PredictBias

identification of genomic and pathogenicity islands in prokaryotic genome
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A) Input parameters
Genomefrancisella.gbThreshold dinucleotide bias2
Threshold codon bias4Threshold %GC bias3
E-value (RPSBlast)0.05Genome (non-pathogenic)
 
B) Compare a potential GI or PAI in related non-pathogenic sp. (phylogenetic tree)
Potential GI or PAI start    end  
Select Organism     
 
C) Potential GIs and PAIs in NC_006570 (download)
S.NoStartEndBiasVirulenceInsertion elementsPrediction
1FTT_0030cFTT_0045Y        NNGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0030c0194.753548ferric uptake regulation protein
FTT_00311195.950353NADH dehydrogenase I subunit A
FTT_0032-1165.222335NADH dehydrogenase subunit B
FTT_0033-2154.625304NADH dehydrogenase I
FTT_0034-2154.522799NADH dehydrogenase subunit D
FTT_0035-1134.027463NADH dehydrogenase I subunit E
FTT_0036-1133.875395NADH dehydrogenase I subunit F
FTT_00370142.657867NADH dehydrogenase subunit G
FTT_00383182.509026NADH dehydrogenase I subunit H
FTT_00393172.328692NADH dehydrogenase subunit I
FTT_00403172.213177NADH dehydrogenase I subunit J
FTT_00412182.318345NADH dehydrogenase I subunit K
FTT_00421172.429610NADH dehydrogenase I subunit L
FTT_0043-2152.321426NADH dehydrogenase I subunit M
FTT_0044-1143.036076NADH dehydrogenase I subunit N
FTT_00452142.916439hypothetical protein
2FTT_0069cFTT_0077Y        NNGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0069c-1133.285355hypothetical protein
FTT_0070c-2133.503058major facilitator superfamily transporter
FTT_0071c-2144.049470citrate synthase
FTT_0072-2144.321456succinate dehydrogenase cytochrome b556
FTT_0073-1134.579615succinate dehydrogenase hydrophobic membrane
FTT_0074-1124.246404succinate dehydrogenase catalytic and
FTT_0075-1113.345042succinate dehydrogenase iron-sulfur subunit
FTT_0076-1103.4888572-oxoglutarate dehydrogenase E1
FTT_00770113.285151dihydrolipoamide succinyltransferase component
3FTT_0277cFTT_0284Y        NNGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0277c4132.929974hypothetical protein
FTT_0278c4132.840427cytochrome d terminal oxidase polypeptide
FTT_0279c4132.805233cytochrome d terminal oxidase polypeptide
FTT_0280c5141.719782major facilitator transporter
FTT_02817132.300577cytochrome O ubiquinol oxidase subunit II
FTT_02826131.707683cytochrome O ubiquinol oxidase subunit I
FTT_02833140.362639cytochrome O ubiquinol oxidase subunit III
FTT_02843140.054689cytochrome O ubiquinol oxidase subunit IV
4FTT_0456cFTT_0473Y        Y        NPathogenicity Island (biased-composition)
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0456c28-0.529017hypothetical protein
FTT_0457c1110.678447anaerobic sulfite reductase subunit
FTT_04581120.339792stringent starvation protein A
FTT_0459113-0.253554periplasmic protease
FTT_0460290.247965DNA polymerase III subunit delta'
FTT_0461070.773966RNA-binding protein
FTT_0462-170.593324delta-aminolevulinic acid dehydratase
FTT_0463-27-0.055416tRNA/rRNA methyltransferase
FTT_0464-27-0.168662periplasmic L-asparaginase II
FTT_0466c-27-0.017807arginyl-tRNA synthetase
FTT_0467-28-0.239653organic solvent tolerance protein
FTT_0468270.547066peptidyl-prolyl cis-trans isomerase
FTT_0469270.274089dimethyladenosine transferase
FTT_0470110-0.477201diadenosine tetraphosphatase
FTT_0471212-0.5416183-dehydroquinate dehydratase
FTT_0472212-1.121703acetyl-Coa carboxylase biotin carboxyl carrier
FTT_0473210-1.249672acetyl-Coa carboxylase biotin carboxylase
ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
FTT_0468PF04605250.006 Virulence-associated protein D (VapD)
		>PF04605#Virulence-associated protein D (VapD)

