PredictBias

identification of genomic and pathogenicity islands in prokaryotic genome

Home \| Help \| Analyzed genomes

A) Input parameters
Genome	NC_010611.gbk	Threshold dinucleotide bias	2
Threshold codon bias	4	Threshold %GC bias	3
E-value (RPSBlast)	0.05	Genome (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_010611 (download)

S.No

Start

End

Bias

Virulence

Insertion elements

Prediction

1

ACICU_RS15210

ACICU_RS15240

N

Y

N

Pathogenicity Island (unbiased-composition)

	LocusTag	DNBias	CDNBias	%GCBias	Product
	ACICU_RS15210	-9223372036854775808	12	0.000000	response regulator
	ACICU_RS15220	-9223372036854775808	16	0.000000	response regulator
	ACICU_RS15225	-9223372036854775808	21	0.000000	hypothetical protein
	ACICU_RS15235	-9223372036854775808	18	0.000000	efflux RND transporter periplasmic adaptor
	ACICU_RS15240	-9223372036854775808	14	0.000000	AcrB/AcrD/AcrF family protein

	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS15280	HTHFIS	31	5e-05	FIS bacterial regulatory protein HTH signature.
	>HTHFIS#FIS bacterial regulatory protein HTH signature. Length = 484 Score = 31.3 bits (71), Expect = 5e-05 Identities = 14/43 (32%), Positives = 18/43 (41%) Query: 2 ARILIVDDSPTETFRFKEILTKHGYDVLEASNGADGVTLAKAE 44 A IL+ DD + L++ GYDV SN A A Sbjct: 4 ATILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWIAAG 46
	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS15285	HTHFIS	35	2e-06	FIS bacterial regulatory protein HTH signature.
	>HTHFIS#FIS bacterial regulatory protein HTH signature. Length = 484 Score = 35.2 bits (81), Expect = 2e-06 Identities = 9/36 (25%), Positives = 13/36 (36%) Query: 9 KVMVIDDSKTIRRTAETLLQREGCEVITAVDGFEAL 44 ++V DD IR L R G +V + Sbjct: 5 TILVADDDAAIRTVLNQALSRAGYDVRITSNAATLW 40
	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS15290	MYCMG045	27	0.001	Hypothetical mycoplasma lipoprotein (MG045) signature.
	>MYCMG045#Hypothetical mycoplasma lipoprotein (MG045) signature. Length = 483 Score = 27.4 bits (60), Expect = 0.001 Identities = 11/39 (28%), Positives = 21/39 (53%) Query: 1 MNKRMKYAFYRNCLSVFIGIASCGALFFSSPTLAANAAP 39 M K++KY F+ +S+ ++SCG+ F + +P Sbjct: 1 MKKQLKYCFFSLFVSLSSILSSCGSTTFVLANFESYISP 39
	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS15300	ACRIFLAVINRP	40	5e-08	Acriflavin resistance protein family signature.
	>ACRIFLAVINRP#Acriflavin resistance protein family signature. Length = 1034 Score = 39.8 bits (93), Expect = 5e-08 Identities = 9/39 (23%), Positives = 21/39 (53%) Query: 5 RISVKYPVFTIMMMLSLMVLGLASWKRMTVEEFPNIDFP 43 ++ P+F ++ + LM+ G + ++ V ++P I P Sbjct: 3 NFFIRRPIFAWVLAIILMMAGALAILQLPVAQYPTIAPP 41

2

ACICU_RS16815

ACICU_RS16845

N

Y

N

Pathogenicity Island (unbiased-composition)

	LocusTag	DNBias	CDNBias	%GCBias	Product
	ACICU_RS16815	-9223372036854775808	24	0.000000	pilus assembly protein PilE
	ACICU_RS16820	-9223372036854775808	20	0.000000	pilin
	ACICU_RS16825	-9223372036854775808	20	0.000000	pilus assembly protein tip-associated adhesin
	ACICU_RS16830	-9223372036854775808	21	0.000000	hypothetical protein
	ACICU_RS16835	-9223372036854775808	19	0.000000	pilus assembly protein PilW
	ACICU_RS16840	-9223372036854775808	18	0.000000	type IV pilus modification protein PilV
	ACICU_RS16845	-9223372036854775808	18	0.000000	prepilin-type cleavage/methylation

	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS16835	BCTERIALGSPG	44	5e-10	Bacterial general secretion pathway protein G signa...
	>BCTERIALGSPG#Bacterial general secretion pathway protein G signature. Length = 145 Score = 44.5 bits (105), Expect = 5e-10 Identities = 15/43 (34%), Positives = 27/43 (62%) Query: 2 KNGFTLIEIMIVVAIIAILAAIATPSYLQYLRKGHRTAVQSEM 44 + GFTL+EIM+V+ II +LA++ P+ + K + S++ Sbjct: 7 QRGFTLLEIMVVIVIIGVLASLVVPNLMGNKEKADKQKAVSDI 49
	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS16840	BCTERIALGSPG	40	3e-08	Bacterial general secretion pathway protein G signa...
	>BCTERIALGSPG#Bacterial general secretion pathway protein G signature. Length = 145 Score = 39.9 bits (93), Expect = 3e-08 Identities = 14/33 (42%), Positives = 23/33 (69%) Query: 11 QGVTLIELMVVIVIVAIFASIAIPSYQSYSRRA 43 +G TL+E+MVVIVI+ + AS+ +P+ +A Sbjct: 8 RGFTLLEIMVVIVIIGVLASLVVPNLMGNKEKA 40
	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS16855	BCTERIALGSPG	28	5e-04	Bacterial general secretion pathway protein G signa...
	>BCTERIALGSPG#Bacterial general secretion pathway protein G signature. Length = 145 Score = 28.3 bits (63), Expect = 5e-04 Identities = 9/31 (29%), Positives = 20/31 (64%), Gaps = 1/31 (3%) Query: 7 SNKEQGFTLIELIVALA-LGLILVAAATQLF 36 ++K++GFTL+E++V + +G++ L Sbjct: 4 TDKQRGFTLLEIMVVIVIIGVLASLVVPNLM 34
	ORFs having significant similarity with Known Virulence factors
	LocusTag	Hits	Score	E-value	Comments
	ACICU_RS16865	BCTERIALGSPG	39	6e-08	Bacterial general secretion pathway protein G signa...
	>BCTERIALGSPG#Bacterial general secretion pathway protein G signature. Length = 145 Score = 39.1 bits (91), Expect = 6e-08 Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 1/42 (2%) Query: 1 MRGIIPQEGFTLVELMVTIAVMAIIALMAAPS-MSNLLESKR 41 MR Q GFTL+E+MV I ++ ++A + P+ M N ++ + Sbjct: 1 MRATDKQRGFTLLEIMVVIVIIGVLASLVVPNLMGNKEKADK 42


Contact Sachin Pundhir for Bugs/Comments. For best view 1024 x 768 resolution & IE 6.0 or above recommended.