. 2009 Sep 25;191(23):7182–7192. doi: 10.1128/JB.00895-09

TABLE 1.

Nucleotide sequence variation in ompA genotype variants compared with the respective prototype strain

Genotype (no. of variants)	No. of variable sites	MOMP region	Nucleotide position^a	Amino acid change^b	Type of change^c				No. of isolates (x/y)^d	dN/dS (SE)
Genotype (no. of variants)	No. of variable sites	MOMP region	Nucleotide position^a	Amino acid change^b	New	B cell	T cell	Loop	No. of isolates (x/y)^d	dN/dS (SE)
A (1)	1	CDIII	736	Val → Ile	x	x			1/1	—^e
B (3)	15	CDI	154	Thr → Ala					2/3	0.35 (0.19)
			163/164	Val → Cys				E	3/3
			184/186	Met → Val					2/3
			195						2/3
			198						2/3
			216						3/3
			228						2/3
			246						2/3
			249						2/3
		VDI	268	Thr → Ala					2/3
		VDI	286/287	Val → Thr					2/3
		VDII	514	Ala → Thr		x			3/3
C (3)	5	CDI	155	Thr → Ile	x				1/3	0.59 (0.51)
		CDI	183		x				1/3
		VDI	284	Gly → Asp	x	x		E	1/3
		CDIII	693		x		C		1/3
		VDIV	1003	Ala → Ser		x			3/3
D (12)	2	VDII	488	Glu → Gly	x			E	1/12	—
D (12)	2	VDIV	976	Ala → Thr		x			12/12	—
Da (65)	6	VDII	485	Asn → Ser					11/65	0.29 (0.25)
		CDIII	636						46/65
		VDIV	939			x			61/61
			976	Ala → Thr		x			11/58
			997	Thr → Ala		x			57/57
		CDV	1050		x				1/1
E (7)	5	VDII	512	Asn → Ser	x	x			1/7	—
		VDII	514	Ser → Ala	x	x	C		1/7
		CDIII	568	Ala → Thr	x		C		2/7
		VDIV	995	Ser → Asn	x	x			1/7
		VDIV	997	Ala → Thr		x			2/7
F (6)	6	CDI	167	Asp → Gly	x			E	1/6	1.53 (1.60)
		CDI	180	Met → Ile	x				1/6
		CDII	388	Ile → Val	x				1/6
		CDIII	703	Phe → Leu	x				1/6
		CDIV	780						1/6
		CDIV	802	Asp → Asn	x			P	1/6
G (54)	7	CDI	228						15/54	2.48 (2.55)
		CDII	374	Cys → Tyr	x			P	1/54
		VDII	487	Gly → Ser					24/54
		CDIII	700	Glu → Gln				P	15/54
		CDIV	857	Thr → Ile	x		W		1/54
		VDIV	1003	Ser → Ala					29/49
			1003	Ser → Thr					12/49
			1015	Ile → Val	x				1/45
H (18)	4	VDI	272	Asn → Ser		x			18/18	0.30 (0.29)
		CDII	327		x				1/18
		CDII	383	Ala → Val	x				1/18
		CDIV	850				W		18/18
I (1)	1	VDIII	764	Ile → Thr	x	x			1/1	—
Ia (49)	14	CDI	129						1/1	0.84 (0.45)
			184/186	Val → Met					47/47
			228						47/47
		VDI	277	Ile → Val					2/49
		VDII	526	Ile → Val					22/49
		CDIII	571	Asn → Asp				P	49/49
		CDIII	577	Thr → Ala	x				1/1
		VDIII	764	Ile → Thr		x			47/47
		CDIV	837				W		46/46
			840				W		46/46
			932	Lys → Arg	x				1/44
		CDV	1141	Ala → Thr					1/1
		CDV	1188						1/1
J (8)	10	CDI	213		x				1/6	0.22 (0.13)
		CDII	369						7/8
		CDIII	684		x				1/8
			720		x				1/8
		VDIII	742	Ala → Thr	x	x			1/8
			753		x	x			1/8
			782	Ala → Glu	x			E	1/7
		VDIV	991	Thr → Ala					1/7
			1000	Ala → Ser	x				1/7
			1020	Asp → Glu		x		E	1/7
Ja (3)	2	VDII	544	Asn → Asp	x			E	2/3	0.50 (0.25)
Ja (3)	2	CDIII	634		x				1/3	0.50 (0.25)
L2 (2)	2	VDII	485	Asn → Ser		x			2/2	—
L2 (2)	2	VDII	517	Leu → Phe	x	x			1/2	—

Based on the alignment of the strains belonging to the same genotype.

Amino acid change presented by the variant clinical specimen compared with the prototype strain of the respective ompA genotype.

Mutations that were observed only for the Portuguese clinical specimens or that occurred within well-defined B-cell epitopes (x), mutations that occurred within (W) or in close proximity (C) to T-cell (CTL and Th) epitopes, and mutations found in MOMP external loops (E) or periplasmic turns (P). For this last type of mutation, only the residues known to be involved in MOMP structural constrains were considered for this analysis.

x represents the total number of clinical specimens sharing the same variable site; y represents the total number of clinical specimens for which the nucleotide sequence involving the variable site is available.

—, calculation of the dN/dS ratio was not feasible for these genotypes as they presented solely nonsynonymous mutations.