Table 4

Copy number of coding tandem repeats.

Repeats

Strains

MC58

44/76

NGE30

BZ133

92001

94/155

A22

Z2491

FAM18

L18

L12

L22

FA1090

FA19

26034

Repeat length

Nature *

TR1

2

2

2

2

2

2

2

2

2

2

2

2

3

2

2

30 bp / 10 aa

no new

TR2

3

4

2

2

2

2

2

2

2

2

2

np

2

2

2

33 bp / 11 aa

more

TR3

1

2

2

2

2

2

2

2

2

2

np

np

2

2

2

18 bp / 6 aa

no new

TR4

3

2

3

3

3

3

3

4

3

np

1

1

2

2

1

87 bp / 29 aa

more

TR5 †

2 / 4

2 / 5

2 / 3

2 / 4

2 / 1

2 / 3

2 / 5

2 / 3

0 / 0‡

np

np

np

1 / 1

1 / 2

1 / 2

†

more

TR6

2

2

2

2

2

2

2

2

2

2

2

2

3

2

2

15 bp / 5 aa

no new

TR7

2

2

2

2

3

2

2

3

2

2

3

2

3

3

2

12 bp / 4 aa

no new

TR8

2

2

2

2

2

3

2

3

4

2

2

2

2

2

2

30 bp / 10 aa

more

TR9

2

2

2

2

2

2

2

2

2

1

1

1

1

1

1

30 bp / 10 aa

species

TR10

3

3

2

3

3

3

3

2

3

2

0

2

1

1

1

207 bp / 69 aa

more

TR11

2

2

3

3

4

3

3

3

3

3

3

3

3

4

4

15 bp / 5 aa

more

TR12

1

1

1

3

3

1

1

3

1

1

1

1

1

1

1

21 bp / 7 aa

no new

TR13

2

2

7

2

2

3

2

2

4

np

np

np

3

3

3

21 bp / 7 aa

more

TR14

3

3

3

3

3

3

3

3

3

np

np

np

2

2

2

240 bp / 80 aa

species

TR15

14

14

15

15

10

14

15

14

13

np

np

np

12

18

16

15 bp / 5 aa

more

TR16

3

3

3

2

3

2

np

2

2

3

3

3

3

3

3

12 bp / 4 aa

no new

TR17

2

np

2

2

2

np

2

2

2

np

np

np

1

np

1

57 bp / 19 aa

species

TR18

3

3

3

3

3

3

3

3

3

3

3

2

2

2

2

12 bp / 4 aa

species§

TR19a

3

3

3

3

3

3

3

3

3

np

np

np

2

2

2

18 bp / 6 aa

species

TR19b

1

1

1

1

1

1

1

1

1

4

4

4

4

4

4

9 bp / 3 aa

species

TR20 ||

4

4

8

1

2

2

1

1

1

5

8

11

2

2

nd

108 bp / 36 aa

more

TR21

6

6

6

6

6

6

6

6

6

np

np

np

2

2

2

6 bp / 2 aa

species

TR22

7

11

19

5

6

9

16

9

26

np

np

np

2

2

2

9 bp / 3 aa

more

TR24

15

14

3

np

np

5

14

---

---

np

np

np

---

np

np

18 bp / 6 aa

more

TR26

2

2

2

2

2

1¶

2

2

2

np

np

np

2

2

2

273 bp / 91 aa

none

TR27

2

2

2

2

2

2

2

2

2

np

np

np

2

2

2

261 bp / 87 aa

none

TR28

2

2

2

2

2

2

2

2

2

2

2

2

2

2

2

258 bp / 86 aa

none

Repeats

Strains

FA1090

MS11

FA19

F62

25534

28539

26034

26241

27921

29528

28516

27806

TR23

3

3

3

3

5

3

3

3

3

3

3

3

18 bp / 6 aa

more

TR25

3

3

3

3

3

3

3

3

3

3

3

3

30 bp / 10 aa

none

np – no product nd – not done * Nature of the length variations of the coding tandem repeat: species – observed lengths are associated with species; more – lengths in addition to what is seen in the three sequence strains used in genome comparison analysis; no new – no new lengths observed in addition to those seen in the sequenced strains used in genome comparison analysis; none – no length differences observed. † Compound tandem repeat, the first is 66 bp / 11 aa and the second is 24 bp / 8 aa ‡ PilQ is frame-shifted in the genome sequence due to a large deletion starting 50 bp into the 66 bp component of the compound tandem repeat element and ending 361 bp after the region that contains the repeats in other strains. § Length differences were only seen in the non-pathogen, N. lactamica. || From [15]. ¶ The CDS in this strain contains a 303 bp deletion, which begins 63 bp before the first copy of the tandem repeat in the other strains and ends 32 bp before the second copy of the tandem repeat in the other strains. Thus this strain has one full copy of the tandem repeat and 32 bp remaining of a second copy.

Jordan et al. BMC Microbiology 2003 3:23   doi:10.1186/1471-2180-3-23

Open Data