Editing Sequence motif (section)

===Motifs and consensus sequences===

The notation <code>[XYZ]</code> means <code>X</code> or <code>Y</code> or <code>Z</code>, but does not indicate the likelihood of any particular match.  For this reason, two or more patterns are often associated with a single motif: the defining pattern, and various typical patterns.

For example, the defining sequence for the [[IQ motif]] may be taken to be:

: <code>[FILV]Qxxx[RK]Gxxx[RK]xx[FILVWY]</code>

where <code>x</code> signifies any amino acid, and the square brackets indicate an alternative (see below for further details about notation).

Usually, however, the first letter is <code>I</code>, and both <code>[RK]</code> choices resolve to <code>R</code>. Since the last choice is so wide, the pattern <code>IQxxxRGxxxR</code> is sometimes equated with the IQ motif itself, but a more accurate description would be a ''[[consensus sequence]] for the IQ motif''.