530.4117Neighbours312BLASTN+1462135.gbk
91549744*156891619173Island text1.4958137.135250.1096Neighbours312BLASTN+1549744.gbk
101818500*183909920600Island text1.5753534.84428.0467Neighbours355BLASTN+1818500.gbk
112038118205650218385Island text1.5120430.058435.6986Neighbours312BLASTNIslandViewer 2038118.gbk
122147268*216760520338Island text1.5214131.980828.7087Neighbours312BLASTN+2147268.gbk