The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Paz-y-Miño C., Guillermo; Espinosa, Avelina; Bai, Chunyan Y.

doi:10.1007/s12052-011-0329-2

Table 3 Jackprot probabilities applied to the genomic sequence coding for 160 amino acids (aa) and a stop codon of KcsA

From: The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

aa	Acronym	Codon	No. of simulations under selection required to generate correct nucleotide sequence per position			Total observed with selection^a	Expected with selection^b	Expected without selection^c
aa	Acronym	Codon	1st	2nd	3rd	Total observed with selection^a	Expected with selection^b	Expected without selection^c
M	met	atg	1	2	4	7	12	64
P	pro	cca	4	6	2	12	12	64
P	pro	ccc	3	5	4	12	12	64
M	met	atg	6	3	9	18	12	64
L	leu	ctg	5	3	5	13	12	64
S	ser	tcc	2	5	2	9	12	64
G	gly	ggt	2	1	2	5	12	64
L	leu	ctt	3	4	3	10	12	64
L	leu	ctg	1	4	1	6	12	64
A	ala	gcc	1	2	2	5	12	64
R	arg	aga	3	1	4	8	12	64
L	leu	ttg	6	1	1	8	12	64
V	val	gtc	3	3	3	9	12	64
K	lys	aaa	2	2	2	6	12	64
L	leu	ctg	1	12	5	18	12	64
L	leu	ctg	2	4	5	11	12	64
L	leu	ctc	3	1	2	6	12	64
G	gly	ggg	10	7	2	19	12	64
R	arg	cgc	3	4	3	10	12	64
H	hys	cac	3	2	5	10	12	64
G	gly	ggc	3	8	9	20	12	64
S	ser	agt	4	3	1	8	12	64
A	ala	gcg	1	1	6	8	12	64
L	leu	ctg	2	3	4	9	12	64
H	hys	cac	1	5	6	12	12	64
W	trp	tgg	4	4	3	11	12	64
R	arg	agg	6	5	2	13	12	64
A	ala	gcc	4	7	1	12	12	64
A	ala	gcg	1	5	8	14	12	64
G	gly	ggt	1	3	1	5	12	64
A	ala	gcc	9	2	2	13	12	64
A	ala	gcg	3	1	2	6	12	64
T	thr	acg	1	1	3	5	12	64
V	val	gtc	10	4	6	20	12	64
L	leu	ctc	2	2	2	6	12	64
L	leu	ctg	1	2	5	8	12	64
V	val	gtg	3	5	2	10	12	64
I	ile	atc	1	1	2	4	12	64
V	val	gtc	2	8	5	15	12	64
L	leu	ctc	5	1	2	8	12	64
L	leu	ctc	1	17	1	19	12	64
A	ala	gcg	2	9	2	13	12	64
G	gly	ggc	1	3	2	6	12	64
S	ser	tcg	1	7	2	10	12	64
Y	tyr	tac	5	1	1	7	12	64
L	leu	ttg	1	9	6	16	12	64
A	ala	gcc	1	4	1	6	12	64
V	val	gtc	1	2	2	5	12	64
L	leu	ctg	5	2	1	8	12	64
A	ala	gct	4	4	1	9	12	64
E	glu	gag	1	5	8	14	12	64
R	arg	cgc	2	2	8	12	12	64
G	gly	ggc	1	2	2	5	12	64
A	ala	gca	7	2	2	11	12	64
P	pro	ccg	3	5	5	13	12	64
G	gly	ggc	9	5	1	15	12	64
A	ala	gcg	5	3	7	15	12	64
Q	gln	cag	2	18	2	22	12	64
L	leu	ctg	1	2	3	6	12	64
I	ile	atc	2	2	1	5	12	64
T	thr	acg	2	2	4	8	12	64
Y	tyr	tat	1	3	1	5	12	64
P	pro	ccg	2	5	3	10	12	64
R	arg	cgg	4	1	1	6	12	64
A	ala	gcg	3	4	6	13	12	64
L	leu	ctg	1	5	1	7	12	64
W	trp	tgg	9	8	5	22	12	64
W	trp	tgg	3	4	1	8	12	64
S	ser	tcc	2	2	2	6	12	64
V	val	gtg	2	3	5	10	12	64
E	glu	gag	6	1	3	10	12	64
T	thr	acc	8	4	2	14	12	64
A	ala	gcg	4	2	1	7	12	64
T	thr	acg	1	7	4	12	12	64
T	thr	acc	4	2	10	16	12	64
V	val	gtc	3	2	5	10	12	64
G	gly	ggc	2	2	4	8	12	64
Y	tyr	tac	1	4	2	7	12	64
G	gly	ggc	2	4	5	11	12	64
D	asp	gac	2	3	4	9	12	64
L	leu	ctg	3	1	3	7	12	64
Y	tyr	tac	1	4	1	6	12	64
P	pro	ccc	2	2	7	11	12	64
V	val	gtg	3	3	4	10	12	64
T	thr	act	4	2	14	20	12	64
L	leu	ctg	9	4	1	14	12	64
W	trp	tgg	2	2	1	5	12	64
G	gly	ggc	3	1	1	5	12	64
R	arg	cgg	11	1	6	18	12	64
L	leu	ctc	3	5	6	14	12	64
V	val	gtg	8	3	14	25	12	64
A	ala	gcc	3	13	5	21	12	64
V	val	gtg	5	4	6	15	12	64
V	val	gtg	1	4	1	6	12	64
V	val	gtg	2	7	3	12	12	64
