EMBOSS: patmatmotifs

| patmatmotifs

## Function

Scan a protein sequence with motifs from the PROSITE database

## Description

patmatmotifs reads a protein sequence and searches it against the PROSITE database of motifs. It writes a standard EMBOSS report file with details of the location and score of any matching motifs. Optionally, full documentation for matching patterns is given in the report. Optionally, simple post-translational modification sites are not reported. PROSITE must be processed by running prosextract before running patmatmotifs.

The home web page of PROSITE is: http://www.expasy.ch/prosite/. Quoting from the PROSITE 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)."

It is common to find that a search of the PROSITE database against a protein sequence will report many matches to the short motifs that are indicative of the post-translational modification sites, such as glycolsylation, myristylation and phosphorylation sites. These reports are often unwanted and are not normally reported. You can turn reporting of these short motifs on by giving the `-noprune` option on the command-line.

## Usage

Here is a sample session with patmatmotifs

    % patmatmotifs -full
    Scan a protein sequence with motifs from the PROSITE database
    Input protein sequence: tsw:opsd_human
    Output report [opsd_human.patmatmotifs]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Protein sequence filename and optional
                                      format, or reference (input USA)
      [-outfile]           report     [*.patmatmotifs] Output report file name

       Additional (Optional) qualifiers:
       -full               boolean    [N] Provide full documentation for matching
                                      patterns
       -[no]prune          boolean    [Y] Ignore simple patterns. If this is true
                                      then these simple post-translational
                                      modification sites are not reported:
                                      myristyl, asn_glycosylation,
                                      camp_phospho_site, pkc_phospho_site,
                                      ck2_phospho_site, and tyr_phospho_site.

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -rformat2           string     Report format
       -rname2             string     Base file name
       -rextension2        string     File name extension
       -rdirectory2        string     Output directory
       -raccshow2          boolean    Show accession number in the report
       -rdesshow2          boolean    Show description in the report
       -rscoreshow2        boolean    Show the score in the report
       -rstrandshow2       boolean    Show the nucleotide strand in the report
       -rusashow2          boolean    Show the full USA in the report
       -rmaxall2           integer    Maximum total hits to report
       -rmaxseq2           integer    Maximum hits to report for one sequence

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-outfile] (Parameter 2) | Output report file name | Report output file | <*>.patmatmotifs
Additional (Optional) qualifiers | Allowed values | Default
-full | Provide full documentation for matching patterns | Boolean value Yes/No | No
-[no]prune | Ignore simple patterns. If this is true then these simple post-translational modification sites are not reported: myristyl, asn_glycosylation, camp_phospho_site, pkc_phospho_site, ck2_phospho_site, and tyr_phospho_site. | Boolean value Yes/No | Yes
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

patmatmotifs reads a protein sequence USA.

### Input files for usage example

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:opsd_human

    ID   OPSD_HUMAN              Reviewed;         348 AA.
    AC   P08100; Q16414; Q2M249;
    DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
    DT   01-AUG-1988, sequence version 1.
    DT   20-MAR-2007, entry version 91.
    DE   Rhodopsin (Opsin-2).
    GN   Name=RHO; Synonyms=OPN2;
    OS   Homo sapiens (Human).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
    OC   Catarrhini; Hominidae; Homo.
    OX   NCBI_TaxID=9606;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RX   MEDLINE=84272729; PubMed=6589631;
    RA   Nathans J., Hogness D.S.;
    RT   "Isolation and nucleotide sequence of the gene encoding human
    RT   rhodopsin.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
    RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
    RT   "Genome-wide discovery and analysis of human seven transmembrane helix
    RT   receptor genes.";
    RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
    RN   [3]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    RC   TISSUE=Retina;
    RG   The German cDNA consortium;
    RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
    RN   [4]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    RX   PubMed=15489334; DOI=10.1101/gr.2596504;
    RG   The MGC Project Team;
    RT   "The status, quality, and expansion of the NIH full-length cDNA
    RT   project: the Mammalian Gene Collection (MGC).";
    RL   Genome Res. 14:2121-2127(2004).
    RN   [5]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
    RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
    RA   Bennett J., Beller B., Sun D., Kariko K.;
    RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
    RT   rhodopsin-encoding gene.";
    RL   Gene 167:317-320(1995).
    RN   [6]
    RP   REVIEW ON RP4 VARIANTS.
    RX   MEDLINE=94004905; PubMed=8401533;
    RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
    RA   Bhattacharya S.;

