                                   pepcoil



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Function

   Predict coiled coil regions in protein sequences

Description

   pepcoil calculates the probability of a coiled-coil structure for
   windows of (by default) 28 residues through a protein sequence using
   the method of Lupas A, van Dyke M & Stock J (1991); Science 252:1162-4.
   It reads one or more sequences and writes a standard EMBOSS report file
   including the location and score of the putative coiled-coil structures
   and their score for each input sequence. Optionally, coiled coil
   regions, non-coiled coil regions and coil frameshifts are reported.

Usage

   Here is a sample session with pepcoil


% pepcoil
Predict coiled coil regions in protein sequences
Input protein sequence(s): tsw:gcn4_yeast
Window size [28]:
Output report [gcn4_yeast.pepcoil]:


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

Command line arguments

Predict coiled coil regions in protein sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
   -window             integer    [28] Window size (Integer from 7 to 28)
  [-outfile]           report     [*.pepcoil] Output report file name (default
                                  -rformat motif)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -[no]coil           boolean    [Y] Report coiled coil regions
   -frame              boolean    [Yes if -coil is true] Show coil frameshifts
   -other              boolean    [N] Report non coiled coil regions

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each 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

   pepcoil reads one or more protein sequences.

   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:gcn4_yeast' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:gcn4_yeast

ID   GCN4_YEAST              Reviewed;         281 AA.
AC   P03069; D3DLN9; P03068; Q70D88; Q70D91; Q70D96; Q70D99; Q70DA0;
AC   Q96UT3;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   13-JUN-2012, entry version 139.
DE   RecName: Full=General control protein GCN4;
DE   AltName: Full=Amino acid biosynthesis regulatory protein;
GN   Name=GCN4; Synonyms=AAS3, ARG9; OrderedLocusNames=YEL009C;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
OC   Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=85038531; PubMed=6387704; DOI=10.1073/pnas.81.20.6442;
RA   Hinnebusch A.G.;
RT   "Evidence for translational regulation of the activator of general
RT   amino acid control in yeast.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:6442-6446(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=84298088; PubMed=6433345; DOI=10.1073/pnas.81.16.5096;
RA   Thireos G., Penn M.D., Greer H.;
RT   "5' untranslated sequences are required for the translational control
RT   of a yeast regulatory gene.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:5096-5100(1984).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS PRO-24; SER-62;
RP   ALA-82; ALA-91; ALA-125 AND GLU-196.
RC   STRAIN=CLIB 219, CLIB 382, CLIB 388, CLIB 410, CLIB 413, CLIB 556,
RC   CLIB 630, CLIB 95, K1, R12, R13, Sigma 1278B, YIIc12, and YIIc17;
RX   PubMed=15087486; DOI=10.1093/nar/gkh529;
RA   Leh-Louis V., Wirth B., Despons L., Wain-Hobson S., Potier S.,
RA   Souciet J.-L.;
RT   "Differential evolution of the Saccharomyces cerevisiae DUP240
RT   paralogs and implication of recombination in phylogeny.";
RL   Nucleic Acids Res. 32:2069-2078(2004).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204511 / S288c / AB972;
RX   MEDLINE=97313264; PubMed=9169868;
RA   Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA   Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA   Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G.,
RA   Hunicke-Smith S., Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H.,
RA   Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P.,
RA   Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T.,
RA   Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";


  [Part of this file has been deleted for brevity]

