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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.