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Table 4 Amino acid similarities and identities between ICE Hptfs4a -encoded proteins and proteins from ICE Hptfs3 and ICE Hptfs4b/c islands

From: A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity

Gene P12

Size (aa)

Identity/similarity ICEHptfs4b1

Identity/similarity ICEHptfs4c1

Orthologous gene on ICEHptfs3

Identity/similarity ICEHptfs31

Putative function

hpp12_437

357

56/73

98/98

hpb8_521/pz40

63/76

XerT

hpp12_438

227

missing

95/97

hpb8_524/pz37

77/83

 

hpp12_439

432

32/49

93/95

hpb8_527/pz34

23/42 2

VirB6

hpp12_440

92

missing

93/96

missing

-

 

hpp12_441

466

40/60

96/97

hpb8_526/pz35

23/46 2

 

hpp12_442/443

737

94/95

94/95

hpb8_543/pz15

32/50

 

hpp12_444/445

464

28/46

97/993

hpb8_529/pz32

26/53 4

 

hpp12_446

340

28/43

95/973

hpb8_530/pz31

30/47

 

hpp12_447

2808

94/96

92/95

pz21

89/93

 

hpp12_448

218

98/99

97/99

hpb8_532/pz29

67/81

ParA

hpp12_449

94

98/100

94/94

hpb8_533/pz28

37/69

 

hpp12_450

392

92/96

missing

missing

-

 

hpp12_451

637

93/95

35/51

hpb8_519,517/pz41

35/56

VirD2

hpp12_452

104

97/98

n.d.5

missing

-

 

hpp12_453

93

98/100

n.d.5

missing

-

 

hpp12_454

575

98/99

62/77

hpb8_538/pz20

50/66

VirD4

hpp12_455

170

98/98

46/60 6

hpb8_538/pz206

32/50

 

hpp12_456

96

97/98

n.d.5

missing

-

 

hpp12_457

151

97/97

35/51

missing

-

 

hpp12_458

313

99/99

58/74

hpb8_540/pz18

42/64

VirB11

hpp12_459

99

98/100

n.d.5

missing

-

 

hpp12_460

87

93/96

n.d.5

missing

-

 

hpp12_461

97

97/97

91/93

missing

-

 

hpp12_462

421

80/84

92/95

hpb8_544/pz14

53/69

VirB10

hpp12_463

510

97/98

94/97

hpb8_545/pz13

47/66

VirB9

hpp12_464

389

55/73

98/99

hpb8_546/pz12

38/62

VirB8

hpp12_465

38

55/75

55/75

hpb8_547/pz11

44/58

VirB7

hpp12_466

677

45/62

94/97

hpb8_537/pz24

45/61

TopA

hpp12_467

807

44/63

96/97

hpb8_548/pz10

38/58

VirB4

hpp12_468

88

54/75

95/97

hpb8_550/pz8

39/58

VirB3

hpp12_469

100

42/63

93/97

hpb8_551/pz7

30/45

VirB2

hpp12_470/471

508

34/54

94/96

hpb8_528/pz33

35/51

 

hpp12_472

97

missing

90/93

missing

-

 

hpp12_473

259

34/57

92/93

hpb8_554/pz5

37/63

 
  1. 1numbers printed in normal face correspond to >90% identity (identical genes), and numbers in bold face to 40-85% similarity.
  2. 2genes hpb8_526 and pz35, as well as hpb8_527 and pz34 share only 61/73% and 54/70% identity/similarity, respectively, to each other, but are equally similar to hpp12_441 and hpp12_439, respectively.
  3. 3some ICEHptfs4c islands contain the ICEHptfs4b versions with lower similarities in these sites.
  4. 4similarities confined to short regions only.
  5. 5no significant similarity detectable, but gene with similar size and orientation present.
  6. 6ICEHptfs4c and ICEHptfs3 islands contain fusions of hpp12_454 and hpp12_455.
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BMC Genomics

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