      [Part of this file has been deleted for brevity]

    FT                                /FTId=VAR_004816.
    FT   VARIANT     209    209       V -> M (effect not known).
    FT                                /FTId=VAR_004817.
    FT   VARIANT     211    211       H -> P (in RP4).
    FT                                /FTId=VAR_004818.
    FT   VARIANT     211    211       H -> R (in RP4).
    FT                                /FTId=VAR_004819.
    FT   VARIANT     216    216       M -> K (in RP4).
    FT                                /FTId=VAR_004820.
    FT   VARIANT     220    220       F -> C (in RP4).
    FT                                /FTId=VAR_004821.
    FT   VARIANT     222    222       C -> R (in RP4).
    FT                                /FTId=VAR_004822.
    FT   VARIANT     255    255       Missing (in RP4).
    FT                                /FTId=VAR_004823.
    FT   VARIANT     264    264       Missing (in RP4).
    FT                                /FTId=VAR_004824.
    FT   VARIANT     267    267       P -> L (in RP4).
    FT                                /FTId=VAR_004825.
    FT   VARIANT     267    267       P -> R (in RP4).
    FT                                /FTId=VAR_004826.
    FT   VARIANT     292    292       A -> E (in CSNBAD1).
    FT                                /FTId=VAR_004827.
    FT   VARIANT     296    296       K -> E (in RP4).
    FT                                /FTId=VAR_004828.
    FT   VARIANT     297    297       S -> R (in RP4).
    FT                                /FTId=VAR_004829.
    FT   VARIANT     342    342       T -> M (in RP4).
    FT                                /FTId=VAR_004830.
    FT   VARIANT     345    345       V -> L (in RP4).
    FT                                /FTId=VAR_004831.
    FT   VARIANT     345    345       V -> M (in RP4).
    FT                                /FTId=VAR_004832.
    FT   VARIANT     347    347       P -> A (in RP4).
    FT                                /FTId=VAR_004833.
    FT   VARIANT     347    347       P -> L (in RP4; common variant).
    FT                                /FTId=VAR_004834.
    FT   VARIANT     347    347       P -> Q (in RP4).
    FT                                /FTId=VAR_004835.
    FT   VARIANT     347    347       P -> R (in RP4).
    FT                                /FTId=VAR_004836.
    FT   VARIANT     347    347       P -> S (in RP4).
    FT                                /FTId=VAR_004837.
    SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
         MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
         VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
         GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
         EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
         ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
         YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
    //

## Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.

By default patmatmotifs writes a 'dbmotif' report file.

### Output files for usage example

### File: opsd_human.patmatmotifs

    ########################################
    # Program: patmatmotifs
    # Rundate: Tue 15 Jul 2008 12:00:00
    # Commandline: patmatmotifs
    #    -full
    #    -sequence tsw:opsd_human
    # Report_format: dbmotif
    # Report_file: opsd_human.patmatmotifs
    ########################################

    #=======================================
    #
    # Sequence: OPSD_HUMAN     from: 1   to: 348
    # HitCount: 2
    #
    # Full: Yes
    # Prune: Yes
    # Data_file: ../prosextract-keep/PROSITE/prosite.lines
    #
    #=======================================

    Length = 17
    Start = position 123 of sequence
    End = position 139 of sequence

    Motif = G_PROTEIN_RECEP_F1_1

    TLGGEIALWSLVVLAIERYVVVCKPMS
         |               |
       123               139

    Length = 17
    Start = position 290 of sequence
    End = position 306 of sequence

    Motif = OPSIN

    PIFMTIPAFFAKSAAIYNPVIYIMMNK
         |               |
       290               306

    #---------------------------------------
    #
    # Motif: G_PROTEIN_RECEP_F1_1
    # Count: 1
    #
    # *****************************************
    # * G-protein coupled receptors signature *
    # *****************************************

