Pre_GI Island

Some Help

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_009089: Clostridium difficile 630, complete genome

NCBI: NC_009089

Host Lineage: Peptoclostridium difficile; Peptoclostridium; Peptostreptococcaceae; Clostridiales; Firmicutes; Bacteria

General Information: This strain is the epidemic type X variant that has been extensively studied in research and clinical laboratories. It produces both toxin A, and B. Causative agent of pseudomembranous colitis. This genus comprises about 150 metabolically diverse species of anaerobes that are ubiquitous in virtually all anoxic habitats where organic compounds are present, including soils, aquatic sediments and the intestinal tracts of animals and humans. This shape is attributed to the presence of endospores that develop under conditions unfavorable for vegetative growth and distend single cells terminally or sub-terminally. Spores germinate under conditions favorable for vegetative growth, such as anaerobiosis and presence of organic substrates. It is believed that present day Mollicutes (Eubacteria) have evolved regressively (i.e., by genome reduction) from gram-positive clostridia-like ancestors with a low GC content in DNA. Some species are capable of producing organic solvents (acetone, ethanol, etc,), molecular hydrogen and other useful compounds. This species is now recognized as the major causative agent of pseudomembranous colitis (inflammation of the colon) and diarrhea that may occur following antibiotic treatment. This bacterium causes a wide spectrum of disease, ranging from mild, self-limiting diarrhea to serious diarrhea and, in some cases, complications such as pseudomembrane formation, toxic megacolon (dilation of the colon) and peritonitis, which often lead to lethality among patients. The bacteria produce high molecular mass polypeptide cytotoxins, A and B. Some strains produce only one of the toxins, others produce both. Toxin A causes inflammatory reaction involving hypersecretion of fluid and hemorrhagic necrosis through triggering cytokine release by neutrophils. Alteration of intestinal microbial balance with antibiotic therapy and increased exposure to the bacterium in a hospital setting allows C. difficile to colonize susceptible individuals. Moreover, it has been shown that subinhibitory concentrations of antibiotics promote increased toxin production by C. difficile.



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
11*3459934599Island text6.1083323.258442.4062Neighbours21BLASTN1.gbk
287581*10818120601Island text2.8595521.692737.8423Neighbours21BLASTN87581.gbk
3117980*16311645137Island text7.6495334.067947.6547Neighbours21BLASTN+117980.gbk
4370555*39409923545Island text6.9374924.57343.8426Neighbours21BLASTN+IslandViewer 370555.gbk
542807546635638282Island text3.2622632.249436.4991Neighbours21BLASTN+IslandViewer 428075.gbk
6478328*51663738310Island text3.21124.513536.7822Neighbours21BLASTN+IslandViewer 478328.gbk
758165560656324909Island text3.1778427.60329.8366Neighbours21BLASTN+IslandViewer 581655.gbk
887329590009926805Island text3.0172123.805937.4153Neighbours21BLASTNIslandViewer 873295.gbk
996595998833722379Island text2.4728621.525436.393Neighbours21BLASTN+IslandViewer 965959.gbk
101093832111768023849Island text3.8222820.619540.7662Neighbours21BLASTN+IslandViewer 1093832.gbk
111202261*123169329433Island text6.0104325.291244.9013Neighbours21BLASTNIslandViewer 1202261.gbk
121283000132421841219Island text3.3075740.731737.2895BLASTN+IslandViewer 1283000.gbk
131329826135215322328Island text2.5344720.491931.8979Neighbours21BLASTN+1329826.gbk
142150062217431124250Island text2.6405923.362329.9659Neighbours21BLASTN+IslandViewer 2150062.gbk
153142976*316557022595Island text6.7235125.902642.4394Neighbours21BLASTNIslandViewer 3142976.gbk
163241918326675524838Island text3.2182421.810336.2407Neighbours21BLASTNIslandViewer 3241918.gbk
173782000380409922100Island text3.0600621.209336.8193Neighbours21BLASTN3782000.gbk
183889811392148531675Island text3.4027738.147432.2125Neighbours21BLASTN+IslandViewer 3889811.gbk
193935500*397916543666Island text3.4268629.761533.4491Neighbours21BLASTN+IslandViewer 3935500.gbk
203998347*402074022394Island text5.5976821.87534.048Neighbours21BLASTN+3998347.gbk
214140764*416313522372Island text7.1674824.063743.4127Neighbours21BLASTN4140764.gbk
224177117420070723591Island text2.9933119.102628.6454Neighbours21BLASTN+IslandViewer 4177117.gbk