Glossary of key terms and abbreviations

See also the Molecular Evolution glossary on Rich's blog.

Term	Related Terms	Description
Convergent evolution	Molecular mimicry	Independent evolutionary origins of the same function or motif on different genetic backgrounds.
Degenerate	Ambiguous	A SLiM position that can have 2+ different amino acids.
Divergent evolution	Conservation	The accumulation of differences over time following shared ancestry. Where such differences are selected against (purifying selection) sequence conservation will be seen.
Domain-Motif Interaction	DMI	PPI mediated by a SLiM in one protein and a SLiM-binding domain in the other.
Intrinsically Disordered Protein/Region	IDP/IDR	A protein/region that lacks a stable three-dimensional structure in the unbound state.
Instance	Occurrence	A single observation of a SLiM in a single protein.
Pattern	Motif definition	The regular expression that defines a motif.
Post-Translational Modification	PTM	A chemical modification of an amino acid that alters its properties, such as phosphorylation of serine, threonine or tyrosine.
Protein-Protein Interaction	PPI	A physical interaction between two proteins.
Regular expression	Regex, PROSITE pattern	A common programming notation for string (text) patterns. For the purposes of this review, variants on the standard regular expression notation are included under the “regex” umbrella.
Short Linear Motif	SLiM, Linear Motif, LM, Minimotif	A short (typically <15aa) linear stretch of protein sequence with specific residues important for function. Within this review, "motif" refers to a SLiM unless otherwise specified.
Support	UP Support	The number of different proteins that contain a given SLiM. “UP” indicates that this is the number of unrelated proteins.
Wildcard		A position in a SLiM that can be any amino acid.