Moreover, similar average proportions of mini-proteins, 11.28%, 11.30% and 9.33%, respectively, are annotated in the genomes of three archaeal phyla.
As shown in Table 1, the overall proportion of mini-proteins among all annotated genomic proteins is 10.99%.
The aforementioned results show that hypothetical proteins accounted for a large proportion of mini-proteins, even among the conserved phylum-shared and domain-shared ones.
In sharp contrast to the C. tetani, these nine genomes contain a normal proportion of mini-proteins, ranging from 14.25% to 8.27%.
Except for these two extremes, other phyla encode similar proportions of mini-proteins, although greater variability is observed when considering individual strains.
Moreover, the proportions of mini-proteins in the genome are actually dissimilar between different isolates of the same species, such as two strains in Spirochaetes, Leptospira interrogans serovar Copenhageni str.
To investigate conservation among mini-proteins, we took several representative phyla to determine the proportion of their mini-proteins that are specific or shared to each taxonomic level (species, genus, family, order, class, phylum and domain).
They are both obligate intracellular pathogens, but they inhabit granulocytes and erythrocyte, respectively [19], [20], therefore, differences in the host intracellular environments might account for the significant differences in relative proportion of the mini-proteins.
It is possible that many small mini-proteins may have been filtered out during annotation, grossly under estimating the actual number of mini-proteins.
In contrast, Aquificae has the least number of mini-proteins, merely encoding 48 mini-proteins in the whole genome, representing 3.08%.
