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patmatmotifs |
Function
Search a PROSITE motif database with a protein sequenceDescription
patmatmotifs takes a protein sequence and compares it to the PROSITE database of motifs.For a description of PROSITE, we can do no better than to quote 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)."
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 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.
Your EMBOSS administrator must have set up the local EMBOSS PROSITE database using the utility 'prosextract' before this program will run.
Usage
Here is a sample session with patmatmotifs
% patmatmotifs -full Search a PROSITE motif database with a protein sequence Input 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 Sequence USA
[-outfile] report Output report file name
Additional (Optional) qualifiers:
-full boolean Provide full documentation for matching
patterns
-[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.
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
-rusashow2 boolean Show the full USA in the report
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
| [-outfile] (Parameter 2) |
Output report file name | Report output file | |
| 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 STANDARD; PRT; 348 AA.
AC P08100; Q16414;
DT 01-AUG-1988 (Rel. 08, Created)
DT 01-AUG-1988 (Rel. 08, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE RHODOPSIN.
GN RHO.
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A.
RX MEDLINE; 84272729.
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 SEQUENCE OF 1-120 FROM N.A.
RA BENNETT J., BELLER B., SUN D., KARIKO K.;
RL Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP REVIEW ON ADRP VARIANTS.
RX MEDLINE; 94004905.
RA AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A.,
RA BHATTACHARYA S.;
RT "Rhodopsin mutations in autosomal dominant retinitis pigmentosa.";
RL Hum. Mutat. 2:249-255(1993).
RN [4]
RP VARIANT ADRP HIS-23.
RX MEDLINE; 90136922.
RA DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S.,
RA YANDELL D.W., SANDBERG M.A., BERSON E.L.;
RT "A point mutation of the rhodopsin gene in one form of retinitis
RT pigmentosa.";
RL Nature 343:364-366(1990).
RN [5]
RP VARIANTS ADRP.
RX MEDLINE; 91051574.
RA FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G.,
RA HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M.,
RA WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A.,
RA BHATTACHARYA S.S., HUMPHRIES P.;
RT "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin
RT proline-->histidine substitution (codon 23) in pedigrees from
RT Europe.";
RL Am. J. Hum. Genet. 47:941-945(1990).
RN [6]
RP VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347.
RX MEDLINE; 91015273.
[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 ADRP).
FT /FTId=VAR_004818.
FT VARIANT 211 211 H -> R (IN ADRP).
FT /FTId=VAR_004819.
FT VARIANT 216 216 M -> K (IN ADRP).
FT /FTId=VAR_004820.
FT VARIANT 220 220 F -> C (IN ADRP).
FT /FTId=VAR_004821.
FT VARIANT 222 222 C -> R (IN ADRP).
FT /FTId=VAR_004822.
FT VARIANT 255 255 MISSING (IN ADRP).
FT /FTId=VAR_004823.
FT VARIANT 264 264 MISSING (IN ADRP).
FT /FTId=VAR_004824.
FT VARIANT 267 267 P -> L (IN ADRP).
FT /FTId=VAR_004825.
FT VARIANT 267 267 P -> R (IN ADRP).
FT /FTId=VAR_004826.
FT VARIANT 292 292 A -> E (IN CSNB4).
FT /FTId=VAR_004827.
FT VARIANT 296 296 K -> E (IN ADRP).
FT /FTId=VAR_004828.
FT VARIANT 297 297 S -> R (IN ADRP).
FT /FTId=VAR_004829.
FT VARIANT 342 342 T -> M (IN ADRP).
FT /FTId=VAR_004830.
FT VARIANT 345 345 V -> L (IN ADRP).
FT /FTId=VAR_004831.
FT VARIANT 345 345 V -> M (IN ADRP).
FT /FTId=VAR_004832.
FT VARIANT 347 347 P -> A (IN ADRP).
FT /FTId=VAR_004833.
FT VARIANT 347 347 P -> L (IN ADRP; COMMON VARIANT).
FT /FTId=VAR_004834.
FT VARIANT 347 347 P -> Q (IN ADRP).
FT /FTId=VAR_004835.
FT VARIANT 347 347 P -> R (IN ADRP).
FT /FTId=VAR_004836.
FT VARIANT 347 347 P -> S (IN ADRP).
FT /FTId=VAR_004837.
SQ SEQUENCE 348 AA; 38892 MW; 07443BEA CRC32;
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, 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: Fri Jul 15 2005 12:00:00
# 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
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123 139
Length = 17
Start = position 290 of sequence
End = position 306 of sequence
Motif = OPSIN
PIFMTIPAFFAKSAAIYNPVIYIMMNK
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290 306
#---------------------------------------
#
# Motif: G_PROTEIN_RECEP_F1_1
# Count: 1
#
# *****************************************
# * G-protein coupled receptors signature *
# *****************************************
#
# G-protein coupled receptors [1 to 4,E1,E2] (also called R7G) are an extensive
# group of hormones, neurotransmitters, odorants and light receptors which
[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 has been 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 |
| digest | Protein proteolytic enzyme or reagent cleavage digest |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Protein pattern search |
| fuzztran | Protein pattern search after translation |
| helixturnhelix | Report nucleic acid binding motifs |
| oddcomp | Find protein sequence regions with a biased composition |
| patmatdb | Search a protein sequence with a motif |
| pepcoil | Predicts coiled coil regions |
| preg | Regular expression search of a protein sequence |
| pscan | Scans proteins using PRINTS |
| sigcleave | Reports protein signal cleavage sites |
Author(s)
Sinead O'Leary (current e-mail address unknown)while she was at:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK