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_011080: Salmonella enterica subsp. enterica serovar Newport str. SL254,

NCBI: NC_011080

Host Lineage: Salmonella enterica; Salmonella; Enterobacteriaceae; Enterobacteriales; Proteobacteria; Bacteria

General Information: The SL254 strain is an MDR strain from one of two distinct lineages of the Newport serovar. Salmonella enterica subsp. enterica serovar Newport is common worldwide. Outbreak investigations and targeted studies have identified dairy cattle as the main reservoir this serotype. Antimicrobial resistance (Newport MDR-AmpC) is particularly problematic in this serotype, and the prevalence of Newport MDR-AmpC isolates from humans in the United States has increased from 0% during 1996-1997 to 26% in 2001. MDR strains have been recorded as resistant to ampicillin, chloramphenicol, streptomycin, sulphonamides and tetracycline (ACSSuT) and many of these strains show intermediate or full resistance to third-generation cephalosporins, kanamycin, potentiated sulphonamides, and gentamicin. This group of Enterobactericiae have pathogenic characteristics and are one of the most common causes of enteric infections (food poisoning) worldwide. They were named after the scientist Dr. Daniel Salmon who isolated the first organism, Salmonella choleraesuis, from the intestine of a pig. The presence of several pathogenicity islands (PAIs) that encode various virulence factors allows Salmonella spp. to colonize and infect host organisms. There are two important PAIs, Salmonella pathogenicity island 1 and 2 (SPI-1 and SPI-2) that encode two different type III secretion systems for the delivery of effector molecules into the host cell that result in internalization of the bacteria which then leads to systemic spread.



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
1257514830822558Island text2.2173732.39616.4149Neighbours41BLASTN25751.gbk
233312135949426374Island text2.3242441.762836.195Neighbours41BLASTNIslandViewer 333121.gbk
338344140609922659Island text2.411137.011431.4801Neighbours51BLASTN+IslandViewer 383441.gbk
461042863159921172Island text2.2248832.451120.0831Neighbours41BLASTN+IslandViewer 610428.gbk
578085080915728308Island text3.6690643.095824.6713Neighbours41BLASTN+IslandViewer 780850.gbk
6819103*84387224770Island text1.8521830.088818.5041Neighbours41BLASTN+IslandViewer 819103.gbk
792432694696322638Island text2.1873537.889718.2927NeighboursBLASTN+IslandViewer 924326.gbk
81166951119330926359Island text2.4922239.103925.5216Neighbours41BLASTN+IslandViewer 1166951.gbk
91209935123471124777Island text1.861233.621122.5454Neighbours41BLASTN+IslandViewer 1209935.gbk
101321268*133914217875Island text1.7711130.854827.5003Neighbours41BLASTNIslandViewer 1321268.gbk
111470794150838537592Island text1.8333334.134134.6054Neighbours41BLASTN+IslandViewer 1470794.gbk
121709612173614226531Island text2.4046237.591221.7946Neighbours41BLASTN+IslandViewer 1709612.gbk
131750000177244622447Island text1.6277232.703132.9334Neighbours41BLASTN1750000.gbk
141944226*198035236127Island text2.4146138.692519.0598Neighbours41BLASTN+IslandViewer 1944226.gbk
152161696219837536680Island text4.3440544.789627.7487Neighbours41BLASTNIslandViewer 2161696.gbk
162342672236709924428Island text1.681437.416527.5496Neighbours51BLASTN+IslandViewer 2342672.gbk
172722492274217119680Island text2.0146531.240325.1492Neighbours41BLASTN+IslandViewer 2722492.gbk
182761403*277959918197Island text1.6045830.913621.1292Neighbours41BLASTN+IslandViewer 2761403.gbk
192789744*281281123068Island text1.5979336.51253.6302Neighbours51BLASTN2789744.gbk
202870428289413023703Island text2.2069837.061728.8054Neighbours41BLASTN+IslandViewer 2870428.gbk
212897977291952121545Island text1.7252331.626127.3825Neighbours41BLASTN+2897977.gbk
222982346303624053895Island text2.2185535.159125.4057Neighbours41BLASTN+2982346.gbk
233875320*390054525226Island text2.8390540.381821.288Neighbours41BLASTNIslandViewer 3875320.gbk
243941909396414422236Island text1.684939.433434.5048Neighbours51BLASTN+3941909.gbk
253976441399977023330Island text1.6725836.516626.3796Neighbours51BLASTNIslandViewer 3976441.gbk
264177443*420040522963Island text1.3142931.408133.8714Neighbours41BLASTN+4177443.gbk
274461851449032128471Island text2.1888537.42538.0377Neighbours41BLASTNIslandViewer 4461851.gbk
284543000457179028791Island text1.9953736.400236.2352Neighbours41BLASTN+IslandViewer 4543000.gbk
294703266472876525500Island text2.764238.008823.4365Neighbours41BLASTN+IslandViewer 4703266.gbk