Fig. 2.
From: Biological function in the twilight zone of sequence conservation
Trends regarding sequence constraint. Protein-coding sites that are highly constrained (d N /d S  → 0) tend to fall within secondary structures within intracellular proteins expressed in many tissues, whereas the less-numerous sites that are evolving either near neutrally (d N /d S  ≈ 1) or in response to positive selection (d N /d S  > 1) tend to lie in disordered regions or in loops in secreted proteins that are expressed in a tissue-restricted manner [73,74,75]. The median value of d N /d S for human and mouse orthologues is 0.095 [76]. Inferences of positive selection (for example using PAML [77]) can be in error due to sequence misalignment [78, 79], or when alignments are short [80], or when d N exceeds d S because of chance fluctuations. d N /d S (also written as K a /K s or ω) [81] is the ratio of the number of nonsynonymous substitutions per nonsynonymous site (d N ) to the number of synonymous substitutions per synonymous site (d S )