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Table 2 PAIs in prokaryotic chromosomes (see supplementary Table 3S for the complete information) [see Additional file 3]

From: A computational approach for identifying pathogenicity islands in prokaryotic genomes

Strain

Size (kb)

Δ G+C (%)a

HGT (%)b

Evidence of GIc

Characteristics

Bacillus halodurans C-125d

8.1

-2.7

100.0

Transposase

ABC transporters

Bacillus subtilis 168d

4.9

-2.3

13.6

-

Flagellar protein

Bordetella bronchiseptica RB50

15.3

-1.6

36.7

tRNA

TTSS

 

8

4.3

93.2

-

Hemin transport system

Bordetella pertussis Tohama I

7.9

4.6

93.1

-

Heme uptake

 

15.3

-1.2

39.8

tRNA

TTSS

Bradyrhizobium japonicum USDA 110d

6.4

-4.3

100.0

-

Nodulation

Chromobacterium violaceum ATCC 12472

11.8

-9.3

100.0

-

TTSS

 

15.5

-6.5

86.4

-

TTSS

Enterococcus faecalis V583

137.5

-4.7

83.8

tRNA

NN in E. faecalis e

Escherichia coli CFT073

7.1

-6.3

85.8

tRNA, integrase, IS

Hypotheticals

 

60.1

-1.8

33.0

tRNA, transposase, phage genes

F1C and S fimbrial protein, iron uptake

 

48.5

-3.5

46.1

tRNA, integrase, transposase

PAI I CFT073 e

 

29.1

2.7

57.8

IS

ISEc8, antigen 43 precursor, fimbrial protein

 

6

-9.8

87.1

-

Fimbrial protein

 

43.3

-2.7

19.7

Transposase

PAI II CFT073 e

Escherichia coli K12d

9.8

-3.8

100.0

Integrase, putative transposase

Fimbrial protein

 

8.5

6.1

43.3

-

Citrate-dependent iron transport

Escherichia coli O157:H7 EDL933

7

-4.9

42.2

Putative transposase

Glucosyltransferase

 

13.5

-4.4

100.0

-

Pilin subunit, transporter and member of exoprotein

 

7

-4.9

42.1

Putative transposase, IS proteins

Glycosyl transferase, IS1 proteins

 

14.9

-13.3

100.0

tRNA

TTSS

 

44.7

-9.2

87.3

tRNA, integrase, phage genes

LEE e

Escherichia coli O157:H7 Sakai

7

-4.6

45.6

Transposase

Ferric enterochelin esterase

 

17

-14.0

100.0

tRNA

TTSS

 

44.7

-9.4

89.7

tRNA

LEE e

Helicobacter pylori 26695

38

-3.0

82.6

Glutamate racemase (glr)

cag PAI e

Helicobacter pylori J99

38.2

-3.1

83.7

Glutamate racemase (murI)

cag PAI e

Mesorhizobium loti MAFF303099d

12.7

-5.5

100.0

-

TTSS, nodulation protein

Nitrosomonas europaea ATCC 19718d

16.9

2.5

34.9

Recombinase

Transmembrane sensors, outer membrane efflux

Photorhabdus luminescens subsp. laumondii TTO1

23.2

8.3

68.2

-

Putative fimbrial proteins

 

36.3

7.7

87.4

tRNA, IS, transposase

Lipoprotein, pilus

 

50.6

-1.5

17.0

-

TTSS locus e

 

34.9

2.1

64.1

Transposase, IS

tc locus e

Salmonella enterica Typhi Ty2

6.7

0.6

26.4

-

Fimbrial protein

 

41.3

-4.7

61.2

tRNA

SPI-2e

 

10.3

-6.5

57.7

tRNA, transposase

SPI-5e

 

6.7

-2.4

95.5

tRNA

Fimbrial protein

 

12.4

-5.2

100.0

-

SPI-1f

 

25.5

-7.3

91.6

-

SPI-4e

Salmonella enterica Typhi CT18 (Salmonella enterica Typhi Typhi)