FT                                /FTId=PRO_0000076490.
FT   DOMAIN      253    274       Leucine-zipper.
FT   DNA_BIND    231    249       Basic motif.
FT   REGION       89    100       Required for transcriptional activation.
FT   REGION      106    125       Required for transcriptional activation.
FT   MOD_RES      17     17       Phosphoserine.
FT   MOD_RES     165    165       Phosphothreonine; by PHO85.
FT   MOD_RES     218    218       Phosphoserine.
FT   VARIANT      24     24       S -> P (in strain: CLIB 219).
FT   VARIANT      62     62       P -> S (in strain: CLIB 630 haplotype
FT                                Ha2).
FT   VARIANT      82     82       T -> A (in strain: CLIB 556 haplotype
FT                                Ha1).
FT   VARIANT      91     91       D -> A (in strain: CLIB 95, CLIB 219,
FT                                CLIB 382, CLIB 388, CLIB 410, CLIB 413,
FT                                CLIB 556, CLIB 630, K1, R12, R13
FT                                haplotype Ha2, Sigma 1278B haplotype Ha1,
FT                                YIIc12 and YIIc17).
FT   VARIANT     125    125       D -> A (in strain: CLIB 556 haplotype
FT                                Ha1).
FT   VARIANT     196    196       D -> E (in strain: CLIB 388, CLIB 410,
FT                                CLIB 413, CLIB 630 haplotype Ha1, K1,
FT                                YIIc12 haplotype Ha2 and YIIc17 haplotype
FT                                Ha1).
FT   MUTAGEN      97     98       FF->AA: Reduces transcriptional
FT                                activation activity; when associated with
FT                                A-107; A-110; A-113; A-120; A-123 and A-
FT                                124.
FT   MUTAGEN     107    107       M->A: Reduces transcriptional activation
FT                                activity; when associated with A-97; A-
FT                                98; A-110; A-113; A-120; A-123 and A-124.
FT   MUTAGEN     110    110       Y->A: Reduces transcriptional activation
FT                                activity; when associated with A-97; A-
FT                                98; A-107; A-113; A-120; A-123 and A-124.
FT   MUTAGEN     113    113       L->A: Reduces transcriptional activation
FT                                activity; when associated with A-97; A-
FT                                98; A-107; A-110; A-120; A-123 and A-124.
FT   MUTAGEN     120    124       WTSLF->ATSAA: Reduces transcriptional
FT                                activation activity; when associated with
FT                                A-97; A-98; A-107; A-110 and A-113.
FT   CONFLICT    239    281       ARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG
FT                                ER -> PGVLVRESCKE (in Ref. 2; AAA65521).
FT   HELIX       230    248
FT   HELIX       251    280
SQ   SEQUENCE   281 AA;  31310 MW;  2ED1B8E35D509578 CRC64;
     MSEYQPSLFA LNPMGFSPLD GSKSTNENVS ASTSTAKPMV GQLIFDKFIK TEEDPIIKQD
     TPSNLDFDFA LPQTATAPDA KTVLPIPELD DAVVESFFSS STDSTPMFEY ENLEDNSKEW
     TSLFDNDIPV TTDDVSLADK AIESTEEVSL VPSNLEVSTT SFLPTPVLED AKLTQTRKVK
     KPNSVVKKSH HVGKDDESRL DHLGVVAYNR KQRSIPLSPI VPESSDPAAL KRARNTEAAR
     RSRARKLQRM KQLEDKVEEL LSKNYHLENE VARLKKLVGE R
//

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 the report is in 'motif' format.

  Output files for usage example

   The SwissProt annotation marks the true leucine zipper motif as from
   253 to 274. The leucine zipper is a special case of a coiled-coil
   region.

  File: gcn4_yeast.pepcoil

########################################
# Program: pepcoil
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: pepcoil
#    -sequence tsw:gcn4_yeast
# Report_format: motif
# Report_file: gcn4_yeast.pepcoil
########################################

#=======================================
#
# Sequence: GCN4_YEAST     from: 1   to: 281
# HitCount: 1
#
# Window size: 28 residues
#
#=======================================

Max_coil_pos at "*"

(1) Score 1.910 length 49 at residues 233->281
                           *
 Sequence: ARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER
           |                                               |
         233                                               281
 Probability: 1.000
 Predict: coiled
 Max_coil_pos: 249


#---------------------------------------
#---------------------------------------

Data files

   None.

Notes

   Coiled coils are formed by two or three alpha helices in parallel and
   in register that cross at an angle of approximately 20 degrees, are
   strongly amphipathic and display a pattern of hydrophilic and
   hydrophobic residues that is repeated every seven residues. The seven
   positions of the heptad repeat are designated a through g, a and d
   being generally hydrophobic, while the others are hydrophilic.

   The parallel two-stranded alpha-helical coiled coil is the most
   frequently encountered subunit-oligomerization motif in proteins.

References

    1. Lupas A, van Dyke M & Stock J; Predicting Coiled Coils from Protein
       Sequences. Science 252:1162-4 (1991)

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name     Description
   garnier          Predict protein secondary structure using GOR method
   helixturnhelix   Identify nucleic acid-binding motifs in protein
                    sequences
   pepnet           Draw a helical net for a protein sequence
   pepwheel         Draw a helical wheel diagram for a protein sequence

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

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

   Original program "PEPCOIL" by Peter Rice (EGCG 1991)

History

   Written (1999) - Alan Bleasby

Target users

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

Comments

   None
