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Table 1 TBSSR family analysis

From: Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes

Famint ID

MGE type

No. prot

No. GI

No. phages

No. prophages

No. plasmids

Putative catalytic motif

0

intG

210

153

10(vir2)

38(pro2)

9(plas226)

no obvious one

1

RIT(A)

64(4)

ND

0

3

33(plas10)

RH-Y

2

RIT(C)

63(4)

ND

0

0

34(plas10)

RH-Y

3

mix

61

0

5(vir2)

15(fam202)

41(plas170)

RK-Y

4

mix

58

0

27(vir2)

29(pro2)

2(plas10)

RH-Y

5

RIT(B)

54(4)

ND

0

0

27(plas10)

RH-Y(1)

6

(pro)phage

52

0

16(vir2)

36(pro2)

0

RH/R-Y

7

(pro)phage

47

0

18(vir2)

29(pro2)

0

RHT/S-Y

8

IntI

44

0

0

1(pro2)

43(plas10)

RH-Y

9

plasmid

43

0

0

0

43(plas10)

RHS-Y(1)

10

plasmid

39

0

0

0

39(plas10)

RH-Y

11

plasmid

37

0

0

0

37(plas101)

R-Y

12

(pro)phage

35

0

8(vir2)

27(pro2)

0

RHT-Y

13

(pro)phage

30

0

11(vir2)

19(pro2)

0

RH-Y

14

Tn4371 (4)

25

13

0

5(pro2)

7(plas226)

RH-Y

15

(pro)phage

22

0

3(418)

19(pro76)

0

RSL or RLY-Y

16

(pro)phage

22

1

12(vir2)

9(pro2)

0

RHT-Y

17

(pro)phage

20

0

13(vir2)

7(pro2)

0

RHS-Y

18

plasmid

16

0

0

0

16(plas101)

RSG-Y

19

BIM(A)(4)

14

ND

0

0

8(plas10)

RH-Y

20

mix

14

0

1(vir2)

9 (pro2)

4(plas226)

R-Y

21

prophage, plasmid

12

0

0

3(pro2)

9(plas226)

RRT-Y

22

plasmid

11

0

0

0

11(plas10)

RRTF-Y

23

plasmid

11

0

0

0

11(plas10)

R-Y

24

prophage

10

0

0

10(pro2)

0

RK-Y

25

(pro)phage

10

0

4(vir2)

6(pro2)

0

RH-Y

26

(pro)phage

9

0

3(vir2)

6(pro2)

0

RH-Y

27

plasmid(5)

9

0

0

0

9(plas454)

RHT-Y(2)

28

phage, plasmid

9

0

0

4(pro2)

5(plas10)

RH-Y

29

mix

9

0

1(vir418)

7(pro76)

1(plas226)

R-Y

30

plasmid

9

0

0

0

9(plas688)

R-Y

31

plasmid

8

0

0

0

8(plas10)

RH-Y

32

plasmid

8

0

0

0

8(plas589)

R-Y

33

plasmid

8

0

0

0

8(plas10)

R-Y(2)

34

plasmid

8

0

0

0

8(plas10)

RAT-Y

35

(pro)phage

8

0

1(vir418)

7(pro76)

0

No R at expected distance from Y

36

plasmid

8

0

0

0

8(plas10)

RH-Y, partner 41, 90

37

mix

7

0

0

6(pro2)

1(plas10)

RH-Y

38

plasmid

7

0

0

0

7(plas101)

RR-Y

39

plasmid

7

0

0

0

7(plas589)

RH-Y(3)

40

plasmid

7

0

0

0

7(plas10)

RHS-Y

41

plasmid

7

0

0

0

7(plas454)

RR-Y

42

mix

6

0

0

1(pro2)

5(plas10)

RH-Y(2)

43

plasmid

6

0

0

0

6(plas10)

RR-Y(2)

44

plasmid

6

0

0

0

6(plas10)

RH-Y

46

plasmid

6

0

0

0

6(plas10)

RHT-Y

47

mix

5

0

3(vir2)

1(pro2)

1(plas226)

RH-Y

48

mix

5

0

3(vir2)

0

2(plas226)

R-Y

49

plasmid

5

0

0

0

5(plas10)

RRTAL-Y

50

(pro)phage

5

0

4(vir2)

1(pro2)

0

RHT-Y

51

(pro)phage

4

0

3(vir2)

1(pro2)

0

RHT-Y

52

prophage

4

0

0

4(pro76)

0

RK-Y(2)

53

plasmid(5)

4

0

0

0

4(plas454)

RH-Y, partner 62, one has no partner

54

plasmid

4

0

0

0

4(plas688)

RHTF-Y

55

plasmid

4

0

0

0

4(plas170)

R-Y

57-68

 

3

     

69-81

 

2

     

82-102

 

1

     
  1. The origins of the proteins can be traced by "vir", "plas" and "pro", which stand for ACLAME family IDs (vir2 is family:vir:2, plas10 is family:plasmids:10, pro2 is family: proph:2, and so on).
  2. (pro)phage: the family contains proteins from both phages and prophages.
  3. Only the most conserved R and adjacent amino-acids and the potential catalytic Y residue are mentioned.
  4. (1) Not all proteins in the family have the conserved residues.
  5. (2) A putative catalytic motif is discernible when two shorter sequences are removed from the alignment.
  6. (3) Distance between RH and Y is around 50 residues.
  7. (4) Some proteins in the family do not originate from ACLAME protein families, which is the reason why the number of GI, phages, prophages and plasmids do not add up to the number of proteins.
  8. (5) Proteins in the family have a long N-terminal extension and are over 700 amino-acids long.
  9. ND: Some proteins in the family could be part of a GI.
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Mobile DNA

ISSN: 1759-8753