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helixturnhelix |
The helix-turn-helix motif was originally identified as the DNA-binding domain of phage repressors. One alpha-helix lies in the wide groove of DNA; the other lies at an angle across DNA.
% helixturnhelix Input sequence: sw:laci_ecoli Output file [laci_ecoli.hth]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outfile] report Output report file name Optional qualifiers: -mean float Mean value -sd float Standard Deviation value -minsd float Minimum SD -eightyseven boolean Use the old (1987) weight data Advanced qualifiers: (none) General qualifiers: -help boolean 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 |
[-outfile] (Parameter 2) |
Output report file name | Report file | |
Optional qualifiers | Allowed values | Default | |
-mean | Mean value | Number from 1.000 to 10000.000 | 238.71 |
-sd | Standard Deviation value | Number from 1.000 to 10000.000 | 293.61 |
-minsd | Minimum SD | Number from 0.000 to 100.000 | 2.5 |
-eightyseven | Use the old (1987) weight data | Yes/No | No |
Advanced qualifiers | Allowed values | Default | |
(none) |
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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default helixturnhelix writes a 'motif' report file.
Here is a sample output:
######################################## # Program: helixturnhelix # Rundate: Mon Feb 11 13:45:02 2002 # Report_file: laci_ecoli.hth ######################################## #======================================= # # Sequence: LACI_ECOLI from: 1 to: 360 # HitCount: 1 # # Hits above +2.50 SD (972.73) # #======================================= Maximum_score_at at "*" (1) Score 2160.000 length 22 at residues 4->25 * Sequence: VTLYDVAEYAGVSYQTVSRVVN | | 4 25 Standard_deviations: 6.54 #--------------------------------------- #---------------------------------------
# Amino acid counts for 91 Helix-turn-helix (presumed) protein motifs # from Dodd IB and Egan JB (1990) Nucl. Acids. Res. 18:5019-5026. # Sample: 91 aligned sequences # # R 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Total Exp # - -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- ----- --- A 2 1 3 14 10 12 75 6 15 9 1 1 4 3 8 15 4 4 4 11 0 10 212 995 C 0 0 1 1 0 0 0 0 0 3 3 1 1 0 0 0 0 0 0 1 0 3 14 106 D 0 1 0 1 14 0 0 14 1 0 5 0 1 2 0 0 0 0 1 1 0 2 43 556 E 4 5 0 11 26 0 0 16 9 3 3 0 3 12 13 0 0 2 0 1 13 6 127 669 F 4 0 4 0 0 4 0 1 0 10 0 0 0 0 1 0 0 1 1 1 22 0 49 358 G 9 7 1 4 0 0 8 0 0 0 50 0 6 0 7 1 0 3 1 1 0 4 102 761 H 4 3 1 1 2 0 0 3 2 0 5 0 3 3 0 2 0 2 4 5 0 2 42 225 I 10 0 13 3 2 15 0 4 9 4 0 17 0 2 0 1 31 1 4 8 16 1 141 583 K 4 4 6 11 12 1 1 14 11 0 5 2 2 7 2 1 0 5 8 4 5 15 120 516 L 16 1 17 0 1 35 0 3 12 31 0 22 0 2 1 1 22 1 1 12 20 0 198 954 M 7 0 2 1 1 1 0 0 5 7 1 10 0 0 2 0 2 0 0 2 0 1 42 275 N 0 8 0 1 0 0 0 2 1 1 14 0 8 1 4 2 0 4 9 0 0 11 66 383 P 1 6 0 1 0 0 0 0 0 0 0 0 3 13 7 0 0 0 0 0 0 3 34 403 Q 2 1 21 9 11 0 0 9 8 0 0 2 1 17 7 12 0 3 12 5 3 9 132 437 R 9 10 14 9 5 0 1 16 10 0 1 0 1 17 8 7 0 17 28 3 0 16 172 609 S 2 17 0 8 4 1 6 1 2 2 3 0 37 1 25 5 0 29 3 0 1 5 152 552 T 6 24 3 12 1 5 0 2 2 4 0 5 20 4 3 39 0 4 1 0 4 3 142 512 V 7 3 1 1 2 16 0 0 2 12 0 29 0 5 3 3 32 0 7 8 7 0 138 724 W 2 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 2 21 0 0 27 105 Y 2 0 4 3 0 1 0 0 2 4 0 1 1 2 0 2 0 15 5 7 0 0 49 267
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 |
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 |
pepcoil | Predicts coiled coil regions |
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 "HELIXTURNHELIX" by Peter Rice (EGCG 1990)