Table 1 The information of the organisms used in the current study.

From: Comparative analysis of essential genes in prokaryotic genomic islands

Organism

RefSeq

Groupa

No.egb

IslandPath-DIMOB(%)c

SIGI-HMM(%)c

Integrated method (%)c

A. baylyi ADP1

NC_005966

Bacteria(−)

499

0.4

5.88

15.18

0.6

7.5

15.18

1

6.41

15.3

B. subtilis 168

NC_000964

Bacteria(+)

271

0

0

6.97

1.11

2.61

6.6

1.11

0.89

6.98

B. fragilis 638R

NC_016776

Bacteria(−)

547

3.84

11.67

12.8

8.59

17.03

12.46

10.06

13.96

12.63

B. thetaiotaomicron VPI-5482

NC_004663

Bacteria(−)

325

2.46

3.15

7.01

2.15

2.73

7.03

5.23

3.46

7.18

B. pseudomallei K96243

NC_006350

Bacteria(−)

505

6.34

15.46

14.82

4.16

9.86

15.2

6.93

8.37

15.77

B. thailandensis E264

NC_007651

Bacteria(−)

406

3.2

4.98

13.03

0

0

12.7

3.2

4.68

13.11

C. crescentus NA1000

NC_011916

Bacteria(−)

480

1.25

4.55

12.63

0.83

3.64

12.61

1.88

5.56

12.65

E. coli MG1655

NC_000913

Bacteria(−)

609

5.26

15.53

14.67

5.09

10.44

15.04

9.03

14.55

14.73

F. novicida U112

NC_008601

Bacteria(−)

392

1.02

12.5

23

0.26

20

22.81

1.02

8.33

23.22

H. influenzae Rd KW20

NC_000907

Bacteria(−)

642

1.25

44.44

39.82

0.62

17.39

40.2

2.34

32.61

40.09

H. pylori 26695

NC_000915

Bacteria(−)

323

1.24

8.89

22.4

0

−

−

1.24

8.89

22.4

M. maripaludis S2

NC_005791

Archaeon

519

0.58

7.69

30.66

0

−

−

0.58

7.69

30.66

M. tuberculosis H37Rv

NC_000962

Bacteria(−)

687

1.6

8.53

17.9

0.58

40

17.53

2.18

11.36

17.81

M. pulmonis UAB CTIP

NC_002771

Mycoplasmas

310

0.65

9.52

40.47

0

−

−

0.65

9.52

40.47

P. aeruginosa PAO1

NC_010729

Bacteria(−)

463

2.16

6.9

23.3

0

0

22.41

2.16

6.67

23.36

P. gingivalis ATCC 33277

NC_002516

Bacteria(−)

117

0

0

2.12

0

0

2.13

0

0

2.16

P. aeruginosa UCBPP-PA14

NC_008463

Bacteria(−)

335

0

0

5.83

0

0

5.7

1.19

1.69

5.85

S. aureus N315

NC_004631

Bacteria(+)

358

0.84

0.86

8.86

0

−

−

1.12

0.69

9.39

S. oneidensis MR-1

NC_016810

Bacteria(−)

353

2.83

7.3

7.96

9.63

11.6

7.68

10.48

9.54

7.79

S. pneumoniae

NC_016856

Bacteria(+)

105

1.91

0.73

2.04

13.33

4.13

1.83

13.33

2.57

1.91

S. sanguinis SK36

NC_003197

Bacteria(+)

230

1.74

1.15

5.51

6.52

5

5.18

7.83

4.04

5.29

S. Typhi Ty2

NC_004347

Bacteria(−)

403

0

−

−

0

0

10.07

0

0

10.07

S. Typhimurium SL1344

NC_009511

Bacteria(−)

535

2.24

6.9

11.18

0.19

1.59

11.16

2.24

5.74

11.27

S. Typhimurium str. 14028S

NC_002745

Bacteria(−)

302

0

0

12.09

0

0

11.84

0

0

12.19

S. typhimurium LT2

NC_007795

Bacteria(−)

351

1.14

16.67

12.65

0

0

12.69

1.14

16.67

12.65

S. wittichii RW1

NC_003028

Bacteria(−)

244

0

0

11.84

0

−

−

0

0

11.84

S. aureus NCTC 8325

NC_009009

Bacteria(+)

218

0

0

9.66

0

0

9.91

0

0

9.97

V. cholerae N16961

NC_002505

Bacteria(−)

779

2.44

18.81

31.24

2.31

17.82

31.28

3.08

19.05

31.35

  1. aBacteria(+), Gram-positive bacteria; Bacteria(−), Gram-negative bacteria.
  2. bNumber of essential genes of the organism.
  3. cThe dataset classified by IslandPath-DIMOB (or SIGI-HMM, Integrated method) contain three numbers (%): X, Y, Z. X% is the percentage of essential genes which located in the GIs detected by the IslandPath-DIMOB (or SIGI-HMM, Integrated method) among the total essential genes of the organism. Y% is the percentage of essential genes in GIs. Z% is the percentage of essential genes outside GIs. The character ‘–’ in the column of IslandPath-DIMOB or SIGI-HMM means no genomic island is detected by the corresponding method.
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