Sequence motif

In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue. When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein. Nevertheless, motifs need not be associated with a distinctive secondary structure. "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes the case. For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. They are able to recognize motifs through contact with the double helix's major or minor groove. Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation. Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. Such techniques belong to the discipline of bioinformatics. See also consensus sequence. Consider the N-glycosylation site motif mentioned above: Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro This pattern may be written as N{P}[ST]{P} where N = Asn, P = Pro, S = Ser, T = Thr; {X} means any amino acid except X; and [XY] means either X or Y. The notation [XY] does not give any indication of the probability of X or Y occurring in the pattern.