Pre_GI: SEQWORD Parameters

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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




Query: NC_017179:905347 Clostridium difficile BI1, complete genome

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

General Information: Clostridium difficile BI1 is a human strain isolated in the United States in 1988. 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. C. difficile infection represents one of the most common nosocomial (originating in a hospital) infections. 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. Cytotoxin B depolymerizes actin, the major protein of the cytoskeleton, and thus aids in destruction of tissues. The combined action of the toxins results in necrosis of superficial epithelium and edema (fluidic swelling) in affected areas of intestine. Proliferation of C. difficile is normally prevented by normal intestinal microflora, which is believed to inhibit attachment of the bacterium and its toxins to intestinal walls. 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.



Query GRV_RV = 7.29776

Lower LimitUpper Limit



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

IslandHost DescriptionGRV_RVNeighboursBLASTN
NC_010511:7553703*Methylobacterium sp. 4-46 chromosome, complete genome5.79981NeighboursBLASTN
NC_016024:1876000Candidatus Chloracidobacterium thermophilum B chromosome chromosome5.80687NeighboursBLASTN
NC_013315:3689422Clostridium difficile CD196 chromosome, complete genome5.81212NeighboursBLASTN
NC_009092:1599526Shewanella loihica PV-4, complete genome5.82606NeighboursBLASTN
NC_015913:35837*Candidatus Arthromitus sp. SFB-mouse-Japan, complete genome5.83789NeighboursBLASTN
NC_017294:71494Candidatus Arthromitus sp. SFB-mouse-Yit, complete genome5.84125NeighboursBLASTN
NC_011748:2324495Escherichia coli 55989, complete genome5.84485NeighboursBLASTN
NC_012796:4075583*Desulfovibrio magneticus RS-1, complete genome5.84605NeighboursBLASTN
CU928145:2324495Escherichia coli 55989 chromosome, complete genome5.84666NeighboursBLASTN
NC_020418:603750*Morganella morganii subsp. morganii KT, complete genome5.84822NeighboursBLASTN
NC_012796:2757500Desulfovibrio magneticus RS-1, complete genome5.84904Neighbours
NC_009617:5545477Clostridium beijerinckii NCIMB 8052 chromosome, complete genome5.85403NeighboursBLASTN
NC_003030:303812*Clostridium acetobutylicum ATCC 824, complete genome5.87106NeighboursBLASTN
NC_014815:2363460*Micromonospora sp. L5 chromosome, complete genome5.88334NeighboursBLASTN
NC_003366:1Clostridium perfringens str. 13, complete genome5.89146NeighboursBLASTN
NC_015687:303810*Clostridium acetobutylicum DSM 1731 chromosome, complete genome5.91524NeighboursBLASTN
NC_017297:33519*Clostridium botulinum F str. 230613 chromosome, complete genome5.92341NeighboursBLASTN
NC_017295:1375180Clostridium acetobutylicum EA 2018 chromosome, complete genome5.92443NeighboursBLASTN
NC_004557:32094*Clostridium tetani E88, complete genome5.93466NeighboursBLASTN
NC_009617:68779*Clostridium beijerinckii NCIMB 8052 chromosome, complete genome5.93601NeighboursBLASTN
NC_010516:42475*Clostridium botulinum B1 str. Okra, complete genome5.96074NeighboursBLASTN
NC_010723:420025*Clostridium botulinum E3 str. Alaska E43, complete genome5.97158NeighboursBLASTN
NC_012563:36000*Clostridium botulinum A2 str. Kyoto, complete genome5.98722NeighboursBLASTN
NC_007929:428743*Lactobacillus salivarius subsp. salivarius UCC118, complete genome5.99004NeighboursBLASTN
NC_011745:2399313*Escherichia coli ED1a chromosome, complete genome5.99048NeighboursBLASTN
NC_009480:99640Clavibacter michiganensis subsp. michiganensis NCPPB 382, complete5.99256NeighboursBLASTN
