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patmatmotifs |
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Function
Scan a protein sequence with motifs from the PROSITE databaseDescription
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:6.4.0.0
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
-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 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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
sequence | Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat dbmotif) | <*>.patmatmotifs |
| Additional (Optional) qualifiers | ||||
| -full | boolean | Provide full documentation for matching patterns | Boolean value Yes/No | No |
| -[no]prune | boolean | 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 | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated sequence qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of the sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated report qualifiers | ||||
| -rformat2 -rformat_outfile |
string | Report format | Any string | dbmotif |
| -rname2 -rname_outfile |
string | Base file name | Any string | |
| -rextension2 -rextension_outfile |
string | File name extension | Any string | |
| -rdirectory2 -rdirectory_outfile |
string | Output directory | Any string | |
| -raccshow2 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N |
| -rdesshow2 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N |
| -rscoreshow2 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | Y |
| -rstrandshow2 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y |
| -rusashow2 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N |
| -rmaxall2 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 |
| -rmaxseq2 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
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 15-JUN-2010, entry version 128.
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
//
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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: Fri 15 Jul 2011 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).
#
# ***************
#
#
#---------------------------------------
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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:
- Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic Acids Research, Vol 22, No.17 3583-3589.
- Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
- Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd Edition.
- 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).
- 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 0Known bugs
None.See also
| Program name | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Search for patterns in protein sequences |
| fuzztran | Search for patterns in protein sequences (translated) |
| patmatdb | Searches protein sequences with a sequence motif |
| 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 formerly at:HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.