Bioinformatics Interview Question:

Have the proteins of a family generally acquired distinctive properties within each of these three kingdoms for ancient families that arose before bacteria, archaea and eukaryotes diverged?

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Proteins from 20 large ubiquitous families represented in all three domains to see if proteins from each domain exhibit distinctive characteristics. The archaeal integral membrane proteins are consistently smaller than their bacterial homologues, while the eukaryotic homologues are much larger. Moreover, among transporters in the three major eukaryotic kingdoms of plants, animals and fungi, the animal and fungal homologues are of comparable size, whereas the plant homologues are substantially smaller. Although these surprising observations presumably reflect evolutionary pressures during protein sequence divergence, we do not know what those pressures were.
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