EMOTIF is a research system that forms motifs for subsets of aligned sequences.

A motif is expressed as a pattern specifying the amino acids that can occur at each position in a sequence. The possibilities are

`.', which allows any amino acid,
a specific amino acid, or
a group of amino acids that share some physico-chemical property, e.g. charge, hydrophobicity, size

The possible groups in the third category are determined by the `amino acid groups' selector above. In future, we will allow you to specify your own groups.

EMOTIF ranks the motifs that it finds by both their specificity (expected false positives) and the number of supplied sequences that it covers (true positives). The twenty highest-scoring motifs are returned, and can be used to search the entire SWISS-PROT database.

Input format

We currently accept:

plain text sequences, with no extraneous numbers or symbols.


LEEVKQGNLERECLEEACSLEEAREVFEDAEQTDEFWSKY
LEEMKQGNIERECNEERCSKEEAREAFEDNEKTEEFWNIY
LEEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKY
LEELLPGSLERECREELCSFEEAHEIFRNEERTRQFWVSY
LEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISY
SGVAGAPPNPIEAQREVCELSPDCNELADELGFQEAYQRR

BLOCKS format


ID   GLU_CARBOXYLATION; BLOCK
AC   BL00011; distance from previous block=(1,64)
DE   Vitamin K-dependent carboxylation domain proteins.
BL   ECA motif; width=40; seqs=34; 99.5%=1833; strength=1412
FA10_BOVIN (  45) LEEVKQGNLERECLEEACSLEEAREVFEDAEQTDEFWSKY  31

FA10_CHICK (  45) LEEMKQGNIERECNEERCSKEEAREAFEDNEKTEEFWNIY  46

FA10_HUMAN (  45) LEEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKY  33
 FA7_BOVIN (   5) LEELLPGSLERECREELCSFEEAHEIFRNEERTRQFWVSY  57
 FA7_HUMAN (  65) LEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISY  42

OSTC_CHICK (   6) SGVAGAPPNPIEAQREVCELSPDCNELADELGFQEAYQRR  94

The sequences must be aligned; there must be some similarity in columns. Extra characters at the beginning and end will cause EMOTIF to fail.

For multiple alignments from Clustal, GCG, Phylip, PIR, etc, use the reformatter