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Table 4 Top 60 most divergent (>2 SD) genes by DNS in H. pylori strain 26695 plus those additional genes in the top 50 genes from TNS and HNS

From: Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

DNS order

annotation

HP#

J99 #

J99 DNS order

TNS order

HNS order

1

cag pathogenicity island protein (cag7)

HP0527

JHP0476

2

1

1

2

vacuolating cytotoxin (vacA) paralog

HP0289

JHP0274

4

2

4

3

poly E-rich hypothetical protein

HP0322

JHP0305

5

8

5

4

hypothetical protein

HP0609

JHP0556*

3

6

9

5

hypothetical protein

HP0996

JHP0942

6

14

46

6

vacuolating cytotoxin (vacA) paralog

HP0922

JHP0856

7

5

3

7

hypothetical protein

HP0488

JHP0440

13

10

12

8

hypothetical protein

HP1116

JHP1044

10

11

13

9

hypothetical protein

HP0080

JHP0074

12

18

122

10

hypothetical protein

HP0489

JHP0441

115

36

582

11

cag pathogenicity island protein (cag3)

HP0522

JHP0471

21

48

100

12

hypothetical protein

HP1089

JHP0336

27

67

59

13

vacuolating cytotoxin (vacA) paralog

HP0610

JHP0556*

3

12

17

14

hypothetical protein

HP0427

JHP0952

1

3

737

15

hypothetical protein

HP1408

JHP1300

9

4

738

16

type III restriction enzyme R protein (res)

HP0592

NAH

-

30

35

17

hypothetical protein

HP0119

NAH

-

7

2

18

vacuolating cytotoxin (vacA)

HP0887

JHP0819

59

25

34

19

N-methylhydantoinase

HP0696

JHP0632

20

35

43

20

hypothetical protein

HP1115

JHP1042

14

33

866

21

urease beta subunit (urea amidohydrolase) (ureB)

HP0072

JHP0067

32

38

87

22

DNA mismatch repair protein (MutS)

HP0621

JHP0565

45

137

64

23

cag island protein (cagT)

HP0532

JHP0481

25

87

693

24

hypothetical protein

HP0756

JHP0693

19

71

1548

25

integrase/recombinase (xerD)

HP0995

JHP0941

33

39

448

26

outer membrane protein

HP0486

JHP0438

22

147

142

27

cytochrome oxidase (cbb3 type) (fixN)

HP0144

JHP0132

41

102

168

28

type IIS restriction enzyme R and M protein (ECO57IR)

HP1517

NAH

-

42

14

29

DNA transfer protein (cagE)

HP0441

JHP0492

49

51

22

30

DNA polymerase I (polA)

HP1470

JHP1363

46

77

54

31

cag island protein (cagA)

HP0547

JHP0495

17

15

7

32

iron(III) dicitrate transport protein (fecA)

HP1400

JHP1426

28

99

129

33

flagellin A (flaA)

HP0601

JHP0548

34

40

180

34

outer membrane protein (omp26)

HP1157

JHP1084

24

17

25

35

DNA repair protein (recN)

HP1393

JHP1434

51

154

207

36

type I restriction enzyme R protein (hsdR)

HP0464

NAH

-

90

26

37

cell division protein (ftsK)

HP1090

JHP0335

67

181

90

38

hypothetical protein

HP1003

NAH

-

61

170

39

histidine-rich, metal binding polypeptide (hpn)

HP1427

NAH

-

26

1449

40

hypothetical protein

HP1333

JHP1253

40

53

296

41

hypothetical protein

HP0788

JHP0725

68

72

256

42

hypothetical protein

HP0906

JHP0842

42

22

16

43

hypothetical protein

HP0059

JHP0052

26

21

320

44

GMP reductase (guaC)

