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_015571: Porphyromonas gingivalis TDC60, complete genome

NCBI: NC_015571

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

General Information: 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
1168617*19730428688Island text2.1443735.872631.7871Neighbours312BLASTN+IslandViewer 168617.gbk
2260664*27999219329Island text1.5664830.297528.819Neighbours312BLASTNIslandViewer 260664.gbk
3290355*31493124577Island text2.0364532.323136.3016Neighbours312BLASTN+290355.gbk
441115643280321648Island text2.5786432.617128.3551Neighbours21BLASTN+IslandViewer 411156.gbk
5440605*46793427330Island text1.6791538.266931.6303Neighbours355BLASTN+440605.gbk
6722815*74581723003Island text2.2214231.295229.021Neighbours312BLASTN722815.gbk
780171582667424960Island text2.4519933.025714.456Neighbours312BLASTN+IslandViewer 801715.gbk
81030527106170831182Island text2.327234.08519.5776Neighbours312BLASTN+IslandViewer 1030527.gbk
91065775108656820794Island text1.6012730.984736.6307Neighbours21BLASTN+1065775.gbk
101207000122958422585Island text2.5029333.951822.9029Neighbours312BLASTN1207000.gbk
111265121*128814623026Island text1.4828237.749346.1932Neighbours312BLASTN+IslandViewer 1265121.gbk
121495286*151559920314Island text1.5478435.001226.7054Neighbours355BLASTN1495286.gbk
132002489*204114838660Island text1.649231.347520.483Neighbours21BLASTN+IslandViewer 2002489.gbk
142044000210147957480Island text3.0632633.331418.8686Neighbours21BLASTN+IslandViewer 2044000.gbk
152273503*229324619744Island text1.6028832.601248.2321Neighbours312BLASTN2273503.gbk