6.7

0.6

26.4

-

Fimbrial protein

 

6.7

-2.5

95.5

tRNA

Fimbrial protein

 

10.3

-6.6

57.7

tRNA, transposase

SPI-5e

 

41.3

-4.7

61.2

tRNA

SPI-2e

 

12.4

-5.2

100.0

IS, transposase

SPI-1f

 

25.5

-7.3

91.6

-

SPI-4e

Salmonella typhimurium LT2 (S. enterica serovar Typhimurium LT2)

6.7

0.6

26.4

-

Fimbrial protein

 

8.3

-3.5

77.4

-

Fimbrial protein

 

9.5

-6.6

52.2

tRNA

SPI-5 e

 

41.6

-4.7

60.9

tRNA

SPI-2 e

 

15.1

0.6

100.0

Putative transposase

Flagellar synthesis, siderophore receptor protein

 

12.4

-5.3

100.0

-

SPI-1 f

 

18

-4.5

56.8

tRNA

SPI-3 e

 

25.5

-7.5

97.8

-

SPI-4 e

Shigella flexneri 2a 2457T

50.1

-1.9

17.2

tRNA

SHI-1 e

 

25

-2.3

31.5

tRNA

SHI-2 e

 

22.6

-4.1

48.0

tRNA, recombinase

Fimbrial protein

Shigella flexneri 2a 301

13.7

1.8

83.6

Putative transposase

Enterochelin esterase, oxidoreductase (Fe-S subunit)

 

7.5

-3.1

54.8

tRNA

Oxidoreductases (Fe-S subunit)

 

53.5

-2.1

8.1

tRNA, integrase, transposase

SHI-1 e

 

28.1

-2.5

48.2

tRNA, integrase, transposase

SHI-2 e

 

28.9

-3.4

50.1

tRNA, transposase, integrase

Fimbrial protein

Staphylococcus aureus Mu50

5.3

-7.0

100.0

tRNA

SaPIm3f

Staphylococcus aureus MW2

6.3

0.4

43.8

-

ν Saβg

Staphylococcus aureus N315

5.3

-6.9

100.0

tRNA

SaPIn3f

Vibrio cholerae N16961

4.3

-11.5

87.9

Transposase

VPI e

 

8.8

-3.2

100.0

-

CTX locus g

Vibrio parahaemolyticus RIMD 2210633 chromosome I

16.7

2.9

39.6

-

TTSS

 

11.3

0.0

11.1

-

TTSS, iron transport

Vibrio parahaemolyticus RIMD 2210633 chromosome II

9

0.5

26.1

-

Flagellar biosynthesis

 

3.7

4.9

79.2

-

Iron transport

Xanthomonas campestris pv. campestris ATCC 33913

23.1

-1.8

10.0

Transposase

Hrp PAI e

Yersinia pestis CO92

34.7

9.1

73.1

tRNA, integrase

HPI e

 

8

-1.7

48.7

Transposase

Iron transport system

 

6.1

-0.9

100.0

Transposase

Fimbrial protein, secreted protein

Yersinia pestis KIM

34.7

9.1

76.8

tRNA, integrase

HPI e

 

14.6

-0.6

5.6

-

Iron/siderophore ABC transporters, antigen chaperone

  1. aDeviation of the G+C content of the cPAI as compared to that of the whole genome
  2. bLength percentage of horizontally transferred genes in the cPAI
  3. cGenes involved in the transfer mechanism (integrase, transposase, IS element, or tRNA gene at the boundaries)
  4. dNon-pathogenic bacterium
  5. ecPAI that entirely matches to a PAI identified from the genome sequencing paper
  6. fcPAI that matches to one end of a PAI identified from the genome sequencing paper. The other end of the PAI is present in a PAI-like region not overlapping GIs.
  7. gcPAI that partly matches to a PAI identified from the genome sequencing paper
  8. Bold characters denote that a sequenced strain containing the cPAI is the same as or closely related to the host strain of the queried PAI loci.
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BMC Bioinformatics

ISSN: 1471-2105

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