Length = 125

Score = 25.2 bits (55), Expect = 0.006
Identities = 6/18 (33%), Positives = 7/18 (38%)

Query: 20 LNNAYSDISSSMFQNAFN 37
YS I M +N F
Sbjct: 24 TREPYSLIKKFMLENGFE 41


5FTT_0659FTT_0666cY        NNGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0659-112-3.038864DNA recombination protein RmuC family protein
FTT_0660113-3.289340hypothetical protein
FTT_0661c114-3.366732hypothetical protein
FTT_0663215-3.753775hypothetical protein
FTT_0664c216-2.808116histidine decarboxylase
FTT_0665c115-2.635498aldolase
FTT_0666c215-2.525969methylpurine-DNA glycosylase family protein
6FTT_0757FTT_0772Y        Y        YPathogenicity Island (biased-composition)
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0757113-3.312168UTP-glucose-1-phosphate uridylyltransferase
FTT_075919-2.565320hypothetical protein
FTT_0760c-110-2.788433lipoprotein
FTT_0761c09-2.363703hypothetical protein
FTT_0762c110-2.377103DNA replication and repair protein RecF
FTT_0763c19-1.768245TatD related DNAse family protein
FTT_076419-0.040891glycyl-tRNA synthetase subunit beta
FTT_07651120.212502transposase
FTT_07662120.467227purine nucleoside phosphorylase
FTT_0767c2120.592318hypothetical protein
FTT_0768c2100.029072hypothetical protein
FTT_07692100.809276preprotein translocase subunit SecA
FTT_0772212-0.76427250S ribosomal protein L21
ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
FTT_0769SECA538e-13 SecA protein signature.
		>SECA#SecA protein signature.

Length = 901

Score = 53.3 bits (128), Expect = 8e-13
Identities = 21/44 (47%), Positives = 35/44 (79%)

Query: 1 MLSLVQKIIGSRNERFIKKVSRIVQKINSLEPEFEKLSDEQLKA 44
++ L+ K+ GSRN+R ++++ ++V IN++EPE EKLSDE+LK
Sbjct: 2 LIKLLTKVFGSRNDRTLRRMRKVVNIINAMEPEMEKLSDEELKG 45


7FTT_0791FTT_0796Y        Y        NPathogenicity Island (biased-composition)
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0791011-3.785620UDP-glucose 4-epimerase
FTT_0792114-5.397416glycosyl transferase family protein
FTT_0793015-5.863215ABC transporter ATP-binding protein/permease
FTT_0794114-5.749447hypothetical protein
FTT_0795114-6.161877hypothetical protein
FTT_0796010-4.574970hypothetical protein
ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
FTT_0791NUCEPIMERASE463e-10 Nucleotide sugar epimerase signature.
		>NUCEPIMERASE#Nucleotide sugar epimerase signature.

Length = 334

Score = 45.9 bits (109), Expect = 3e-10
Identities = 17/36 (47%), Positives = 23/36 (63%)

Query: 4 KILVTGGVGYIGSHTVVELLDRDYQVVVVDNLSNSK 39
K LVTG G+IG H LL+ +QVV +DNL++
Sbjct: 2 KYLVTGAAGFIGFHVSKRLLEAGHQVVGIDNLNDYY 37


8FTT_0834FTT_0862cY        Y        YPathogenicity Island (biased-composition)
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_08343151.371607chorismate mutase
FTT_08351130.744651CDP-alcohol phosphatidyltransferase
FTT_0836c1131.320184hypothetical protein
FTT_08372130.994763TolQ protein
FTT_08382140.809644TolR protein
FTT_08391120.831193hypothetical protein
FTT_08401130.798676TolB protein precursor
FTT_08410131.324321lipoprotein
FTT_08420130.562284peptidoglycan-associated lipoprotein
FTT_0845114-0.267004hypothetical protein
FTT_0846113-0.323558deoxyribodipyrimidine photolyase
FTT_0847314-1.557227hypothetical protein
FTT_0848415-2.553473hypothetical protein
FTT_0849415-2.912803bile acid symporter family protein
FTT_0850415-3.298705hypothetical protein
FTT_0851413-3.135950hypothetical protein
FTT_0853413-1.981811*arsenite permease family protein
FTT_0854c315-1.643210hypothetical protein
FTT_0855c216-1.489882hypothetical protein
FTT_0856c216-0.6169984-hydroxybenzoate polyprenyltransferase
FTT_0857c3180.455433hypothetical protein
FTT_08583170.963375ribonuclease PH
FTT_0859c316-0.843958hypothetical protein
FTT_0860c214-1.110534hypothetical protein
FTT_0861c214-1.118688Type IV pili fiber building block protein
FTT_0862c214-1.678301heat shock protein HtpX
ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
FTT_0854cMALTOSEBP260.005 Maltose binding protein signature.
		>MALTOSEBP#Maltose binding protein signature.

