Molecular biology in the internet

Main page








Sequence comparisons

Homology searches

Motif searches

Hidden Markov models

Hydrophobicity analyses

Topology and helix packing

Protein localization

Secondary structure

Super-secondary structure

3D structure


PROSITE pattern (as listed in the PA line):

The PA (PAttern) lines contains the definition of a PROSITE pattern. The patterns are described using the following conventions.

  • The standard IUPAC one-letter codes for the amino acids are used.
  • The symbol 'x' is used for a position where any amino acid is accepted.
  • Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses '[ ]'. For example: [ALT] stands for Ala or Leu or Thr.
  • Ambiguities are also indicated by listing between a pair of curly brackets '{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met.
  • Each element in a pattern is separated from its neighbor by a '-'.
  • Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x.
  • When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a '<' symbol or respectively ends with a '>' symbol. In some rare cases (e.g. PS00267 or PS00539), '>' can also occur inside square brackets for the C-terminal element. 'F-[GSTV]-P-R-L-[G>]' means that either 'F-[GSTV]-P-R-L-G' or 'F-[GSTV]-P-R-L>' are considered.
  • A period ends the pattern.

  • [AC]-x-V-x(4)-{ED}.
    • This pattern is translated as: [Ala or Cys]-any-Val-any-any-any-any-{any but Glu or Asp}
  • <A-x-[ST](2)-x(0,1)-V.
    • This pattern, which must be in the N-terminal of the sequence ('<'), is translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val


Latest update of content: October 4, 2004

Ralf Koebnik
Institut für Genetik
Abt. Pflanzengenetik
Weinbergweg 10
06120 Halle/Saale
Telefon: 0345 / 55 26 293 (Büro) bzw. 296 (Labor)
Fax: 0345 / 55 27 151
Email: koebnik (at)
Please replace (at) by @.

Home Back to previous page