Comparison of the amino acid composition of Hsp60 with the
proteomic composition
Amino acid composition (X ) as a percentage of 20 amino acid
residues in the sequence was determined for each of the Hsp60 sequences
in database 1. Then the average amino acid composition (X̅ ) of
Hsp60s was determined for each of the 19 phyla.
To estimate the tendency to decrease or increase in the content of
certain amino acids in the Hsp60 sequences, it is necessary to calculate
the amino acid profile (X̅n ). For this, the
average amino acid composition of Hsp60 (X̅ ) for each of the 19
phyla was compared with the average amino acid composition of the
corresponding proteomes (X̅p ) (Supplementary, AA
composition of proteomes) using the following conditions:
- If X̅i > X̅piand p-value < alpha error, average percentage
(X̅i ) of i -amino acid for Hsp60s is
considered greater than proteomic value (X̅pi ),X̅ni = 1;
- If X̅i < X̅piand p-value < alpha error, average percentage content
(X̅i ) of i -amino acid for Hsp60s is
considered lower than proteomic value (X̅pi ),X̅ni = -1;
- If the p-value of the statistical test is higher than the alpha error,
the average percentage (X̅i ) of i -amino
acid for Hsp60s is considered comparable to the proteomic value
(X̅pi ), X̅ni = 0,
where X̅ni is the normalized value of the average
percentage of i -amino acid for Hsp60s (X̅i )
relative to the average proteomic value (X̅pi ) for
the corresponding phylum.
The amino acid profile of phylum (X̅n ) includesX̅ni values for all amino acid residues. Average
proteomic amino acid compositions (X̅p ) were
calculated using 8747 reference proteomes obtained from the UniProt
Proteomes database
(https://www.uniprot.org/proteomes/).
Using the normalized values X̅ni of 19 phyla, the
average normalized value ‹X̅ni› can be calculated.
The summary amino acid profile includes ‹X̅ni›values for all phyla. In should be noted that such an amino acid profile
is only meaningful if the groups included have similar amino acid
profiles.
In this work, the amino acid profiles of the Hsp60 sequences for 19
phyla and the total amino acid profile were calculated.