Length = 396

Score = 25.9 bits (56), Expect = 0.005
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 6/34 (17%)

Query: 16 FGAYAEHGLKSQISAEH------FNFIMTALRYN 43
FG YA+ GL ++I+ + + F A+RYN
Sbjct: 93 FGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYN 126


9FTT_0965cFTT_0987Y        Y        NPathogenicity Island (biased-composition)
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_0965c212-0.145308hypothetical protein
FTT_0966113-0.301233translation initiation factor IF-1
FTT_0968c010-0.926996amino acid antiporter
FTT_0969c010-1.084856potassium transporter peripheral membrane
FTT_097029-0.664602hypothetical protein
FTT_097129-0.925759cysteine desulfurase
FTT_0972-110-3.846498ABC transporter ATP-binding protein
FTT_0973011-4.164712hypothetical protein
FTT_0975114-4.056055hypothetical protein
FTT_0976016-5.034604thioredoxin
FTT_0977c116-5.449131hypothetical protein
FTT_0978c116-5.514961hypothetical protein
FTT_0979c116-4.679671amino-acid permease
FTT_0980-114-4.680595hypothetical protein
FTT_0981-116-5.146319hypothetical protein
FTT_0982120-2.652984hypothetical protein
FTT_0984c213-4.592457Mutator protein
FTT_0985111-2.596757hypothetical protein
FTT_0986011-2.548863hypothetical protein
FTT_0987-110-3.126012hypothetical protein
ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
FTT_0975FRAGILYSIN230.045 Fragilysin metallopeptidase (M10C) enterotoxin signat...
		>FRAGILYSIN#Fragilysin metallopeptidase (M10C) enterotoxin

signature.
Length = 405

Score = 23.1 bits (49), Expect = 0.045
Identities = 8/36 (22%), Positives = 15/36 (41%), Gaps = 1/36 (2%)

Query: 8 ITLISIFATTSLAIACDNDYLDHNTIKYSTQAETTV 43
+ L+ + T +L AC N+ D T ++
Sbjct: 12 VKLLLMLGTAALLAACSNE-ADSLTTSIDAPVTASI 46


