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Table 1 Modular complements of tfs ICE conserved and variable genes in reference H. pylori genomes

From: Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

    

tfs ICE present in reference H. pylori genomes and gene annotationa

    

tfs4

tfs3

tfs gene assignmentb (t3_ or t4_)

tfs segment

Gene homologue

pz homologuec

P12 (L2C1R2)

Shi470 (L1C1R1)

SouthAfrica7 (LmC2R2)

Gambia 94/24

India7

C1.1/C1.2

tfs4 Left (L1/L2) and

tfs3 Left segment

xer

40

437

4480

7710

7345

3725

V1

–

37

438

–

7705

7360

NA

C2.1/C2.2

virB6

34

439

4485

7700

7375

3760

V2

–

–

440

–

7695

–

–

C3.1/C3.2

–

35

441

4490

7690

7370

3755

C4.1/C4.2

–

15

442, 443

4495

7685

7480

3850

C5.1/C5.2

–

32

444

4500

NA

7385

3770

C6.1/C6.2

–

31

446

4505

7670

7390

3775

V3

–

–

NA

–

–

–

–

V4

tfs4 Central (C1/C2) and

tfs3 Left and Right segments

methylase

21

447

4510

7665

NA

3820

C7

virC1

29

448

4515

7660

7400

3785

C8

–

28

449

4520

7655

7405

3790

V5

–

–

450

4525

–

–

–

C9.1/C9.2

virD2

41

451

4530

7650

7340

3720

V6

–

–

–

–

7640

–

–

V7

–

–

452

4535

–

–

–

V8

–

–

453

4540

–

–

–

C10.1/C10.2

virD4

20

454

4545

7635

7455

3825

V9

–

20

455

4550

7635

–

–

V10

–

–

456

4555

–

–

–

V11

–

–

–

–

7630

–

–

V12.1/V12.2

–

–

457

4560

7625

–

–

C11.1/C11.2

virB11

18

458

4565

7620

7465

3835

V13

–

–

459

4570

–

–

–

V14

–

–

–

–

7615

–

–

V15

–

–

460

4575

–

–

–

V16

–

–

–

–

7610

–

–

V17

–

–

461

4580

7605

–

–

V18

–

–

–

4585

–

–

–

C12

virB10

14

462

4590

7600

7485

3855

C13

virB9

13

463

4595

7595

7490

3860

C14.1/C14.2

tfs4 Right (R1/R2) and

tfs3 Right segment

virB8

12

464

4600

7590

7495

3865

C15.1/C15.2

virB7

11

465

4605

NA

7500

3870

C16.1/C16.2

topA

24

466

4610

7585, 7570

7425

3810

C17.1/C17.2

virB4

10

467

4615

7565

7505

3875

C18.1/C18.2

virB3

8

468

4620

7560

7515

3885

C19.1/C19.2

virB2

7

469

4625

7555

7520

3890

C20.1/C20.2

–

33

471

4630-35

7550

7380

3765

V19

–

–

472

–

7545

–

–

C21.1/C21.2

–

5

473

4640

7540

7535

3900

V20

tfs3 Left segment

–

39

–

–

–

7350

3730

V21

–

38

–

–

–

7355

3735

V22.1/V22.2

fic

–

–

–

–

–

–

V23

ctkA

–

–

–

–

–

–

V24.1-V24.4

–

36

–

–

–

7365

3750

V25.1-V25.3

–

30

–

–

–

7395

3780

V26

–

27

–

–

–

7410

3795

V27

–

26

–

–

–

7415

3800

V28

–

25

–

–

–

7420

3805

V29

tfs3 Central variable

–

23

–

–

–

7430

3815

V30

–

–

–

–

–

NA

–

V31

–

22

–

–

–

7435

–

V32

–

–

–

–

–

7440

–

V33

tfs3 Right segment

–

19

–

–

–

7460

3830

V34

–

17

–

–

–

7470

3840

V35

–

16

–

–

–

7475

3845

V36.1-V36.3

–

9

–

–

–

7510

3880

V37

–

6

–

–

–

7525

3895

V38

–

–

–

–

–

7530

NA

  1. Bold text highlights conserved tfs3/4 homologous genes
  2. NA ‘not annotated’ in reference genome
  3. aAutomated gene numbering increases in multiples of either 1 or 5 (strains Shi470, PeCan4 and SouthAfrica7) in the Genbank annotation of the selected genome sequences
  4. bNomenclature used in the study for reference to tfs ICE genes. tfs3 or tfs4 (t3_ or t4_) genes are assigned a C or V prefix depending on whether they are (C) conserved in all tfs ICE types, or are (V) variably present, as defined by absence in at least one tfs ICE type. Numbering proceeds as genes are encountered in order, first from left to right of tfs4, then left to right of tfs3. Distinct alleles of any particular tfs gene are indicated by additional numbering after the period, for example t4_C9.1 and t4_C9.2 represent two distinct alleles of the tfs4 virD2 gene
  5. cpz nomenclature initially used in the early description of the tfs3 ICE from strain PeCan18b [41]