Searches sequences with a sequence motif using patmatdb program from the EMBOSS package.
Patterns for patmatdb are based on the format of pattern used in the PROSITE database

Motif	Example : MKK[KP]K
Database	Amacrogynus Amellifera Athaliana Bdendrobatidis Celegans Chlorella Cintestinalis Cpneumoniae Creinhardtii Ddiscoideum Dmelanogaster Drerio Ecoli Ehuxleyi Glamblia Hsapiens Lbicolor Mbrevicollis Micromonas Mmusculus Mverticillata Ngruberi Otauri Panserina Pfalciparum Pinfestans Ppatens Ptetraurelia Ptricornutum Rnorvegicus Rprowazekii Scerevisiae Smediterranea Smoellendorffii Spombe Spunctatus Synechocystis Tadhaerens Tbrucei Tgondii Tparva Tpseudonana Tthermophila Xlaevis

The PROSITE pattern definition from the PROSITE documentation follows.

• The symbol "X" is used for a position where any residues is accepted.
• Ambiguities are indicated by listing the acceptable residues 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 residues 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 "-". (Optional in patmatdb).
• 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.

For more information please see the documentation page