10FTT_1030FTT_1052cY        NNGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1030211-1.800285hypothetical protein
FTT_1031312-1.502010lipoate-protein ligase B
FTT_1034c29-1.466734NADH dehydrogenase
FTT_1035c210-0.706401RNA polymerase sigma-70 factor
FTT_1036c-110-0.987822DNA primase
FTT_1037c-214-0.561805hypothetical protein
FTT_1038c-215-0.29580130S ribosomal protein S21
FTT_1039-113-0.535307D-alanyl-D-alanine carboxypeptidase
FTT_1040014-0.646401lipoprotein
FTT_1041015-2.192164hypothetical protein
FTT_1042114-2.151488C32 tRNA thiolase
FTT_1043112-3.102093FKBP-type peptidylprolyl isomerase
FTT_1044c-113-3.087212octaprenyl-diphosphate synthase
FTT_1045c-213-3.223620hypothetical protein
FTT_1046c-114-3.194200hypothetical protein
FTT_1047c-116-2.594040hypothetical protein
FTT_1048c-113-3.425130hypothetical protein
FTT_1050c113-1.537341sulfate adenylyltransferase
FTT_1051c512-1.920095hypothetical protein
FTT_1052c212-1.252323hypothetical protein
11FTT_1065cFTT_1087cY        NYGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1065c215-3.670432transposase
FTT_1066c217-3.670432hypothetical protein
FTT_1068c317-3.254889hypothetical protein
FTT_1069c116-1.661285hypothetical protein
FTT_1071c116-0.465055hypothetical protein
FTT_1072214-2.338046hypothetical protein
FTT_1074215-2.133428transposase
FTT_1075217-2.838502transcriptional regulator
FTT_1076115-3.096105transcriptional regulator
FTT_1079c113-3.561527hypothetical protein
FTT_1080c09-3.116647hypothetical protein
FTT_1081c-110-1.599863hypothetical protein
FTT_1082111-1.701782hypothetical protein
FTT_1083c111-1.480936hypothetical protein
FTT_1084c111-1.986178recombination associated protein
FTT_1085011-2.197753hypothetical protein
FTT_1086c-111-3.256649hypothetical protein
FTT_1087c-110-3.093209ATP-dependent DNA helicase
12FTT_1134FTT_1152Y        NYGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1134215-0.936878Type IV pili polytopic inner membrane protein
FTT_1136c220-1.522537hypothetical protein
FTT_1137c220-0.648228hypothetical protein
FTT_1138117-2.030619ferrochelatase
FTT_1140216-2.653799hypothetical protein
FTT_1142c013-1.728858transposase
FTT_11430110.327883hypothetical protein
FTT_11450110.079098cation transport regulator
FTT_1147c0100.0380284'-phosphopantothenoylcysteine decarboxylase
FTT_1148c0100.431117major facilitator transporter
FTT_1149c1121.186353amino acid transporter family protein
FTT_1150c1131.175405bifunctional proline
FTT_1151c2120.293205hypothetical protein
FTT_11522130.187486hypothetical protein
13FTT_1214cFTT_1237Y        NYGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1214c2140.415809haloacid dehalogenase
FTT_1215c112-0.018845S-adenosylmethionine--tRNA
FTT_1216c212-0.551599hypothetical protein
FTT_1217c110-0.450632monooxygenase family protein
FTT_1218c09-0.9622912-octaprenyl-6-methoxyphenyl hydroxylase
FTT_1219c011-2.756090hypothetical protein
FTT_1220111-3.3140545-formyltetrahydrofolate cyclo-ligase
FTT_1221114-1.501681hypothetical protein
FTT_1222210-0.751768DedA family protein
FTT_1223-190.244826DedA family protein
FTT_1224c-1110.570739DNA repair protein RecO
FTT_1225c-1121.135134hypothetical protein
FTT_1226c-1110.706510cysteine desulfurase
FTT_1227-1130.344227ribonuclease E
FTT_12282110.377500prolipoprotein diacylglyceryl transferase
FTT_1229010-0.405828thymidylate synthase
FTT_1230010-0.630603D-3-phosphoglycerate dehydrogenase
FTT_123119-1.697217PP-loop family protein
FTT_1232110-1.907102transposase
FTT_1233c111-3.162835proton-dependent oligopeptide transport (POT)
FTT_1234014-4.708037choloylglycine hydrolase family protein
FTT_1235c113-5.484667glycosyl transferase family protein
FTT_1236013-4.560787hypothetical protein
FTT_1237-111-3.470602glycosyl transferase family protein
14FTT_1331FTT_1371Y        NYGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1331213-0.072710fructokinase
FTT_1332210-0.441692polysaccharide biosynthesis protein
FTT_1333c3110.201264hypothetical protein
FTT_1334c2100.578590hypothetical protein
FTT_13351110.108594cysteine/glutathione ABC transporter
FTT_1336112-0.318525cysteine/glutathione ABC transporter
FTT_1337c116-1.168905C4-dicarboxylate transport protein
FTT_1338c117-1.027433translation initiation inhibitor
FTT_1339c-115-2.821720sulfate permease family protein
FTT_1340c017-4.986439transposase
FTT_1341117-5.269738hypothetical protein
FTT_1342018-5.282556hypothetical protein
FTT_1343c016-5.992777hypothetical protein
FTT_1344017-6.333638**hypothetical protein
FTT_1345117-6.497815hypothetical protein
FTT_1346117-6.222647hypothetical protein
FTT_1347217-6.158948hypothetical protein
FTT_1348217-6.830564hypothetical protein
FTT_1349117-6.303317hypothetical protein
FTT_1350216-6.834833hypothetical protein
FTT_1351314-6.451889hypothetical protein
FTT_1352313-5.985979hypothetical protein
FTT_1353211-5.093495hypothetical protein
FTT_1354211-4.402041hypothetical protein
FTT_1355210-2.657014hypothetical protein
FTT_1356c39-2.087063intracellular growth locus subunit D
FTT_1357c19-0.776732intracellular growth locus subunit C
FTT_1358c09-0.089313intracellular growth locus subunit B
FTT_1359c090.736939intracellular growth locus subunit A
FTT_1360c-191.266430hypothetical protein
FTT_1363c-2104.008458transposase
FTT_1365c-1123.911221fructose-1,6-bisphosphate aldolase
FTT_1366c0133.430300pyruvate kinase
FTT_1367c-1132.691943phosphoglycerate kinase
FTT_1368c-1132.498191glyceraldehyde-3-phosphate dehydrogenase
FTT_1369c0152.101672transketolase
FTT_13702181.369305hypothetical protein
FTT_13712192.02572750S ribosomal protein L32
15FTT_1443cFTT_1457cY        Y        NPathogenicity Island (biased-composition)
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1443c-1143.362901recombination factor protein RarA
FTT_1444c0123.001507exopolyphosphatase
FTT_14451133.599814thioredoxin
FTT_14460132.800932transcription termination factor Rho
FTT_1447c2140.911380phosphomannomutase
FTT_1448c314-0.049980mannose-1-phosphate guanylyltransferase
FTT_1450c414-1.236562dTDP-D-glucose 4,6-dehydratase
FTT_1451c214-1.478389glucose-1-phosphate thymidylyltransferase
FTT_1452c215-3.158668glycosyltransferase
FTT_1453c113-4.304253O-antigen flippase
FTT_1454c013-3.903671hypothetical protein
FTT_1455c-114-2.864322sugar transamine/perosamine synthetase
FTT_1456c014-3.110754asparagine synthase
FTT_1457c014-3.738386glycosyl transferase family protein
ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
FTT_1450cNUCEPIMERASE349e-06 Nucleotide sugar epimerase signature.
		>NUCEPIMERASE#Nucleotide sugar epimerase signature.

