Table 1

Putative horizontally transferred genes and pseudogenes

Species

Gene

Pseudogene

Failed transfer index




All

HT

All

HT


Archaea

A. pernix

615

45

4

2

6.8

S. solfataricus

2,235

231

48

6

1.2

S. tokodaii

1,797

185

35

19

5.3

P. aerophilum

1,855

171

10

3

3.3

Halobacterium sp. NRC-1

1,383

100

1

1

13.8

M. thermautotrophicus

1,350

122

5

5

11.1

M. jannaschii

1,280

106

15

8

6.4

P. abyssi

891

75

6

2

4.0

P. horikoshii

553

50

8

0

0.0

T. acidophilum

1,169

106

5

4

8.8

T. volcanium

1,061

100

16

6

4.0

Non-pathogenic bacteria

A. aeolicus

1,244

107

3

0

0.0

Synechocystis sp. PCC 6803

2,696

237

5

1

2.3

Nostoc sp. PCC 7120

3,672

332

10

2

2.2

S. coelicolor

6,012

536

14

4

3.2

B. halodurans

3,279

299

11

3

3.0

B. subtilis

1223

102

44

3

0.8

L. innocua

2,924

263

1

1

11.1

C. acetobutylicum

3,129

295

5

1

2.1

L. lactis subsp. lactis

1,870

156

13

2

1.8

C. vibrioides

2,699

231

6

1

1.9

M. loti

5,235

476

14

3

2.4

S. meliloti

2,985

240

9

6

8.3

E. coli K12

2,897

230

63

23

4.6

T. maritima

1,445

137

8

0

0.0

D. radiodurans

1,964

134

9

1

1.6

Pathogenic bacteria

Buchnera sp. APS

477

42

5

2

4.5

U. urealyticum

467

40

2

1

5.8

M. pneumoniae

610

55

30

19

7.0

B. burgdorferi

590

63

1

0

0.0

M. pulmonis

595

53

2

1

5.6

C. trachomatis

597

67

3

1

3.0

C. muridarum

815

81

2

0

0.0

R. prowazekii

504

49

7

1

1.5

T. pallidum

727

64

12

5

4.7

C. pneumoniae J138

839

74

1

0

0.0

C. pneumoniae AR39

831

70

5

1

2.4

C. pneumoniae CWL029

845

71

7

0

0.0

R. conorii

695

67

9

0

0.0

M. leprae

1,440

119

271

53

2.4

C. jejuni

1,291

108

2

0

0.0

H. pylori J99

856

70

5

1

2.4

H. pylori 26695

1,055

90

13

3

2.7

S. pyogenes M1 GAS

1,348

108

14

1

0.9

S. pneumoniae

1,632

114

54

2

0.5

N. meningitidis Z2491

1,432

112

26

4

2.0

P. multocida

1,035

96

7

2

3.1

N. meningitidis MC58

1,466

121

44

14

3.9

X. fastidiosa

1,550

152

15

1

0.7

S. aureus subsp. aureus N315

1,557

140

4

2

5.6

S. aureus subsp. aureus Mu50

1,563

138

4

2

5.7

L. monocytogenes

2,799

231

2

0

0.0

C. perfringens

1,943

165

2

0

0.0

B. melitensis

2,948

216

5

0

0.0

R. solanacearum

3,032

252

5

0

0.0

V. cholerae

2,846

216

24

5

2.7

M. tuberculosis CDC1551

2,837

262

49

7

1.5

M. tuberculosis H37Rv

1,446

130

38

4

1.2

Y. pestis

3,533

282

51

4

1.0

S. typhi CT18

3,986

338

147

18

1.4

S. typhimurium LT2

4,308

349

22

5

2.8

E. coli O157:H7

3,424

266

120

16

1.7

E. coli O157:H7 EDL933

4,322

353

73

5

0.8

P. aeruginosa

3,716

281

7

3

5.7

Total

123,420

10,571

1,458

290

2.3


All genes and pseudogenes and the fraction having atypical codon-position-specific GC contents in the 64 genomes studied. The failed horizontal transfer index was computed as described in Materials and methods.

Liu et al. Genome Biology 2004 5:R64   doi:10.1186/gb-2004-5-9-r64

Open Data