A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity

Table 3 Properties of ICE elements identified in draft genome sequences

Strain	Population¹	ICE type	Integration site (P12)	Motif	Pos. LJ⁴	Size (kb)⁵	Complete T4SS (Y/N)
196A	hpEurope	none				n.a.
166	hpEurope	ICEHptfs4c	hpp12_1518-1519	AAAGAATG	1613471	39.6	Y
175	hpEurope	ICEHptfs3	hpp12_1366³	TAAGAATG	1440427	(10.8)	N
175	hpEurope	ICEHptfs4b	hpp12_120	GAAGAATG	126992	(39.0)⁶	N
175	hpEurope	ICEHptfs4c	hpp12_1510	TAAGAATG	1602176	39.3	Y
328	hpEurope	ICEHptfs4a	hpg27_335	AAAGAATA	366213	(2.3)	N
328	hpEurope	ICEHptfs4b	hpp12_1365	AAAGAATG	1436629	40.2	Y
ATCC43526	hpEurope	ICEHptfs3/4a²	hpp12_1508	TAAGAATG	1598758	(47.5)	N
ATCC43526	hpEurope	ICEHptfs4a	hpp12_189-188	TAAGAATG	191853	(22.6)	N
P1	hpEurope	ICEHptfs3	hpp12_746-745	AAACAATA	800162	(13.3)	N
P1	hpEurope	ICEHptfs4b	hpp12_1366	TAAGAATG	1439080	39.4	Y
1_17C	hpAfrica1	ICEHptfs4a/b	hpp12_994-5S-rRNA		1054197	(37.6)	N
6_17A	hpAfrica1	ICEHptfs4a/b	hpp12_994-5S-rRNA		1054197	(37.7)	N
6_28C	hpAfrica1	ICEHptfs4a	hpp12_994-5S-rRNA		1054197	(1.6)	N
6_28C	hpAfrica1	ICEHptfs4b	hpp12_438	AAAGAATG	453993	(35.5)	N

¹inferred from the Neighbor-joining tree shown in Figure 2.
²resulting from insertion of two genome islands and rearrangements associated with IS element insertion and two copies of pz21/hpp12_447-like genes.
³associated with a genome rearrangement between hpp12_1366 and hpp12_1298.
⁴genomic position of AAGAATG motif in strain P12.
⁵numbers in parentheses indicate incomplete ICE elements.
⁶contains 28 kb of prophage-related sequences.

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