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Table 2 Mean of the observed and expected combined values of the cognate recognition sites in H. pylori whole genome sequences and MLS for hspAmerind and hpEurope strains

From: Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance

RMS

Mean ± SD frequency/1.00 bp

O/E ratiob

Endonuclease/ Methylase

Cognate recognition sitea

MLS (N = 73)

WGS (N = 6)

  

Observed

Expected

Observed

Expected

MLS (N = 73)

WGS (N = 6)

Hpy 166III

CCTC

2.7 ± 0.41

5.49 ± 0.07

2.93 ± 0.02

4.50 ± 0.03

0.50 c

0.65

Hpy178VI

GGATG

1.48 ± 0.23

1.59 ± 0.03

0.81 ± 0.00

1.37 ± 0.01

0.93

0.59

Hpy17VII

GGCC

1.24 ± 0.31

1.96 ± 0.05

0.98 ± 0.02

1.43 ± 0.02

0.63

0.68

Hpy188I

TCBGA

1.02 ± 0.21

3.70 ± 0.03

0.81 ± 0.02

3.53 ± 0.01

0.28

0.23

Hpy188III

TCBBGA

1.11 ± 0.22

3.70 ± 0.04

1.19 ± 0.02

3.53 ± 0.01

0.30

0.34

Hpy8I

GTNNAC

0.40 ± 0.35

3.70 ± 0.03

0.22 ± 0.01

3.53 ± 0.01

0.11

0.06

Hpy8II

GTSAC

0.00 ± 0.00

1.56 ± 0.02

0.05 ± 0.00

1.37 ± 0.01

0.00

0.04

Hpy8III

GWGCWC

0.07 ± 0.12

0.66 ± 0.01

0.19 ± 0.01

0.19 ± 0.00

0.10

0.36

Hpy99I

CGWCG

0.28 ± 0.06

1.13 ± 0.02

0.15 ± 0.01

0.88 ± 0.01

0.25

0.17

Hpy99III

GCGC

4.62 ± 0.64

1.96 ± 0.05

3.73 ± 0.11

1.43 ± 0.02

2.36

2.60

Hpy99IV

CCNNGG

1.62 ± 0.26

1.96 ± 0.05

0.70 ± 0.01

1.43 ± 0.03

0.83

0.49

Hpy99VIP

GATC

5.48 ± 0.44

3.70 ± 0.03

3.19 ± 0.04

3.53 ± 0.01

1.48

0.90

Hpy99XIIP

GTAC

0.37 ± 0.20

3.70 ± 0.04

0.07 ± 0.00

3.53 ± 0.01

0.10

0.02

HpyAV

CCTTC(6/5)

0.58 ± 0.12

1.58 ± 0.02

0.80 ± 0.02

1.37 ± 0.01

0.37

0.58

HpyC1I

CCATC(4/5)

1.94 ± 0.26

1.94 ± 0.26

1.60 ± 0.02

1.39 ± 0.01

1.22

1.01

HpyCH4II

CTNAG

0.60 ± 0.28

3.70 ± 0.03

1.84 ± 0.04

3.53 ± 0.01

0.16

0.52

HpyCH4III

ACNGT

0.89 ± 0.22

3.70 ± 0.04

0.34 ± 0.00

3.53 ± 0.01

0.24

0.10

HpyCH4IV

ACGT

0.39 ± 0.22

3.70 ± 0.04

0.18 ± 0.01

3.53 ± 0.01

0.11

0.05

HpyCH4V

TGCA

3.85 ± 0.75

3.70 ± 0.03

3.45 ± 0.03

3.53 ± 0.03

1.04

0.98

HpyCI

GATATC

0.00 ± 0.03

0.31 ± 0.01

0.02 ± 0.00

0.33 ± 0.00

0.01

0.07

HpyF10VI

GCNNNNNNNGC

2.70 ± 0.35

1.96 ± 0.04

2.97 ± 0.09

1.43 ± 0.02

1.38

2.07

HpyF14I

CGCG

2.26 ± 0.46

1.96 ± 0.05

1.55 ± 0.05

1.43 ± 0.02

1.15

1.08

HpyF2I

CTRYG

1.16 ± 0.17

0.92 ± 0.01

0.37 ± 0.01

0.88 ± 0.00

1.26

0.42

HpyF36IV

GDGCHC

0.20 ± 0.21

1.22 ± 0.03

0.31 ± 0.01

0.93 ± 0.01

0.16

0.33

Hpy44II

GGNNCC

1.21 ± 0.38

1.96 ± 0.05

0.44 ± 0.00

1.43 ± 0.02

0.62

0.31

HpyII

GAAGA

2.29 ± 0.23

2.14 ± 0.03

2.87 ± 0.02

2.16 ± 0.00

1.07

1.33

HpyIP

CATG

4.63 ± 0.25

3.70 ± 0.03

4.43 ± 0.04

3.53 ± 0.01

1.25

1.25

HpyIV

GANTC

1.70 ± 0.25

3.70 ± 0.04

1.66 ± 0.02

3.53 ± 0.01

0.46

0.47

HpyNI

CCNGG

2.04 ± 0.30

1.96 ± 0.05

0.87 ± 0.02

1.43 ± 0.02

1.04

0.61

HpyPORF1389P

GAATTC

0.01 ± 0.05

0.31 ± 0.01

0.11 ± 0.00

0.33 ± 0.00

0.03

0.32

HpyV

TCGA

0.95 ± 0.25

3.70 ± 0.03

0.18 ± 0.00

3.53 ± 0.01

0.26

0.05

HpyVIII

CCGG

1.92 ± 0.30

1.96 ± 0.04

1.06 ± 0.02

1.43 ± 0.02

0.98

0.74

  1. aRestriction endonucleases with palindromic recognition sites are indicated in bold. Code of degenerate nucleotide letters: R = G or A; Y = C or T; S = G or C; W = A or T; D = not C (A or G or T); H = not G (A or C or T); N = any nucleotide.
  2. bO/E ratio indicates the observed/expected (O/E) ratio values. O/E ratios that are significantly (p-value <0.05) different from unity are highlighted in bold and bigger font.
  3. cExclusively underrepresented in hpEurope MLS.