      [Part of this file has been deleted for brevity]

    # Count: 1
    #
    # *************************************************
    # * Visual pigments (opsins) retinal binding site *
    # *************************************************
    #
    # Visual pigments [1,2] are the light-absorbing  molecules that  mediate vision.
    # They consist of  an apoprotein, opsin,  covalently  linked  to the chromophore
    # cis-retinal.  Vision is  effected through  the absorption of a  photon by cis-
    # retinal  which is isomerized to  trans-retinal.  This isomerization leads to a
    # change  of conformation  of the protein. Opsins are integral membrane proteins
    # with  seven transmembrane regions that belong to family 1 of G-protein coupled
    # receptors (see <PDOC00210>).
    #
    # In vertebrates four different pigments are generally found.   Rod cells, which
    # mediate vision in dim light, contain the pigment rhodopsin.  Cone cells, which
    # function in bright light, are responsible  for  color vision and contain three
    # or more color pigments (for example, in mammals: red, blue and green).
    #
    # In Drosophila, the  eye   is composed   of 800   facets  or   ommatidia.  Each
    # ommatidium contains eight photoreceptor cells (R1-R8):  the R1 to R6 cells are
    # outer cells,  R7  and R8 inner cells. Each of the three types of cells (R1-R6,
    # R7 and R8) expresses a specific opsin.
    #
    # Proteins evolutionary related to opsins include squid retinochrome, also known
    # as retinal  photoisomerase, which converts various isomers of retinal into 11-
    # cis retinal and mammalian retinal pigment  epithelium (RPE) RGR [3], a protein
    # that may also act in retinal isomerization.
    #
    # The attachment  site  for  retinal in the above proteins is a conserved lysine
    # residue in  the  middle  of  the  seventh  transmembrane helix. The pattern we
    # developed includes this residue.
    #
    # -Consensus pattern: [LIVMWAC]-[PGAC]-x(3)-[SAC]-K-[STALIMR]-[GSACPNV]-[STACP]-
    #                     x(2)-[DENF]-[AP]-x(2)-[IY]
    #                     [K is the retinal binding site]
    # -Sequences known to belong to this class detected by the pattern: ALL.
    # -Other sequence(s) detected in SWISS-PROT: NONE.
    # -Last update: July 1998 / Pattern and text revised.
    #
    # [ 1] Applebury M.L., Hargrave P.A.
    #      Vision Res. 26:1881-1895(1986).
    # [ 2] Fryxell K.J., Meyerowitz E.M.
    #      J. Mol. Evol. 33:367-378(1991).
    # [ 3] Shen D., Jiang M., Hao W., Tao L., Salazar M., Fong H.K.W.
    #      Biochemistry 33:13117-13125(1994).
    #
    # ***************
    #
    #
    #---------------------------------------

## Data files

Data and documentation from PROSITE files is automatically read. This must be generated and formatted by running prosextract before running patmatmotifs.

## Notes

Program is only useful when prosextract is used beforehand.

## References

If you want to refer to PROSITE in a publication you can do so by citing:

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 analyze derived 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).

## Warnings

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

## Diagnostic Error Messages

The error message:

    "Either EMBOSS_DATA undefined or PROSEXTRACT needs running"

indicates that your local EMBOSS administrator has not yet correctly set up the local EMBOSS PROSITE database using the utility 'prosextract'.

## Exit status

It always exits with status 0

## Known bugs

None.

## See also

Program name | Description
--- | ---
antigenic | Finds antigenic sites in proteins
digest | Reports on protein proteolytic enzyme or reagent cleavage sites
epestfind | Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro | Search for patterns in protein sequences
fuzztran | Search for patterns in protein sequences (translated)
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
oddcomp | Identify proteins with specified sequence word composition
patmatdb | Searches protein sequences with a sequence motif
pepcoil | Predicts coiled coil regions in protein sequences
preg | Regular expression search of protein sequence(s)
pscan | Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave | Reports on signal cleavage sites in a protein sequence

## Author(s)

Sinead O'Leary (current e-mail address unknown)
while she was at:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

Completed May 13 1999.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None