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In total, 5% of proteins fell into poorly characterized categories (COG groups S and R), whereas 16% could not be identified in any COG grouping.
Additionally, the poorly characterized categories S and R are more abundant among paralogs in Clade 1, indicating putative novel inventions in these organisms.
The other tree KOG categories [ 20], namely information storage and processing, metabolism, and poorly characterized categories seem to be less informative (Fig. 2).
The number of genes classified into Metabolism and Poorly characterized categories was similar between the genome database and poly(A) data set.
The "Metabolism" and "Poorly Characterized" categories were the most affected by incomplete lineage sorting, as their consensus trees differed precisely in those branches where incomplete lineage sorting was a factor.
The consensus trees obtained for the "Information Storage and Processing" and "Cellular Processes and Signaling" categories also indicated the 370SBP topology, whereas the consensus trees for the "Metabolism" and "Poorly Characterized" categories differed from one another and from the 370SBP topology.
Similar(54)
Moreover, the "Poorly characterized" category performs better than other categories related with metabolism or cellular processes.
Proteins in the "Unclassified, poorly characterized" category were classified as "Unclassified".
The remaining items shown in white belong to the Poorly characterized category.
For all the technologies, the most abundant characterized category was COG category C (Energy production and conversion).
The "Poorly Characterized" category had the most diverged orthologous genes, with most genes (28%) having six to eight expected substitutions per site per phylogeny.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com