                                patmatmotifs



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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

Scan a protein sequence with motifs from the PROSITE database
Version: EMBOSS:6.6.0.0

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

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   patmatmotifs reads a single protein sequence.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

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

  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   13-JUN-2012, entry version 145.
DE   RecName: Full=Rhodopsin;
DE   AltName: Full=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; DOI=10.1073/pnas.81.15.4851;
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;
RX   PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA   Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA   Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
RA   Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
RA   Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
RT   "The full-ORF clone resource of the German cDNA consortium.";
RL   BMC Genomics 8:399-399(2007).
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.";


  [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; dbSNP:rs28933993).
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; dbSNP:rs29001653).
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; dbSNP:rs29001566).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4; dbSNP:rs29001637).
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, dasgff, debug, listfile, dbmotif, diffseq,
   draw, restrict, excel, feattable, motif, nametable, 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: Mon 15 Jul 2013 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        Find antigenic sites in proteins
   epestfind        Find PEST motifs as potential proteolytic cleavage sites
   fuzzpro          Search for patterns in protein sequences
   fuzztran         Search for patterns in protein sequences (translated)
   patmatdb         Search protein sequences with a sequence motif
   preg             Regular expression search of protein sequence(s)
   pscan            Scan protein sequence(s) with fingerprints from the PRINTS
                    database
   sigcleave        Report on signal cleavage sites in a protein sequence

Author(s)

   Sinead O'Leary formerly at:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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
