PredictBias

identification of genomic and pathogenicity islands in prokaryotic genome
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A) Input parameters
GenomeCP011004.gbkThreshold 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 CP011004 (download)
S.NoStartEndBiasVirulenceInsertion elementsPrediction
1UQ86_09415UQ86_09450N        Y        NPathogenicity Island (unbiased-composition)
LocusTagDNBiasCDNBias%GCBiasProduct
UQ86_09415-9223372036854775808170.000000amino acid ABC transporter substrate-binding
UQ86_09420-9223372036854775808180.000000polar amino acid ABC transporter ATPase
UQ86_09425-9223372036854775808180.000000polar amino acid ABC transporter permease
UQ86_09430-9223372036854775808130.000000histidine kinase
UQ86_09435-9223372036854775808110.000000adenine deaminase
UQ86_09440-9223372036854775808130.000000hypothetical protein
UQ86_09445-9223372036854775808140.000000NAD-dependent dehydratase
UQ86_09450-9223372036854775808150.000000transcriptional regulator
ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
UQ86_09415ADHESNFAMILY280.001 Adhesin family signature.
		>ADHESNFAMILY#Adhesin family signature.

Length = 309

Score = 27.5 bits (61), Expect = 0.001
Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 1 MKKGLLITVMLMVMLALGACSSGESKEDQWSRIK 34
MKK + V+ + + L AC+SG+ ++K
Sbjct: 1 MKKLGTLLVLFLSAIILVACASGKKDTTSGQKLK 34


ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
UQ86_09435UREASE240.029 Urea amidohydrolase (urease) protein signature.
		>UREASE#Urea amidohydrolase (urease) protein signature.

Length = 570

Score = 23.5 bits (51), Expect = 0.029
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 3/28 (10%)

Query: 16 GRAKADLVIKNGRIINVFSG---EIMDG 40
G KAD+ +K+GRI + ++ G
Sbjct: 82 GIVKADIGLKDGRIAAIGKAGNPDMQPG 109


ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
UQ86_09445NUCEPIMERASE391e-07 Nucleotide sugar epimerase signature.
		>NUCEPIMERASE#Nucleotide sugar epimerase signature.

Length = 334

Score = 38.6 bits (90), Expect = 1e-07
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 6/41 (14%)

Query: 1 MKILVFGGTRFFGKKLVERLVSEGHEVTIGTRGKTEDNFGD 41
MK LV G F G + +RL+ GH+V +G DN D
Sbjct: 1 MKYLVTGAAGFIGFHVSKRLLEAGHQV-VGI-----DNLND 35


ORFs having significant similarity with Known Virulence factors
LocusTagHitsScoreE-valueComments
UQ86_09450HTHFIS316e-05 FIS bacterial regulatory protein HTH signature.
		>HTHFIS#FIS bacterial regulatory protein HTH signature.

Length = 484

Score = 31.3 bits (71), Expect = 6e-05
Identities = 7/31 (22%), Positives = 18/31 (58%)

Query: 3 KVYIVEDDEVIRDTIRKHLSKWGFEIGVVED 33
+ + +DD IR + + LS+ G+++ + +
Sbjct: 5 TILVADDDAAIRTVLNQALSRAGYDVRITSN 35



 
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