The complete genome and methylome of Helicobacter pylori hpNEAfrica strain HP14039

Table 2 Methylated motifs detected in HP14039

Recognition site^a	Modification type	No. detected	No. in genome	Detected (%)	Restriction component(s)			Methylation component(s)			Refs
Recognition site^a	Modification type	No. detected	No. in genome	Detected (%)	Locus tag	Ortholog	% identity	Locus tag	Ortholog	% identity	Refs
5′-ACNGT	m4c	976	1112	87.8	HP14039_01407-01406	K747_11000	94.1, 93.9	HP14039_01408	K747_10995	95.5	[8]
5′-ATTAAT	m6a	949	952	99.7	HP14039_01410	jhp0431	94.1	HP14039_01411	jhp0430	94.9	[26, 29]
5′-CATG	m6a	14,872	14,874	100	HP14039_00716	hp1209	93.3	HP14039_00717	hp1208	93.8	[29]
5′-CCATC	m6a	2190	2199	99.6	HP14039_00375-00376	K747_12645	95.7, 92.7	HP14039_00372-00373	K747_03690	96.2, 97.7	[8]
5′-CCGG	m4c	3535	3542	99.8	HP14039_01604	hp0262	96.1	HP14039_01603	hp0263	94.2	[29]
5′-CTNAG	m4c	6164	6172	99.9	HP14039_01555	HpyHI	96	HP14039_01554	M.HpyHI	94.9	[30]
5′-GAGG	m6a	4672	4718	99	HP14039_00203^b	–	–	HP14039_00204	hp0050	95.2	[26, 29]
5′-GATC	m6a	10,541	10,548	99.9	HP14039_00158	hp0091	93.7	HP14039_00157	hp0092	92.8	[29]
5′-GTAC	m6a	300	304	98.7	HP14039_01382-01381	jhp0455	93.4, 93.7	HP14039_01383	jhp0454	95.8	[26, 31]
5′-GTNNAC	m6a	820	826	99.3	HP14039_00987	hp0909	91.7	HP14039_00986	hp0910	96.1	[29]
5′-TCGA	m6a	610	612	99.7	–	–	–	HP14039_01606-01607	hp0260	96.1, 97.6	[32]
5′-TCNNGA	m6a	3795	3808	99.7	HP14039_00847-00846	jhp1013^c	96.8, 97.5	HP14039_00848	jhp1012	96.1	[26]
5′-TGCA	m6a	11,060	11,072	99.9	HP14039_00305	HpyCH4 V	96.6	HP14039_00306	M.HpyCH4 V	93.4	[12, 30]
5′-CTANNNNNNNTAYG	m6a	191	192	99.5	–	–	–	HP14039_00325^d	K747_03505	93	[8]
5′-WCANHNNNNTG	m6a	1732	4440	39	–	–	–	HP14039_01429^e	K747_10905	92	[8]

^aThe methylated base within the motif is underlined while the modified base in the complementary strand is highlighted in red
^bThe 1–563 bp and 550–918 bp regions of HP14039_00203 demonstrated significant nucleotide sequence homology to the N-terminus of hp0052 and the C-terminus of hp0051, respectively
^cPutative type II restriction enzyme probably recognising TCNNGA
^dPredicted type I DNA methylase probably recognising CTANNNNNNNTAYG based on high sequence similarity with K747_03505 that recognises a closely related sequence motif, which is GANNNNNNNTAYG
^ePredicted type I DNA methylase probably recognising WCANHNNNNTG. This gene is highly similar to K747_10905, which encodes a type I DNA methylase that recognises CCANNNNNNTC sequence motif

ISSN: 1757-4749