unix % patmatmotifs
Search a motif database with a protein sequence
Input sequence: xlrhodop.pep
Output file [xlrhodop_1.patmatmotifs]: xlrhodop.patmatmotifs
unix % more xlrhodop.patmatmotifs
Number of matches found in this Sequence = 1
Length of the sequence = 354 basepairs
Start of match = position 123 of sequence
End of match = position 139 of sequence
Length of motif = 17
patmatmotifs of G_PROTEIN_RECEPTOR with XLRHODOP+1 from 123 to 139\\
TLGGEVALWSLVVLAVERYMVVCKPMA
| |
123 139
Number of matches found in this Sequence = 1
Length of the sequence = 354 basepairs
Start of match = position 290 of sequence
End of match = position 306 of sequence
Length of motif = 17
patmatmotifs of OPSIN with XLRHODOP+1 from 290 to 306
PVFMTVPAFFAKSSAIYNPVIYIVLNK
| |
290 306
In our case we already know that our sequence is a rhodopsin. However, if you had an unknown sequence, we hope you can see that identifying motifs might provide you with information to help you plan further experiments.