Skip to main content

Table 3 Families of SLS containing repeated sequences.

From: Systematic identification of stem-loop containing sequence families in bacterial genomes

Species

Family

This work

Literature

Type

Notes

  

size

copies

size

copies

ref.

  

B. anthracis

Bant-1

72

104(29)

   

I

 
 

Bcr1

167

31(21)

147

12

[24]

I

 

B. halodurans

Bhal-1

74

36(32)

   

I

 
 

Bhal-2

76

50(41)

   

I

contains CRISPR repeats

C. perfringens

Clop-1

93

44(28)

   

I

 

C. tetani

Clot-1

74

19(16)

   

I

 
 

Clot-2

31

34(32)

    

contains CRISPR repeats

 

Clot-3

90

24(17)

   

I

contains CRISPR repeats

E. faecalis

Efa-1

163

65 (18)

   

I

 
 

Efa-2

292

11(9)

   

G

 

L. johnsonii

Lac-1

231

34(6)

   

G

 

S. aureus

Sta-1

105

25(25)

   

I

 
 

Sta-2

460

9(8)

   

S

 
 

Sta-3

136

24(15)

   

I

 
 

Sta-4

99

46(27)

   

I

 

S. pneumoniae

BOX

84

205(105)

100–200

127

[25]

I

 
 

RUP

63

110(99)

108

54

[26]

I

 
 

Stre-1

45

241(225)

   

G

 

B. melithensis

Bru-RS

118

222(69)

103–105

35–40

[27]

I

 

R. conorii

Rpe-4

100

97(74)

95

94

[28]

I

 
 

Rpe-5

115

45(35)

115

55

[28]

I

 
 

Rpe-6

108

123(74)

136

168

[28]

  
 

Rpe-7

123

186 144)

99

223

[28]

  

M. genitalium

Myg-1

259

10(7)

   

I

 

M. pneumoniae

Myp-1

143

25(18)

   

G

part of REPMP1 repeat

 

Myp-2

158

42(16)

   

G

part of REPMP4 repeat

 

Myp-3

558

11(8)

   

G

part of REPMP5 repeat

 

Myp-4

364

8(7)

   

G

part of REPMP5 repeat

 

Myp-5

426

8 (8)

   

G

part of REPMP5 repeat

 

Myp-6

468

11(11)

   

G

part of REPMP2/3 repeat

 

Myp-8

674

9(9)

   

G

part of REPMP2/3 repeat

 

Myp-9

226

9(9)

   

G

part of REPMP2/3 repeat

 

Myp-10

330

12 (12)

   

G

part of REPMP2/3 repeat

 

Myp-7

131

42(22)

   

G

 

C. diphtheriae

Cod-1

140

17(16)

   

I

 
 

Cod-2

32

43(39)

   

G

 
 

Cod-3

170

23(20)

     
 

Cod-5

74

35(29)

   

I

 

M. tuberculosis

Myt-1

72

75(70)

     
 

Myt-2

115

769(223)

   

G

located within PE genes

 

Myt-3

81

81(77)

   

G

located within PE genes

 

Myt-4

83

196(68)

   

G

located within PE genes

 

Myt-5

71

41(2)

   

G

contains CRISPR repeats

 

Myt-7

136

278(68)

   

G

located within PE genes

 

Myt-8

92

33(25)

     
 

Myt-9

67

53(15)

     
 

Myt-10

154

62(59)

   

G

located within PE genes

 

Myt-11

65

56(21)

    

contains MIRU repeats

M. leprae

REPLEP

740

29(9)

400–880

15

[29]

I

 
 

RLEP

641

38(30)

601–1075

37

[29]

S

 
 

Myl-1

371

7(4)

   

S

part of LEPREP repeat

 

Myl-2

1979

9(7)

   

S

part of LEPREP repeat

B. bronchiseptica

Bor-1

117

196(92)

   

I

 
 

Bor-2

167

17(6)

   

I

 
 

Bor-3

134

34(32)

   

G

 
 

Bor-4

81

164(114)

   

G

 
 

Bor-5

112

135(101)

   

G

 
 

Bor-6

147

37(31)

   

G

 

B. pertussis

Bor-1

93

128(78)

   

I

 

N. meningitidis

ATR

206

14(9)

183

13

[30]

I

 
 

Nem-2

341

11(7)

     
 

Nem-3

127

10(9)

   

G

 
 

Nem-4

36

412(362)

   

I

contains DUS repeats

 

dRS3

33

755(708)

20

770

[30]

I

 
 

NEMIS

46

262(81)

106–158

250

[13]

I

 
 

Rep2

65

22(18)

59–154

26

[30]

I

 

P. multocida

Pam-1

155

12(12)

   

S

contains DUS repeats

E. coli

BoxC

50

22(20)

56

32

[31]

  
 

Eco-1

734

9(7)

   

G

 
 

ERIC

140

19(19)

127

21

[32]

S

 
 

PU-BIME

108

301(199)

40

485

[31]

  

H. influenzae

Hin-1

31

53(51)

   

I

contains DUS repeats

P. aeruginosa

Pae-1

84

133(61)

   

I

 
 

Pae-2

287

65(24)

   

G

 
 

Pae-3

220

16(13)

   

G

 
 

Pae-4

52

41(35)

     

P. putida

Ppu-1

617

39(28)

   

I

 
 

Ppu-2

2056

10(8)

   

S

 
 

Ppu-3

251

27(23)

   

G

 
 

Ppu-4

81

41(24)

   

I

 
 

Ppu-9

124

57(31)

   

I

 
 

REP

39

588(496)

30

804

[33]

I

 

S. typhi

PU-BIME

43

146(126)

40

100

[31]

I

 
 

PU-BIME*

80

59(37)

40

>100

[31]

  

S. typhimurium

PU-BIME

78

142(94)

40

82

[31]

  
 

Sal-1

115

27(17)

   

I

 
 

Sal-2

120

33(3)

   

G

contains CRISPR repeats

V. cholerae

ERIC

103

97(66)

127

80

[31]

I

 
 

Vic-1

184

14(1)

   

I

 

Y. pestis

ERIC

115

241(128)

69–127

167

[16]

I

 
 

YPAL

168

101(68)

169

30

[17]

I

 
 

YPAL*

136

26(13)

130

10

[17]

I

 
  1. The final set of 92 families of repeated sequences is reported, grouped by species. For each family, the length of the model and the number of sequences fitting the model are given. The number of complete sequences, i.e. covering the model from end to end, is reported in parenthesis. Previously described sequence families have been named in column "Family", according to the current literature; for each of them, the number and typical size of its members are also provided, together with references. For novel families, a systematic name was built by fusing a shortened species name to a progressive number. In the column "type", I, G and S indicate the prevalent genomic location of the members of each families within intergenic, genic or border-spanning sequences. For some families, small previously described sequence motifs contribute to the formation of a substantially larger model; for others, their members are frequently located within larger previously described sequences. In both cases, a note is reported in the rightmost column.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us