Increased Frequency of Cysteine, Tyrosine, and Phenylalanine Residues

Last Universal Ancestor
(LUA)

Виды, взятые в исследование:
Aquifex aeolicus, Aae;
Archaeoglobus fulgidus, Afu;
Aeropyrum pernix, Ape;
Bacillus subtilis, BAC;
Chlamydia pneumoniae, CLA;
Campylobacter jejuni, Cje;
Deinococcus radiodurans, Dra;
Escherichia coli K12, ENT;
Helicobacter pylori J9, HPY;
Halobacterium sp. NRC-1, Hbs;
Haemophilus influenzae, Hin;
Mycoplasma pneumoniae, MYC;
Methanococcus jannaschii, Mja;
Methanobacterium thermoautotrophicum, Mth;
Mycobacterium tuberculosis, Mtu;
Neisseria meningitidis, Nme;
Pseudomonas aeruginosa, Pae;
Pyrococcus horikoshii, Pyr;
Rickettsia prowazekii, Rpr;
Borrelia burgdorferi, SPI;
Saccharomyces cerevisiae, Sce;
Synechocystis PCC6803, Ssp;
Thermoplasma acidophilum, Tac;
Thermotoga maritima, Tma;
Vibrio cholerae, Vch;
Xylella fastidiosa, Xfa.
19 бактерий
+ 6 архей
+ 1 эукариот = 26 видов

Набор белков,
включенных в
исследование
59 семейств COG
(clusters of orthologous groups)

Частота каждой аминокислоты в исследованных видах

Относительная изменчивость аминокислот
согласно Dayhoff et al., 1978; Jones et al., 1992; Gonnet et al., 1992

The probability of observing amino acid j in a specific genome:
where i represents each codon assigned to amino acid j;
xi, yi, and zi represent the frequency of occurrence of the first, second, and third nucleotides, respectively, of codon i within coding sequences of that genome;
and λ is a constant such that the sum over all amino acids is equal to one.
The normalization constant λ compensates for probabilities assigned to stop codons.

Частота Cys, Tyr, Phe (наблюдаемая и предсказанная) у 26 исследованных видов

Сравнение частот Cys, Tyr и Phe
Frequency of Cys is significantly less than that predicted in all 26 species (p << 0.01), the mean over all species being 1/3 of that predicted.
Frequency of Tyr is less than predicted in only 15 of the species (p = 0.28, which is not statistically significant), and the mean observed frequency of Tyr 0.0335, is close to that predicted, 0.0358.
Frequency of Phe is higher than predicted in 25 species (p << 0.01), the mean observed frequency, 0.0437, being 40% higher than predicted.