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This practice has not gone unchallenged and may be a suboptimal choice for overall conservation planning.
Finally, CMMB's single species perspective is perhaps its most important limiting factor for overall conservation efficiency.
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Finally, a comprehensive optimization scheme was suggested for the overall conservation planning.
This provides an explanation for the overall conservation of the catalytically dead kinase domain of ERBB3.
Thus, we provide evidence for an overall conservation of the translocation machinery and describe the inventory in 14 different plant species, which might guide future research of plant protein import.
For a comparison between groups values were corrected for branch-depth (overall conservation) by normalizing the values to an identical average in all alignments.
46.54%/29.94% of WMIs are conserved between the two yeasts (more than twice the overall conservation for the S. cerevisiae - S. pombe comparison and 30% higher than any of the previously proposed explanations - see Table 1).
Overall conservation for these proteins is greater than that observed for the eIF3f orthologues and related proteins and the grouping is validated by more robust bootstraps which includes the T. vaginalis eIF3h.
The similarity of these two E3 ubiquitin ligases and their overall conservation for pathologically relevant amino acids prompted us to compare both proteins at a functional level.
Of these pairs, only 10 are showing conservation, which is quite low compared to the overall conservation for correlated mutation pairs (63%, see above); however, one reason might be that the I domain is more variable and less well alignable than the MADS or K-domain.
This overall conservation provides support for the prediction of the P. falciparum hypothetical proteins listed in Tables 1 and 2 as potential important components of the basic transcription machinery.
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