Therefore, we rather assume that subunits have been lost during evolution although we cannot exclude that we might have missed divergent homologs that can only be revealed in experiments, but not sequence based analyses.
To prevent missing highly divergent viruses, the newly found viral sequences were included in the reference protein sequences for a second round of Blastx.
However, the search did correctly identify all KAP-βs detected as NE-associated by proteomics in Trypanosoma brucei [32], suggesting that the dataset is very comprehensive, and only likely to have missed extremely divergent candidates.
Although these methods work very well when sufficient sequence similarity is present, they tend to miss more divergent family members, which lie within and below the so-called twilight zone of below 20% sequence similarity.
Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity.
It may miss more divergent or shorter sequence alignments.
With this strategy, we sought to ensure that we would not miss more divergent myosin homologs, which might have been derived by species-specific inventions or duplications.
With this strategy, we wanted to ensure that we would not miss more divergent tubulin homologs, which might have been derived by species-specific inventions or duplications.
Of course, although complete genome sequences are not available and RT-PCR results can artifactually miss a divergent sequence, these data collectively suggest that an unique event of loss of AR-B occurred early on in the Otophysi lineage.
The viral host Giardia is known to possess the translation machinery with many unusual features, such as the involvement of a 70S instead of a 80S ribosome [48] and the translation initiation factors that are either missing or structurally divergent as compared to that of the higher eukaryotes [49].
Based on earlier work [ 53], we expected chlL to be missing or highly divergent in Welwitschia.
