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any string of characters drawn from the alphabet enclosed in square brackets matches any one of the corresponding amino acids; e.g. [abc] matches any of the amino acids represented by a or b or c. The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation:
This is a graphical representation of the consensus sequence, in which the size of a symbol is related to the frequency that a given nucleotide (or amino acid) occurs at a certain position. In sequence logos the more conserved the residue, the larger the symbol for that residue is drawn; the less frequent, the smaller the symbol.
For example, if the amino acid that attach to the end is phenylalanine, the reaction will be catalyzed by phenylalanine-tRNA synthase to produce tRNA phe. [ 4 ] The other end—the bottom often called the "DNA arm"—consists of a three base sequence that pairs with a complementary base sequence in a mRNA .
In molecular biology, pseudo amino acid composition (PseACC) is a method introduced by Kuo-Chen Chou to convert the protein sequence into a numerical vector for enhancing pattern recognition techniques, such as during discrimination between classes of proteins based on their sequences (e.g. between membrane proteins, transmembrane proteins, cytosolic proteins, and other types). [1]
a conserved pattern of amino acids that is found in two or more proteins. In the Prosite catalog, a motif is an amino acid pattern that is found in a group of proteins that have a similar biochemical activity, and that often is near the active site of the protein. Examples of sequence motif databases are the Prosite catalog and the Stanford ...
The AUG is the initiation codon encoding a methionine amino acid at the N-terminus of the protein. (Rarely, GUG is used as an initiation codon, but methionine is still the first amino acid as it is the met-tRNA in the initiation complex that binds to the mRNA). Variation within the Kozak sequence alters the "strength" thereof.
With apolar amino acid residues at either the e or g position, a heterotetramer consisting of 2 different leucine zippers can be generated in-vitro, which implies that the overall hydrophobicity of the interaction surface and van der Waals interaction may alter the organization of coiled coils and play a role in the formation of leucine zipper ...
A consensus logo is a simplified variation of a sequence logo that can be embedded in text format. Like a sequence logo, a consensus logo is created from a collection of aligned protein or DNA/RNA sequences and conveys information about the conservation of each position of a sequence motif or sequence alignment [1] [4].