Predictions begin from an alignment to a parent protein of known structure and coordinates for the aligned regions are taken directly from the parent structure and serve as a fixed template.
We successfully identified amino acid sequences and parent proteins for 11 of the 47 peptide peaks, as shown in Table 2. BMP, bone morphogenetic protein; FYVE, phenylalanine (F /tyrosine (Y)/valine (V /glutamic acid (E) domain; Rho, Ras homolog; GEF, guanine nucleotide exchange factor; PH, pleckstrin homology.
Furthermore, heat treatments contribute to the breakdown of parent proteins to form lower molecular weight peptides (Gaucheron et al., 1999).
Within this framework, the modular architecture of the parent proteins, some of which are multi-functional proteins, was evaluated together with their gene expression levels.
The pseudogene proteins and nucleotide sequences, number of exons in the coding region of the parent proteins and pseudogenes, number of frameshifts and stop codons in the pseudogenes, length of the pseudogenes and parent proteins were derived from the GeneWise output.
Remarkably, FNoTNc retains the structure of the parent proteins despite the extent of redesign, allowing us to gain insight into which components of each parent protein are responsible for different aspects of its behaviour.
It remains to be seen whether the ribonuclease activity of the ZFY zinc finger and the PPR DYW domains is preserved in their parent proteins and, eventually, is of biological importance.
Yet, their cohesins are clustered on very different branches on the tree, suggesting that their parent proteins are the product of different evolutionary pathways.
HA carries the EvgA receiver and BvgA output domains, fused in the central part of the linker sequences of the parent proteins.
Generally, the amino acid composition of gelatin hydrolysates is very similar to the parent proteins, being rich in residues of Gly, Ala, Pro, Hyp, Glx, and Asx but poor in Met, Cys, His, and Tyr [ 8].
