Herein the biodiesel selected has an acceptable acid value and low glycerin content.
Nevertheless, changes from one profile to another are much easier to detect with our protocol when no acceptable amino acids are common to both than when at least one amino acid remains in the set of acceptable residues.
The second is the "breadth" of evolution, i. e., the diversity of acceptable amino acids, which can be defined as the probability that two independent replacements of a particular amino acid at a site lead to the same amino acid.
The consensus sequences are as follows: Hsp70 family signature 2 [VI]-[FY]-D-L-G(3 -T-F-D-[VI]-S-[IL]-L and Hsp70 family signature 3 -T-F-D-[VI]-S-[IL]-LSM]-[TS]-R-[IM]-P-K-[VI]-[QR]-[QEDK], where the square brackets show a list of acceptable amino acids at the given position and the numerical values between parentheses indicate repetition of the respective amino acid [ 3 -T-F-D-[VI]-S-[IL]-L
For certain positions (1, 3, 5, 6) there were single preferred residues, whilst other positions (2, 4, 7, 8, 9) had several acceptable amino acids.
Thus, at sites which evolve faster, the diversity of acceptable amino acids is also slightly higher.
Evolution at a protein site can be characterized from two different perspectives, by its rate and by the breadth of the set of acceptable amino acids.
In particular, the subset of acceptable amino acids or the exchangeability matrix at a given site may change throughout evolutionary time.
A slowly evolving position is under strong functional pressure that limits not only the number of substitutions, but also the diversity of acceptable amino acids, thus reducing the probability of being affiliated to different profiles in different clades.
B provides an unbiased sample estimate of the effective number of acceptable amino acids at a site, because it can be interpreted as the fraction of pairs of substitutions of the ancestral amino acid where the new amino acids are different from each other.