NC_013315:1370000*Clostridium difficile CD196 chromosome, complete genome5.99391NeighboursBLASTN
NC_009089:1202261*Clostridium difficile 630, complete genome6.01043NeighboursBLASTN
NC_017179:3984000Clostridium difficile BI1, complete genome6.02402NeighboursBLASTN
NC_012796:1645856*Desulfovibrio magneticus RS-1, complete genome6.02723NeighboursBLASTN
NC_011283:1901229*Klebsiella pneumoniae 342 chromosome, complete genome6.02992NeighboursBLASTN
NC_010674:192951*Clostridium botulinum B str. Eklund 17B, complete genome6.04695NeighboursBLASTN
NC_020291:5752099Clostridium saccharoperbutylacetonicum N1-4(HMT), complete genome6.06782NeighboursBLASTN
NC_017179:281069Clostridium difficile BI1, complete genome6.07042NeighboursBLASTN
NC_009089:1*Clostridium difficile 630, complete genome6.10833NeighboursBLASTN
NC_010674:426256*Clostridium botulinum B str. Eklund 17B, complete genome6.13215NeighboursBLASTN
NC_013316:3863728*Clostridium difficile R20291, complete genome6.1334NeighboursBLASTN
NC_014328:1*Clostridium ljungdahlii ATCC 49587 chromosome, complete genome6.13785NeighboursBLASTN
NC_007516:124486*Synechococcus sp. CC9605, complete genome6.15021NeighboursBLASTN
NC_012918:1814000*Geobacter sp. M21 chromosome, complete genome6.16961NeighboursBLASTN
NC_008593:2457594*Clostridium novyi NT, complete genome6.18567NeighboursBLASTN
NC_008261:1*Clostridium perfringens ATCC 13124, complete genome6.19931NeighboursBLASTN
NC_004557:2777291*Clostridium tetani E88, complete genome6.22744NeighboursBLASTN
NC_000854:723000Aeropyrum pernix K1, complete genome6.23495NeighboursBLASTN
NC_012660:1804610*Pseudomonas fluorescens SBW25 chromosome, complete genome6.24355NeighboursBLASTN
NC_008148:583030Rubrobacter xylanophilus DSM 9941, complete genome6.25713NeighboursBLASTN
NC_010516:1*Clostridium botulinum B1 str. Okra, complete genome6.26488NeighboursBLASTN
NC_008262:67711*Clostridium perfringens SM101, complete genome6.27274NeighboursBLASTN
NC_007517:1468719*Geobacter metallireducens GS-15, complete genome6.31106NeighboursBLASTN
NC_012658:1*Clostridium botulinum Ba4 str. 657 chromosome, complete genome6.31179NeighboursBLASTN
NC_009698:1*Clostridium botulinum A str. Hall chromosome, complete genome6.31471NeighboursBLASTN
NC_018664:3009166*Clostridium acidurici 9a chromosome, complete genome6.3183NeighboursBLASTN
NC_006177:2883476Symbiobacterium thermophilum IAM 14863, complete genome6.32967NeighboursBLASTN
NC_012563:1*Clostridium botulinum A2 str. Kyoto, complete genome6.33244NeighboursBLASTN
NC_013316:1081044*Clostridium difficile R20291, complete genome6.34259NeighboursBLASTN
NC_017179:446564*Clostridium difficile BI1, complete genome6.37359NeighboursBLASTN
NC_015578:423000Treponema primitia ZAS-2 chromosome, complete genome6.38283NeighboursBLASTN
NC_009697:1*Clostridium botulinum A str. ATCC 19397 chromosome, complete6.40467NeighboursBLASTN
NC_013315:895500Clostridium difficile CD196 chromosome, complete genome6.41021NeighboursBLASTN
NC_015425:1207314Clostridium botulinum BKT015925 chromosome, complete genome6.42731NeighboursBLASTN
NC_013316:4018451*Clostridium difficile R20291, complete genome6.43869NeighboursBLASTN
NC_010674:3674739*Clostridium botulinum B str. Eklund 17B, complete genome6.48929NeighboursBLASTN
NC_009495:1*Clostridium botulinum A str. ATCC 3502 chromosome, complete genome6.49437NeighboursBLASTN
NC_012563:811993Clostridium botulinum A2 str. Kyoto, complete genome6.51848NeighboursBLASTN
NC_009617:4911595Clostridium beijerinckii NCIMB 8052 chromosome, complete genome6.57167NeighboursBLASTN
NC_012796:1049034*Desulfovibrio magneticus RS-1, complete genome6.62004NeighboursBLASTN
NC_013316:1*Clostridium difficile R20291, complete genome6.62937NeighboursBLASTN