HP0854

JHP0790

107

169

451

45

hypothetical protein

HP0030

JHP0026

23

24

39

46

histidine and glutamine-rich metal-binding protein

HP1432

JHP1321

15

9

1432

47

hypothetical protein

HP0186

JHP0174

29

130

276

48

fucosyltransferase

HP0651

JHP0596

105

43

75

49

translation elongation factor EF-Tu (tufB)

HP1205

JHP1128

81

64

166

50

virulence associated protein homolog (vacB)

HP1248

JHP1169

79

164

160

51

hypothetical protein

HP0449

NAH

-

81

449

52

type III restriction enzyme R protein

HP1371

JHP1285

55

119

23

53

virB4 homolog (virB4)

HP0459

NAH

-

49

28

54

2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB)

HP0104

JHP0096

56

73

68

55

hypothetical protein

HP1479

JHP1372

135

153

127

56

RNA polymerase sigma-70 factor (rpoD)

HP0088

JHP0081

62

55

31

57

hypothetical protein

HP0205

JHP0191

53

78

8

58

hypothetical protein

HP1143

JHP1071

78

29

41

59

hypothetical protein

HP1106

JHP1033

36

272

277

60

cag pathogenicity island protein (cag13)

HP0534

JHP0482

71

225

1021

63

DNA topoisomerase I (topA)

HP0440

NAH

-

149

24

68

outer membrane protein (omp3)

HP0079

JHP0073

796

45

99

69

hypothetical protein

HP0669

JHP0613

44

60

42

74

cag pathogenicity island protein (cag8)

HP0528

JHP0477

72

50

27

75

hypothetical protein

HP0453

NAH

-

58

10

84

DNA-directed RNA polymerase, beta subunit (rpoB)

JHP1121

50

23

19

 

91

hypothetical protein

HP1142

JHP1070

60

19

6

97

multidrug resistance protein (spaB)

HP0600

JHP0547

75

41

30

103

type I restriction enzyme R protein (hsdR)

HP1402

JHP1424

195

86

21

109

adenine/cytosine DNA methyltransferase

HP0054

NAH

-

120

20

119

preprotein translocase subunit (secA)

HP0786

JHP0723

159

176

49

121

hypothetical protein

HP0058

JHP0051

394

16

53

122

hypothetical protein

HP0513

JHP0462

104

28

15

125

type I restriction enzyme M protein (hsdM)

HP1403

JHP1423

299

340

44

132

hypothetical protein

HP0731

JHP0668

110

80

32

139

hypothetical protein

HP0508

JHP0458

84

32

77

142

hypothetical protein

HP1187

JHP1113

274

31

38

167

hypothetical protein

HP1520

NAH

-

20

33

179

hypothetical protein

HP0118

JHP0110

64

27

36

195

type III restriction enzyme R protein (res)

HP1521

JHP1410

161

210

18

209

outer membrane protein (omp17)

HP0725

JHP0662

257

47

101

224

hypothetical protein

HP0733

JHP0670

769

222

48

230

hypothetical protein

HP0611

JHP0299

35

37

1129

249

hypothetical protein

HP0345

NAH

-

46

1338

283

hypothetical protein

HP0120

NAH

-

44

50

291

translation initiation factor IF-2 (infB)

HP1048

JHP0377

330

332

45

297

DNA polymerase III alpha-subunit (dnaE)

HP1460

JHP1353

509

219

47

342

type I restriction enzyme R protein (hsdR)

HP0846

JHP0784

244

101

37

363

adenine specific DNA methyltransferase (mod)

HP1522

JHP1411

857

207

11

410

secreted protein involved in flagellar motility

HP1192

JHP1117

614

13

1256

593

hypothetical protein

HP1516

NAH

-

34

1090

631

hypothetical protein

HP0586

JHP0534

577

163

29

1080

type II restriction enzyme (methyltransferase)

HP0478

JHP0430

953

220

40

  1. * probably frame shifted components of the same vacA related gene
  2. Genes with > 2 SD divergence in each analysis are indicated in bold
  3. NAH indicates No Annotated Homologue in the other sequence