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