Trình tự motiz

Các motif và trình tự bảo thủ (consensus sequences)

The notation [XYZ] means X or Y or Z, 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:

[FILV]Qxxx[RK]Gxxx[RK]xx[FILVWY]

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

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

Phần mềm

There are software programs which, given multiple input sequences, attempt to identify one or more candidate motifs. One example is MEME, which generates statistical information for each candidate.

Discovery through evolutionary conservation

Motifs have been discovered by studying similar genes in different species. For example, by aligning the amino acid sequences specified by the GCM (glial cells missing) gene in man, mouse and D. melanogaster, Akiyama and others discovered a pattern which they called the GCM motif. It spans about 150 amino acid residues, and begins as follows:

WDIND*.*P..*...D.F.*W***.**.IYS**...A.*H*S*WAMRNTNNHN

Here each . signifies a single amino acid or a gap, and each * indicates one member of a closely-related family of amino acids.

The authors were able to show that the motif has DNA binding activity.

Pattern description notations

Several notations for describing motifs are in use but most of them are variants of standard notations for regular expressions and use these conventions:

there is an alphabet of single characters, each denoting a specific amino acid or a set of amino acids;

a string of characters drawn from the alphabet denotes a sequence of the corresponding amino acids;

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:

a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn.

Thus the pattern [AB] [CDE] F matches the six amino acid sequences corresponding to ACF, ADF, AEF, BCF, BDF, and BEF.

Different pattern description notations have other ways of forming pattern elements. One of these notations is the PROSITE notation, described in the following subsection.

Another scheme

This example comes from the paper by Matsuda and colleagues cited below.

The E. coli lactose operon repressor LacI (PDB id 1lccA) and E. coli catabolite gene activator (PDB id 3gapA) both have a helix-turn-helix motif, but their amino acid sequences do not show much similarity, as shown in the table below.

Matsuda and colleagues devised a code called the 3D chain code for representing a protein structure as a string of letters. This encoding scheme reveals the similarity between the proteins much more clearly than the amino acid sequence:

3D chain code Amino acid sequence

1lccA TWWWWWWWKCLKWWWWWWG LYDVAEYAGVSYQTVSRVV

3gapA KWWWWWWGKCFKWWWWWWW RQEIGQIVGCSRETVGRIL