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Homologous sequences are paralogous if they were created by a duplication event within the genome. For gene duplication events, if a gene in an organism is duplicated, the two copies are paralogous. They can shape the structure of whole genomes and thus explain genome evolution to a large extent. Examples include the Homeobox genes in animals.
As with morphological and anatomical structures, sequence similarity might occur because of convergent evolution, or, as with shorter sequences, by chance, meaning that they are not homologous. Homologous sequence regions are also called conserved. This is not to be confused with conservation in amino acid sequences, where the amino acid at a ...
The method of homology modeling is based on the observation that protein tertiary structure is better conserved than amino acid sequence. [3] Thus, even proteins that have diverged appreciably in sequence but still share detectable similarity will also share common structural properties, particularly the overall fold.
First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. Generated with ClustalX. Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
Binding site prediction involves the use of one of the following two methods: [49] Sequence similarity based methods. They consist in the identification of homologous sequences with known DNA binding sites, or by aligning them with query proteins. Their performance is usually low because the DNA binding sequences are less conserved. Structure ...
Structure is much more evolutionarily conserved than sequence, such that proteins with highly similar structures can have entirely different sequences. [7] Over very long evolutionary timescales, very few residues show detectable amino acid sequence conservation, however secondary structural elements and tertiary structural motifs are highly ...
It has been shown that, given the structural alignment between a target and a template sequence, highly accurate models of the target protein sequence can be produced; a major stumbling block in homology-based structure prediction is the production of structurally accurate alignments given only sequence information.
Based on amino acid sequence homologies and mechanistic relatedness, most site-specific recombinases are grouped into one of two families: the tyrosine (Tyr) recombinase family or serine (Ser) recombinase family. The names stem from the conserved nucleophilic amino acid residue present in each class of recombinase which is used to attack the ...