Table 2

Unique genetic loci with polymorphisms resulting in non-synonymous amino acid changes in Helicobacter pylori strains B128 and 7.13, and in vivo-adapted strains isolated from gerbils maintained on iron-depleted or iron-replete diets

Variant			B128 single colonies			7.13 single colonies			7.13 iron-depleted single colonies									7.13 iron-replete single colonies
Location	Gene	HPB8 locus	a	b	c	a	b	c	D1 a	D1 b	D1 c	D2 a	D2 b	D2 c	D3 a	D3 b	D3 c	R1 a	R1 b	R1 c	R2 a	R2 b	R2 c	R3 a	R3 b	R3 c
118890	fliI	124							K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R	K>R
132888	tonB1	138		K>E
211182	babB	237																S>L
211347	babB	237			T>I		T>I	T>I	T>I	T>I			T>I			T>I	T>I	T>I	T>I			T>I			T>I
211415	babB	237		G>R	G>R		G>R	G>R	G>R	G>R						G>R	G>R		G>R			G>R
211583	babB	237							D>N	D>N		D>N	D>N	D>N				D>N	D>N	D>N		D>N			D>N
211592	babB	237	K>E	K>E	K>E	K>E	K>E	K>E	K>E	K>E		K>E	K>E	K>E				K>E	K>E	K>E		K>E			K>E
211690	babB	237	N>K	N>K	N>K	N>K	N>K	N>K	N>K	N>K								N>K		N>K		N>K			N>K
211694	babB	237							E>K	E>K								E>K		E>K		E>K			E>K
211838	babB	237	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q
211844	babB	237	G>S	G>S	G>S	G>S	G>S	G>S										G>S
212150	babB	237							G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S		G>S
212315	babB	237	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S		G>S
263909	rpsL	294	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K	E>K
263985	rpsL	294							R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K	R>K
264366	rpsG	295							T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M	T>M
264374	rpsG	295	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N
273162	Hypothetical	303										E>K
273165	Hypothetical	303										L>V
342359	pal	375	T>A	T>A	T>A
559618	Hypothetical	587	E>K	E>K	E>K
563546	Hypothetical	593													Y>C	Y>C	Y>C
591318	Putative OMP	626		T>S	T>S
591626	Putative OMP	626										A>N	A>N
591635	Putative OMP	626										K>N	K>N
591638	Putative OMP	626										p>Q	p>Q
616637	DNA methyltransferase	642	D>N	D>N	D>N
629024	babA	657	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L	S>L
629189	babA	657		T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I	T>I		T>I			T>I
629257	babA	657	G>R	G>R	G>R	G>R	G>R	G>R	G>R	G>R					G>R	G>R	G>R		G>R			G>R
629425	babA	657	D>N	D>N	D>N	D>N	D>N	D>N	D>N	D>N		D>N	D>N	D>N				D>N	D>N	D>N		D>N			D>N
629434	babA	657	K>E	K>E	K>E	K>E	K>E	K>E	K>E	K>E		K>E	K>E	K>E				K>E	K>E	K>E		K>E			K>E
629532	babA	657		N>K	N>K	N>K	N>K	N>K	N>K	N>K								N>K		N>K		N>K			N>K
629536	babA	657		E>K	E>K	E>K	E>K	E>K	E>K	E>K								E>K		E>K		E>K			E>K
629680	babA	657	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q	K>Q
629686	babA	657	G>S	G>S	G>S	G>S	G>S	G>S										G>S
629992	babA	657	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S		G>S
630157	babA	657	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S	G>S		G>S
692170	cagY	716																						n>T
692262	cagY	716																						L>K
692887	cagY	716										K>R	K>R	K>R
693460	cagY	716										V>A	V>A
693465	cagY	716										K>E	K>E
693471	cagY	716										V>I	V>I	V>I
693483	cagY	716										L>K	L>K	L>K
693497	cagY	716										S>Q	S>Q	S>Q
693505	cagY	716										K>R	K>R	K>R
693508	cagY	716										T>N	T>N	T>N
693513	cagY	716										A>K	A>K	A>K
727820	Hypothetical	750	L>W	L>W	L>W
798239	Glycosyltransferase	817	A>T	A>T	A>T
799896	Glycosyltransferase	818																D>E	D>E				D>E
846179	rnc	865						A>D
913806	mesE	927	P>S	P>S	P>S
1084103	Putative OMP	1104										K>Q	K>Q	K>Q
1084106	Putative OMP	1104										A>S	A>S	A>S
1084553	Putative OMP	1104										Q>E	Q>E	Q>E
1084556	Putative OMP	1104										L>F	L>F	L>F
1084587	Putative OMP	1104										M>I	M>I	M>I
1122559	fur	1145					R>H		R>H	R>H	R>H	R>H	R>H	R>H	R>H	R>H	R>H	R>H	R>H	R>H
1130504	pepP	1155														R>H
1195655	fliF	1220	P>L	P>L	P>L
1221163	Polysaccharide deacetylase	1252	A>T	A>T	A>T
1283634	Conserved hypothetical OMP	1309																		A>E
1289275	oppD	1313																						D>N		D>N
1302387	hcpE	1328										A>V	A>V	A>V
1369139	prfB	1395																A>T
1377477	hcpD	1405																			T>A
1405574	Hypothetical	1436							A>D	A>D	A>D
1533082	Predicted coding region	1561																S>P
1533085	Predicted coding region	1561																S>F
1533088	Predicted coding region	1561																D>N

D1-3 and R1-3 designate independent gerbils maintained on either iron-depleted (n=3) or iron-replete (n=3) diets, respectively, while a–c designate different single colonies isolated from each gerbil. Colour-coded regions represent non-synonymous amino acid changes that result from specific genetic polymorphisms. Specific amino acid changes are designated within each box.