PATMATMOTIFS

Search a PROSITE motif database with a protein sequence

patmatmotifs takes a protein sequence and compares it to thePROSITE database of motifs.

For a description of PROSITE, we can do no better than to quote thePROSITE user's documentation:

PROSITE is a method of determining what is the function of uncharacterized proteins translated from genomic or cDNA sequences. It consists of a database of biologically significant sites and patterns formulated in such a way that with appropriate computational tools it can rapidly and reliably identify to which known family of protein (if any) the new sequence belongs.

In some cases the sequence of an unknown protein is too distantly related to any protein of known structure to detect its resemblance by overall sequence alignment, but it can be identified by the occurrence in its sequence of a particular cluster of residue types which is variously known as a pattern, motif, signature, or fingerprint. These motifs arise because of particular requirements on the structure of specific region(s) of a protein which may be important, for example, for their binding properties or for their enzymatic activity. These requirements impose very tight constraints on the evolution of those limited (in size) but important portion(s) of a protein sequence. To paraphrase Orwell, in Animal Farm, we can say that "some regions of a protein sequence are more equal than others" !

The use of protein sequence patterns (or motifs) to determine the function(s) of proteins is becoming very rapidly one of the essential tools of sequence analysis. This reality has been recognized by many authors, as it can be illustrated from the following citations from two of the most well known experts of protein sequence analysis, R.F. Doolittle and A.M. Lesk:

      "There are  many short  sequences  that  are  often  (but  not  always)      diagnostics of certain binding properties or active sites. These can be      set into a small subcollection and searched against your sequence (1)".      "In some  cases, the structure and function of an unknown protein which      is too  distantly related  to any  protein of known structure to detect      its affinity  by overall  sequence alignment  may be  identified by its      possession of  a particular  cluster of  residues types classified as a      motifs. The  motifs, or  templates, or  fingerprints, arise  because of      particular  requirements  of  binding  sites  that  impose  very  tight      constraint on the evolution of portions of a protein sequence (2)."

The home web page of PROSITE is: http://www.expasy.ch/prosite/

It is common to find that a search of the PROSITE database against aprotein sequence will report many matches to the short motifs that areindicative of the post-translational modification sites, such asglycolsylation, myristylation and phosphorylation sites. These reportsare often unwanted and are not normally reported. You can turnreporting of these short motifs on by giving the '-noprune' option onthe command-line.

Your EMBOSS administrator must have set up the local EMBOSS PROSITEdatabase using the utility 'prosextract' before this program will run.

Bairoch A., Bucher P., Hofmann K. The PROSITE datatase, its status in 1997. Nucleic Acids Res. 24:217-221(1997).

Other references:

1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic Acids Research, Vol 22, No.17 3583-3589.
2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd Edition.
4. Doolittle R.F. (In) Of URFs and ORFs: a primer on how to analyzederived amino acid sequences., University Science Books, Mill Valley,California, (1986).
5. Lesk A.M. (In) Computational Molecular Biology, Lesk A.M., Ed.,pp17-26, Oxford University Press, Oxford (1988).