Sequence divergence

Figure 1. An unrooted phylogenetic tree of the myosins based on the amino acid sequence comparison of their head domains demonstrating the division of the myosin superfamily into nine classes. The lengths of the branches are proportional to the percent of amino acid sequence divergence and a calibration bar for 5% sequence divergence is shovk n. The different classes of myosins have been numbered using Roman numerals in rough order of their discovery and hypothetical models of the different myosin structures are shown. Question marks indicate either hypothetical or unknown structural features, and only a fraction of the known myosins are shown. (Taken, in modified form, from Cheney et al., 1993).

Powers, T.O., Harris, T.S. and Hyman, B.C. (1993) Mitochondrial DNA sequence divergence among Meloidogyne incognita, Romanomermis culcivorax, Ascaris suum and Caenorhabditis elegans. Journal of Nematology 25, 564—572. 

Sequence-divergent units of the ABA-1 polyprotein array of the nematode Ascaris have similar fatty acid and retinol binding properties but different binding site environments. BiochemicalJournal340, 337-343. 

The repeat gene family tandem repeats may increase both intra- and intermolecular recombination events, which result in gene or epitope amplification that is usually followed by sequence divergence. This could be another strategy of adaptation by the virus to keep pace with its evolving host. Because of its potentially large size and sequence diversity, the 540-bp repeat gene family will presumably play an important role. Based upon predicted properties, the 540-bp repeat proteins are believed to function differently than those of the cysteine-rich family. 

Sirtuins have been conserved from bacteria to eukaryotes. Notably, they all possess a conserved catalytic core domain flanked by sequence-divergent N- and C-terminal regions. If bacteria and archaebacteria generally possess one or two sirtuins, this number is higher in eukaryotes, with five sirtuins in Saccharomyces cerevisiae and seven in human. The presence of sirtuins in all phyla of life led to a wealth of structural data, not only on eukaryotic enzymes but also on bacterial and archaebacteria enzymes. 

The age distribution for various genome sequences is done by comparing changes in similar sequences found in older species. This dating has several important assumptions first, that the rate of sequence divergence is constant over time and between lineages and second, that the standard older sequence is in fact a source of the sequence and that the date for this source is appropriate. These assumptions are at best appropriate so that results derived from such studies need to be considered in this light. 

FIGURE 3-33 Evolutionary tree derived from amino acid sequence comparisons. A bacterial evolutionary tree, based on the sequence divergence observed in the GroEL family of proteins. Also included in this tree (lower right) are the chioropiasts (chi.) of some nonbacteriai species. 

In nature, to preserve function a strong selective pressure may act on the secondary structure of functional RNA molecules, while the sequences diverge. This effect... 

Instead, the ankyrin repeat-containing part of a-LTX is broken in several places and forms clearly delimited domains and subdomains, probably reflecting sequence divergence of some repeats and the functional specialization of the subdomains. 

PM Dombrosky, MB Schmid, KD Young. Sequence divergence of the murB and rrfB genes from Escherichia coli and Salmonella typhimurium. Arch Microbiol 161 501-507, 1994. 

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