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EMBOSS: 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 Input sequence: sw:gcn4_yeast Window size [28]: Output file [gcn4_yeast.pepcoil]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -window integer Window size [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -[no]coil bool Report coiled coil regions -frame bool Show coil frameshifts -[no]other bool Report non coiled coil regions General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
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 |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-[no]coil | Report coiled coil regions | Yes/No | Yes |
-frame | Show coil frameshifts | Yes/No | Yes if -coil is true |
-[no]other | Report non coiled coil regions | Yes/No | Yes |
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 |
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 | Finds 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)