Moreover, it is often not possible to identify orthologs of genes in different species by means of protein sequence comparison alone, because serine proteinases and serpins belong to very large gene families in which highly similar members (i.e. paralogs) often have completely unrelated functions [26], [27], [28], [29].
These results illustrate that while signaling pathways components may be "conserved", that does not necessarily mean the protein sequences cease to produce adaptive mutations [ 20].
Finally, in three cases, the variant Hb was only characterized by means of protein sequencing; therefore, the mutated α-globin gene could not be identified unambiguously, and these cases were excluded from further analysis.
'Reverse orientation' simply means that each protein sequence was read and stored sequentially, beginning at the C-terminal end and concluding at the N-terminal end.
The mean length of a protein sequence in the human protein dataset was 487.4 amino acids.
The CH predictor calculates the mean hydrophobicity and the mean net charge for a protein sequence, identifies the part of the charge-hydrophobicity plane that the corresponding point belongs to, and calculates its distance from the separating line.
By "splice site", he means a segment of protein sequence (10 aa residues) flanking an intron position.
Early studies suggested "overprinting" of a protein coding region in a different reading frame as a means of generating new protein sequence space [ 32- 34].
For each protein sequence, the mean fraction of charged residues was determined by counting D, E, K, and R and dividing this sum by the sequence length.
An analysis of the mean distance between protein sequences using the JTT model with gaps excluded in the analysis showed that levels of sequence identity were 64.4%, much larger the 30% expected in the presence of high conservation levels.
