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pepcoil
Function
Predicts coiled coil regions
Description
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.
pepcoil calculates the probability of a coiled-coil structure for
windows of 28 residues through a protein sequence using the method of
Lupas A, van Dyke M & Stock J (1991); Science 252:1162-4
Usage
Here is a sample session with pepcoil
% pepcoil
Predicts coiled coil regions
Input protein sequence(s): tsw:gcn4_yeast
Window size [28]:
Output file [gcn4_yeast.pepcoil]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
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] outfile [*.pepcoil] Output file name
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
-[no]other boolean [Y] 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
-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
-odirectory2 string Output directory
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 dying program messages
Input file format
pepcoil reads in a protein sequence USA.
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; P03068; Q70D88; Q70D91; Q70D96; Q70D99; Q70DA0; Q96UT3;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 20-MAR-2007, entry version 82.
DE General control protein GCN4 (Amino acid biosynthesis regulatory
DE protein).
GN Name=GCN4; Synonyms=AAS3, ARG9; OrderedLocusNames=YEL009C;
OS Saccharomyces cerevisiae (Baker's yeast).
OC Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=4932;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=85038531; PubMed=6387704;
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;
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.";
RL Nature 387:78-81(1997).
[Part of this file has been deleted for brevity]
FT CHAIN 1 281 General control protein GCN4.
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 165 165 Phosphothreonine (by PHO85).
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).
FT HELIX 230 276
FT HELIX 250 276
FT HELIX 251 278
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
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
PEPCOIL of GCN4_YEAST
using a window of 28 residues
Other structures from 1 to 232 (232 residues)
Max score: 1.283 (probability 0.21)
Prediction starts at 233
Probable coiled-coil from 233 to 281 (49 residues)
Max score: 1.910 (probability 1.00)
Data files
None.
Notes
None.
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
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
garnier Predicts protein secondary structure
helixturnhelix Report nucleic acid binding motifs
hmoment Hydrophobic moment calculation
oddcomp Find protein sequence regions with a biased composition
patmatdb Search a protein sequence with a motif
patmatmotifs Search a PROSITE motif database with a protein sequence
pepnet Displays proteins as a helical net
pepwheel Shows protein sequences as helices
preg Regular expression search of a protein sequence
pscan Scans proteins using PRINTS
sigcleave Reports protein signal cleavage sites
tmap Displays membrane spanning regions
Author(s)
Alan Bleasby (ajb ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
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
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