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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 Report nucleic acid binding motifs Input sequence(s): tsw:laci_ecoli Output report [laci_ecoli.hth]: |
Go to the input files for this example
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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 output 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 | Boolean value Yes/No | No |
Advanced qualifiers | Allowed values | Default | |
(none) |
ID LACI_ECOLI STANDARD; PRT; 360 AA. AC P03023; P71309; Q47338; O09196; DT 21-JUL-1986 (Rel. 01, Created) DT 01-NOV-1997 (Rel. 35, Last sequence update) DT 15-DEC-1998 (Rel. 37, Last annotation update) DE LACTOSE OPERON REPRESSOR. GN LACI. OS Escherichia coli. OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae; OC Escherichia. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 78246991. RA FARABAUGH P.J.; RT "Sequence of the lacI gene."; RL Nature 274:765-769(1978). RN [2] RP SEQUENCE FROM N.A. RC STRAIN=K12 / MG1655; RX MEDLINE; 97426617. RA BLATTNER F.R., PLUNKETT G. III, BLOCH C.A., PERNA N.T., BURLAND V., RA RILEY M., COLLADO-VIDES J., GLASNER F.D., RODE C.K., MAYHEW G.F., RA GREGOR J., DAVIS N.W., KIRKPATRICK H.A., GOEDEN M.A., ROSE D.J., RA MAU B., SHAO Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1474(1997). RN [3] RP SEQUENCE FROM N.A. RC STRAIN=K12 / MG1655; RA DUNCAN M., ALLEN E., ARAUJO R., APARICIO A.M., CHUNG E., DAVIS K., RA FEDERSPIEL N., HYMAN R., KALMAN S., KOMP C., KURDI O., LEW H., RA LIN D., NAMATH A., OEFNER P., ROBERTS D., SCHRAMM S., DAVIS R.W.; RL Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases. RN [4] RP SEQUENCE FROM N.A. RA CHEN J., MATTHEWS K.K.S.M.; RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases. RN [5] RP SEQUENCE FROM N.A. RA MARSH S.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [6] RP SEQUENCE OF 1-147; 159-230 AND 233-360. RX MEDLINE; 76091932. RA BEYREUTHER K., ADLER K., FANNING E., MURRAY C., KLEMM A., GEISLER N.; RT "Amino-acid sequence of lac repressor from Escherichia coli. RT Isolation, sequence analysis and sequence assembly of tryptic RT peptides and cyanogen-bromide fragments."; RL Eur. J. Biochem. 59:491-509(1975). RN [7] [Part of this file has been deleted for brevity] 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; V00294; CAA23569.1; -. DR EMBL; J01636; AAA24052.1; -. DR EMBL; AE000141; AAC73448.1; -. DR EMBL; U73857; AAB18069.1; ALT_INIT. DR EMBL; X58469; CAA41383.1; -. DR EMBL; U86347; AAB47270.1; ALT_INIT. DR EMBL; U72488; AAB36549.1; -. DR EMBL; U78872; AAB37348.1; -. DR EMBL; U78873; AAB37351.1; -. DR EMBL; U78874; AAB37354.1; -. DR PIR; A03558; RPECL. DR PIR; S02540; S02540. DR PDB; 1LCC; 31-JAN-94. DR PDB; 1LCD; 31-JAN-94. DR PDB; 1LTP; 31-OCT-93. DR PDB; 1TLF; 31-JUL-95. DR PDB; 1LBG; 11-JUL-96. DR PDB; 1LBH; 11-JUL-96. DR PDB; 1LBI; 11-JUL-96. DR PDB; 1LQC; 12-FEB-97. DR ECO2DBASE; H039.0; 6TH EDITION. DR ECOGENE; EG10525; LACI. DR PFAM; PF00356; lacI; 1. DR PFAM; PF00532; Peripla_BP_like; 1. DR PROSITE; PS00356; HTH_LACI_FAMILY; 1. KW Transcription regulation; DNA-binding; Repressor; 3D-structure. FT DNA_BIND 6 25 H-T-H MOTIF. FT MUTAGEN 17 17 Y->H: BROADENING OF SPECIFICITY. FT MUTAGEN 22 22 R->N: RECOGNIZE AN OPERATOR VARIANT. FT VARIANT 282 282 Y -> D (IN T41 MUTANT). FT CONFLICT 286 286 S -> L (IN AAA24052, REF. 2, 4 AND 5). FT HELIX 6 13 FT TURN 14 14 FT HELIX 17 24 FT HELIX 32 44 FT TURN 49 50 SQ SEQUENCE 360 AA; 38564 MW; 4CA5A1D6 CRC32; MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPSTTIK QDFRLLGQTS VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ // |
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.
######################################## # Program: helixturnhelix # Rundate: Thu Nov 07 14:33:27 2002 # Report_format: motif # 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 |
pestfind | Finds PEST motifs as potential proteolytic cleavage sites |
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)