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Although plant defensins are structurally conserved, their overall homology at the amino acid level is low.
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A benefit of combining such a clustering tree and the visualization of the various predictions is that this allows easy visual verification of the results of the clustering, as modules are usually conserved in their overall arrangement in closely related groups of proteins.
Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants.
Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture clusters of low affinity binding sites is maintained and required for enhancer function.
Most eukaryotes have at least three HP1 isoforms [1], which are conserved in overall structure but bind to different regions within the genome [2].
While the complex is not well conserved, the overall pattern of subunit occurrence argues that this is an ancient complex.
The plastome is highly conserved in overall structure and this provides the basis for comparative studies [ 4].
These results indicate that while gene-gene interactions are not well conserved, the overall network, through the intermediate level of modules, is conserved to a much higher degree.
The interfaces of non-obligate interactions tend to be smaller, less tightly packed, more polar, less conserved, and overall more similar to normal protein surfaces in terms of amino acid composition than those of obligate interactions [ 4- 9].
Finally, the polytomy in the Bayesian tree of mats (Additional file 1: Figure S7) may be caused by very short (226 aa) and highly conserved (the overall mean p-distance = 0.166) sequences.
Isomerases change their overall chemistry and conserve the structure of their substrates more often than conserving the chemistry and changing substrates.
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