NC_001264:28266Deinococcus radiodurans R1 chromosome 2, complete sequence6.66381NeighboursBLASTN
NC_020291:5778999Clostridium saccharoperbutylacetonicum N1-4(HMT), complete genome6.67768NeighboursBLASTN
NC_018664:2459994*Clostridium acidurici 9a chromosome, complete genome6.68162NeighboursBLASTN
NC_010520:1*Clostridium botulinum A3 str. Loch Maree, complete genome6.69632NeighboursBLASTN
NC_009699:1*Clostridium botulinum F str. Langeland chromosome, complete genome6.70524NeighboursBLASTN
NC_009089:3142976*Clostridium difficile 630, complete genome6.72351NeighboursBLASTN
NC_017297:1*Clostridium botulinum F str. 230613 chromosome, complete genome6.74057NeighboursBLASTN
NC_015425:2690448*Clostridium botulinum BKT015925 chromosome, complete genome6.74606NeighboursBLASTN
NC_012796:3600630*Desulfovibrio magneticus RS-1, complete genome6.82162NeighboursBLASTN
NC_020054:6111419Fibrella aestuarina BUZ 2 drat genome6.83811NeighboursBLASTN
NC_008261:551513*Clostridium perfringens ATCC 13124, complete genome6.86122NeighboursBLASTN
NC_010723:3395187*Clostridium botulinum E3 str. Alaska E43, complete genome6.90078NeighboursBLASTN
NC_010520:35845*Clostridium botulinum A3 str. Loch Maree, complete genome6.91446NeighboursBLASTN
NC_013316:3056925*Clostridium difficile R20291, complete genome6.92409NeighboursBLASTN
NC_009089:370555*Clostridium difficile 630, complete genome6.93749NeighboursBLASTN
NC_013850:1658010Klebsiella variicola At-22 chromosome, complete genome6.94131NeighboursBLASTN
NC_009617:1278000Clostridium beijerinckii NCIMB 8052 chromosome, complete genome6.99423NeighboursBLASTN
NC_012658:35500*Clostridium botulinum Ba4 str. 657 chromosome, complete genome7.0216NeighboursBLASTN
NC_013316:371953*Clostridium difficile R20291, complete genome7.04072NeighboursBLASTN
NC_013316:120759*Clostridium difficile R20291, complete genome7.06072NeighboursBLASTN
NC_016935:1365463*Paenibacillus mucilaginosus 3016 chromosome, complete genome7.08197NeighboursBLASTN
NC_008593:2020473*Clostridium novyi NT, complete genome7.11818NeighboursBLASTN
NC_015425:2752482*Clostridium botulinum BKT015925 chromosome, complete genome7.14509NeighboursBLASTN
NC_009089:4140764*Clostridium difficile 630, complete genome7.16748NeighboursBLASTN
NC_010674:1*Clostridium botulinum B str. Eklund 17B, complete genome7.19445NeighboursBLASTN
NC_012880:3421500*Dickeya dadantii Ech703, complete genome7.21071NeighboursBLASTN
NC_017179:905347Clostridium difficile BI1, complete genome7.29776NeighboursBLASTN
NC_014219:3254268*Bacillus selenitireducens MLS10 chromosome, complete genome7.31167NeighboursBLASTN
NC_010723:1*Clostridium botulinum E3 str. Alaska E43, complete genome7.62407NeighboursBLASTN
NC_009089:117980*Clostridium difficile 630, complete genome7.64953NeighboursBLASTN
NC_008148:2498000Rubrobacter xylanophilus DSM 9941, complete genome7.66912NeighboursBLASTN
NC_010723:3530000*Clostridium botulinum E3 str. Alaska E43, complete genome7.67516NeighboursBLASTN
NC_012796:77071*Desulfovibrio magneticus RS-1, complete genome7.69565NeighboursBLASTN
NC_020211:2206500Serratia marcescens WW4, complete genome7.71608NeighboursBLASTN
NC_008593:2527064*Clostridium novyi NT, complete genome7.72049NeighboursBLASTN
NC_011365:592256*Gluconacetobacter diazotrophicus PAl 5 chromosome, complete genome7.85639BLASTN
NC_015315:1Thermoproteus uzoniensis 768-20 chromosome, complete genome7.99056NeighboursBLASTN
NC_002939:2008304Geobacter sulfurreducens PCA, complete genome8.11703NeighboursBLASTN
NC_009656:2422083Pseudomonas aeruginosa PA7 chromosome, complete genome8.19395NeighboursBLASTN
NC_014958:3346500*Deinococcus maricopensis DSM 21211 chromosome, complete genome8.3816NeighboursBLASTN