Though the thermophilic RO homologs identified in this study were present among taxonomically close organisms, their distributions were very specific for certain phyla, often with very low abundance (Fig. 1).
In order to check how the paralogues arrange in a bigger tree, homologous sequences were retrieved from Uniprot databases from close organisms.
Our results showed differences of secondary structures in PSLPINc domains even between phylogenetically close organisms.
For each pair of phylogenetically close organisms, the one with the smaller genome was eliminated, leaving the organism with the larger genome [ 115].
The distance is established by comparing the lineage information; moreover, the system explores the closest organisms which encode the two enzymes.
The closest organisms with available protein sets were the Dipterans, Drosophila melanogaster and Anopheles gambiae, with an estimated divergence time from honey bee (Hymenopteran) of 300 million years.
The inclusion of proteins from taxonomically distant organisms with rich functional annotations such as Vitis vinifera or Ricinus communis, allowed us to annotate new proteins that could be lost if we include proteins only from close organisms.
The principle of our phylogenetic approach is that phylogenetically close organisms are likely to have similarly close regulatory networks; thus independent network inference errors at the leaves get corrected in the ancestral reconstruction process along the phylogeny.