Length = 334

Score = 33.6 bits (77), Expect = 9e-06
Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 22 NILVTGAAGFIGSNYVRMMLSR 43
LVTGAAGFIG + + +L
Sbjct: 2 KYLVTGAAGFIGFHVSKRLLEA 23


16FTT_1472cFTT_1483cY        NYGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1472c2100.446402peptidyl-prolyl cis-trans isomerase
FTT_1473c2100.208688major facilitator superfamily galactose-proton
FTT_1474c212-0.027855major facilitator superfamily galactose-proton
FTT_1475113-0.420251galactose-1-phosphate uridylyltransferase
FTT_1476-2121.371454galactokinase
FTT_1477c-1133.088933hypothetical protein
FTT_1478c0134.0367783-deoxy-manno-octulosonate cytidylyltransferase
FTT_1479c-1143.775158hypothetical protein
FTT_1481c-1133.521468transposase
FTT_1483c-1123.654836dihydrolipoamide dehydrogenase
17FTT_1696FTT_1721cY        NYGenomic Island
LocusTagDNBiasCDNBias%GCBiasProduct
FTT_1696014-3.306716molecular chaperone GroEL
FTT_1697c117-5.099452transposase
FTT_1698c115-6.179069formate dehydrogenase
FTT_1699017-6.333638**hypothetical protein
FTT_1700117-6.497815hypothetical protein
FTT_1701117-6.222647hypothetical protein
FTT_1702217-6.158948hypothetical protein
FTT_1703217-6.830564hypothetical protein
FTT_1704117-6.303317hypothetical protein
FTT_1705216-6.834833hypothetical protein
FTT_1706314-6.451889hypothetical protein
FTT_1707313-5.985979hypothetical protein
FTT_1708211-5.093495hypothetical protein
FTT_1709211-4.402041hypothetical protein
FTT_1710210-2.657014hypothetical protein
FTT_1711c39-2.087063intracellular growth locus subunit D
FTT_1712c-191.005370intracellular growth locus subunit C
FTT_1713c-191.378564intracellular growth locus subunit B
FTT_1714c-1102.149928intracellular growth locus subunit A
FTT_1715c-1102.107491hypothetical protein
FTT_1718c-1124.065708transposase
FTT_1720c-1134.231661phosphoribosylformylglycinamidine synthase
FTT_1721c-1133.124748amidophosphoribosyltransferase

 
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