M	met	atg	3	2	6	11	12	64
V	val	gtc	3	9	2	14	12	64
A	ala	gcc	7	6	4	17	12	64
G	gly	ggg	3	3	2	8	12	64
I	ile	atc	1	3	1	5	12	64
T	thr	acc	6	2	2	10	12	64
S	ser	tcc	7	3	10	20	12	64
F	phe	ttc	2	3	1	6	12	64
G	gly	ggt	10	3	4	17	12	64
L	leu	ctg	2	8	7	17	12	64
V	val	gtg	4	2	3	9	12	64
T	thr	acc	1	4	1	6	12	64
A	ala	gcc	2	6	2	10	12	64
A	ala	gcg	1	1	9	11	12	64
L	leu	ctg	2	8	1	11	12	64
A	ala	gcc	2	8	1	11	12	64
T	thr	acc	8	5	6	19	12	64
W	trp	tgg	1	2	1	4	12	64
F	phe	ttc	5	4	4	13	12	64
V	val	gtc	1	5	9	15	12	64
G	gly	ggc	6	2	1	9	12	64
R	arg	cgg	2	2	1	5	12	64
E	glu	gaa	6	2	4	12	12	64
Q	gln	caa	4	3	4	11	12	64
E	glu	gag	2	7	3	12	12	64
R	arg	cgc	4	7	7	18	12	64
R	arg	cgg	4	5	3	12	12	64
G	gly	ggc	2	1	6	9	12	64
H	his	cac	1	2	11	14	12	64
F	phe	ttc	5	7	11	23	12	64
V	val	gtg	6	2	11	19	12	64
R	arg	cgc	2	1	2	5	12	64
H	his	cac	3	1	4	8	12	64
S	ser	tcc	4	7	1	12	12	64
E	blu	gag	9	1	6	16	12	64
K	lys	aag	4	8	2	14	12	64
A	ala	gcc	9	1	3	13	12	64
A	ala	gcc	1	7	3	11	12	64
E	glu	gag	4	3	13	20	12	64
E	glu	gag	9	3	4	16	12	64
A	ala	gcg	1	1	1	3	12	64
Y	tyr	tac	2	1	5	8	12	64
T	thr	acg	11	5	2	18	12	64
R	arg	cgg	1	1	5	7	12	64
T	thr	acg	2	5	5	12	12	64
T	thr	acc	2	3	3	8	12	64
R	arg	cgg	1	5	2	8	12	64
A	ala	gcg	7	2	4	13	12	64
L	leu	ctg	4	5	8	17	12	64
H	his	cac	3	3	6	12	12	64
E	glu	gag	3	2	6	11	12	64
R	arg	cgt	10	8	9	27	12	64
F	phe	ttc	4	13	2	19	12	64
D	asp	gac	4	1	3	8	12	64
R	arg	cgt	1	8	1	10	12	64
L	leu	ttg	1	2	3	6	12	64
E	glu	gag	1	2	6	9	12	64
R	arg	cga	3	5	2	10	12	64
M	met	atg	6	1	3	10	12	64
L	leu	ctc	1	4	2	7	12	64
D	asp	gac	2	8	3	13	12	64
D	asp	gac	2	4	2	8	12	64
N	asn	aac	1	1	5	7	12	64
R	arg	cgc	1	22	3	26	12	64
R	arg	cgg	3	2	1	6	12	64
Stop		tga	3	2	4	9	12	64
Total			543	646	610	1,799	1,932	10,304
Mean			3.37	4.01	3.78	11.17	12	64
Mode			1	2	2	8	12	64
Median			3	3	3	10	12	64
Max			11	22	14	27	12	64
Min			1	1	1	3	12	64

The total observed-under-selection value of correct nucleotide sequence composition (= 1,799) is lower than and statistically different from the total expected-under-selection value (= 1,932; Chi-square = 339.08; df = 160; p ≤ 0.05), and it does differ from what would be expected by chance without selection (Chi-square = 7081.95; df = 160; p ≤ 0.001). The tinkering effect of selection on mutation rate expedites evolution and the jackprot model shows it. Protein sequence available at NCBI (GenBank Z37969; Swiss-Prot P0A334)
^aData generated from under-selection simulations in which one of four marked marbles (A, G, C, and T), each representing a nucleotide, was drawn from a hat until the matching-to-the-sequence-nucleotide was generated, e.g., atg = one, two, and four times/first, second, and third positions, respectively
^bCorresponds to one in 12, or one divided by 4 + 4 + 4, i.e., the summation of the individual probabilities for each nucleotide position
^cCorresponds to one in 64, or one divided by 4 × 4 × 4, i.e., the total number of possible nucleotides per position multiplied by itself three times

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