pepcoil |
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
% pepcoil Predicts coiled coil regions Input sequence(s): tsw:gcn4_yeast Window size [28]: Output file [gcn4_yeast.pepcoil]: |
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Standard (Mandatory) qualifiers: [-sequence] seqall Sequence database USA -window integer Window size [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -[no]coil boolean Report coiled coil regions -frame boolean Show coil frameshifts -[no]other boolean 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-window | Window size | Integer from 7 to 28 | 28 |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.pepcoil |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-[no]coil | Report coiled coil regions | Boolean value Yes/No | Yes |
-frame | Show coil frameshifts | Boolean value Yes/No | Yes if -coil is true |
-[no]other | Report non coiled coil regions | Boolean value Yes/No | Yes |
ID GCN4_YEAST STANDARD; PRT; 281 AA. AC P03069; P03068; DT 21-JUL-1986 (Rel. 01, Created) DT 21-JUL-1986 (Rel. 01, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE GENERAL CONTROL PROTEIN GCN4 (AMINO ACID BIOSYNTHESIS REGULATORY DE PROTEIN). GN GCN4 OR ARG9 OR AAS3 OR YEL009C. OS Saccharomyces cerevisiae (Baker's yeast). OC Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales; OC Saccharomycetaceae; Saccharomyces. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 85038531. 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 SEQUENCE FROM N.A. RX MEDLINE; 84298088. 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 SEQUENCE FROM N.A. RC STRAIN=S288C / AB972; RA DIETRICH F.S., MULLIGAN J.T., HENNESSEY K.M., ALLEN E., ARAUJO R., RA AVILES E., BERNO A., BRENNAN T., CARPENTER J., CHEN E., CHERRY J.M., RA CHUNG E., DUNCAN M., GUZMAN E., HARTZELL G., HUNICKE-SMITH S., RA HYMAN R., KAYSER A., KOMP C., LASHKARI D., LEW H., LIN D., RA MOSEDALE D., NAKAHARA K., NAMATH A., NORGREN R., OEFNER P., OH C., RA PETEL F.X., ROBERTS D., SEHL P., SCHRAMM S., SHOGREN T., SMITH V., RA TAYLOR P., WEI Y., YELTON M., BOTSTEIN D., DAVIS R.W.; RL Submitted (DEC-1994) to the EMBL/GenBank/DDBJ databases. RN [4] RP DOMAINS. RX MEDLINE; 87002456. RA HOPE I.A., STRUHL K.; RT "Functional dissection of a eukaryotic transcriptional activator RT protein, GCN4 of yeast."; RL Cell 46:885-894(1986). RN [5] RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 250-281. RX MEDLINE; 92054531. RA O'SHEA E.K., KLEMM J.D., KIM P.S., ALBER T.; RT "X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel RT coiled coil."; RL Science 254:539-544(1991). [Part of this file has been deleted for brevity] CC -!- SUBCELLULAR LOCATION: NUCLEAR. CC -!- SIMILARITY: TO OTHER BZIP PROTEINS. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; K02205; AAA34640.1; -. DR EMBL; K02649; AAA65521.1; -. DR EMBL; U18530; AAB64486.1; -. DR PIR; A03604; RGBYA1. DR PIR; A03605; RGBYA2. DR PDB; 1ZTA; 15-APR-93. DR PDB; 2ZTA; 15-OCT-92. DR PDB; 1YSA; 31-OCT-93. DR PDB; 1DGC; 22-JUN-94. DR PDB; 2DGC; 08-MAR-96. DR PDB; 1GCL; 03-JUN-95. DR PDB; 1GCM; 29-JAN-96. DR PDB; 1SWI; 08-NOV-96. DR PDB; 1ZII; 07-JUL-97. DR PDB; 1ZIJ; 07-JUL-97. DR PDB; 1ZIK; 07-JUL-97. DR PDB; 1ZIL; 07-JUL-97. DR PDB; 1ZIM; 07-JUL-97. DR PDB; 1PIQ; 30-SEP-98. DR PDB; 1CE9; 25-MAR-99. DR TRANSFAC; T00321; -. DR SGD; L0000683; GCN4. DR PFAM; PF00170; bZIP; 1. DR PROSITE; PS00036; BZIP_BASIC; 1. KW Amino-acid biosynthesis; Transcription regulation; Activator; KW DNA-binding; Nuclear protein; 3D-structure. FT DOMAIN 106 125 REQUIRED FOR TRANSCRIPTIONAL ACTIVATION. FT DNA_BIND 231 249 BASIC MOTIF. FT DOMAIN 253 274 LEUCINE-ZIPPER. FT CONFLICT 239 281 ARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG FT ER -> PGVLVRESCKE (IN REF. 2). FT HELIX 227 276 FT TURN 277 277 SQ SEQUENCE 281 AA; 31310 MW; A2155238 CRC32; 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 // |
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) |
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 |
Original program "PEPCOIL" by Peter Rice (EGCG 1991)