Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance

Table 2 Polymorphism in cattle

Nucleotide	189	202	455	467	631	681	914	925	978	989
Amino acid	63	68	152	156	211	227	305	309	326	330
Domain	LRR1	LRR1	LRR5	LRR5	LRR7	LRR8	LRR10	LRR11	LRR11	LRR11
Blosum62	2	0	1	-3	3	0	-2	1	0	1
P (all)	0.922	0.735	0.22	0.005	0.942	0	1	0	0.982	0.018
Class (all)	3	3	2	2	3	1	3	1	3	2
Class (ruminants)	2	3	2	3	2	3	3	2	3	2
Codon_wildtype	gag	ggc	cgg	gta	gtt	tta	cac	gtg	cat	agt
Codon_mutant	gat	agc	cag	gga	aat	ttt	ccc	atg	caa	aat
AA_wildtype	E	G	R	V	V	L	H	V	H	S
AA_mutant	D	S	Q	G	I	F	P	M	Q	N
dbSNP_ID (ss#)	95214853	95214854	95214855	95214856	95214857	95214858	95214858	95214859	95214861	95214862
AA	t	g	g	t	a	t	a	g	t	g
FB	t	g	g	t	g/a	t	a	g	t	a
BP	t	g	g	g	g/a	t	a	g	t	g
GA	g/t	g/a	g	t	g	t	a	g	t	g
FV	t	g	g/a	t	g/a	t	a	g/a	t	g
HF	t	g	g	t	a	t	a	g	t	g
LI	t	g	g	t	g/a	t	a	g	t	g
NE	g/t	g/a	g	t	g	a	a	g	a/t	g
SW	g	a	g	t	g	a	c	g	a	g
BH	g	g/a	g	t	g	a/t	a	g	a	g
Nucleotide	1010	1214	1250	1457	1504	1688	1814	1962	1995	2149
Amino acid	337	405	417	486	502	563	605	654	665	717
Domain	LRR11	LRR14	LRR15	LRR18	LRR19	LRRCT	MEM	TIR	TIR	TIR
Blosum62	2	-1	1	2	1	0	-1	-2	0	2
P (all)	0.972	0	0.352	0	0.998	0.776	0.578	0	0.011	0
Class (all)	3	1	2	1	3	3	3	1	2	1
Class (ruminants)	2	2	2	2	2	3	2	2	2	2
Codon_wildtype	aaa	acg	aac	aga	tca	cgc	acg	tgg	cac	ctg
Codon_mutant	aga	atg	agc	aaa	gca	cac	atg	tgt	cag	atg
AA_wildtype	K	T	N	R	S	R	T	W	H	L
AA_mutant	R	M	S	K	A	H	M	C	Q	M
dbSNP_ID (ss#)	95214863	95214864	95214865	95214867	95214868	95214869	95214873	95214874	95214875	95214878
AA	g	c	a	g	t	g/a	c	g	c	c
FB	g	c	a	g	t	g	c	g	c	c
BP	g	c	a	g	t	g	c	g	c	c
GA	g/a	c	a	g	t	g/a	c	g	c	c
FV	g	c	a	g	t	g	c	g	c	c
HF	g	c	a	g	t	g	c	g/t	c	a/c
LI	g	c	a	g/a	t	g	c	g	c	c
NE	a	c	g/a	g	g/t	g/a	c/t	g	g/c	c
SW	a	t	g	g	g	a	c/t	g	g	c
BH	a	c	g	g	t	a	c	g	g	c

Nucleotide: position of the polymorphism in the nucleotide sequence, Amino acid: affected amino acid site, Domain: domain in which the polymorphic site is located, LRRCT: Leucine Rich Repeat C-terminal domain, MEM: transmembrane domain, Blosum62: Blosum62 matrix score of the particular AA exchange, P (all): probablitiy of class assignment in the complete dataset, Class (all): class assignment in the complete dataset (1: purifying selection, 2: neutral, 3: positive selection), Class (ruminants): class assignment in the ruminant subset, dbSNP_ID (ss#): accession number in dbSNP database, AA: Aberdeen Angus, FB: Fighting Bull, BP: Black Pied Gene Reserve, GA: German Angus, FV: Fleckvieh, HF: Holstein Friesian, LI: Limousin, NE: Nelore, SW: Sahiwal, BH: Brahman. The last three breeds are Bos indicus breeds.

ISSN: 2730-7182