| helixturnhelix

## Function

Report nucleic acid binding motifs

## Description

helixturnhelix uses the method of Dodd and Egan and finds helix-turn-helix nucleic acid binding motifs in proteins.

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.

## Usage

Here is a sample session with helixturnhelix

    % 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
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outfile]           report     Output report file name

       Additional (Optional) qualifiers:
       -mean               float      Mean value
       -sd                 float      Standard Deviation value
       -minsd              float      Minimum SD
       -eightyseven        boolean    Use the old (1987) weight data

       Advanced (Unprompted) qualifiers: (none)
       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
       -rformat2            string     Report format
       -rname2              string     Base file name
       -rextension2         string     File name extension
       -rdirectory2         string     Output directory
       -raccshow2           boolean    Show accession number in the report
       -rdesshow2           boolean    Show description in the report
       -rscoreshow2         boolean    Show the score in the report
       -rusashow2           boolean    Show the full USA in the report

       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
[-outfile] (Parameter 2) | Output report file name | Report output file |
Additional (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 (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

helixturnhelix reads one or more protein sequence USAs.

### Input files for usage example

'tsw:laci_ecoli' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:laci_ecoli

    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
    //

## Output file format

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://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.

By default helixturnhelix writes a 'motif' report file.

### Output files for usage example

### File: laci_ecoli.hth

    ########################################
    # Program: helixturnhelix
    # Rundate: Thu Jul 15 2004 12:00:00
    # 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

    #---------------------------------------
    #---------------------------------------

## Data files

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

The data files are stored in the standard EMBOSS data directory. The names are:

- Ehth.dat matrix file
- Ehth87.dat 1987 shorter matrix file

The old (1987) data has a motif length of 20 residues, whilst the default data (Ehth.dat) has a motif length of 22 residues.

With care these can be replaced to suit your data sets. If the files are placed in the following directories they will be used in preference to the files in the EMBOSS distribution data directory:

- . (your current directory)
- .embossdata
- ~/ (your home directory)
- ~/.embossdata

Here is the default file:

    # 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

## Notes

None.

## References

1. Dodd I.B., Egan J.B. (1987) "Systematic method for the detection of potential lambda cro-like DNA-binding regions in proteins." J. Mol. Biol. 194: 557-564.
2. Dodd I.B., Egan J.B. (1990) "Improved detection of helix-turn-helix DNA-binding motifs in protein sequences." Nucleic Acids Res. 18: 5019-5026.

## Warnings

The program will warn you if the data file is not mathematically accurate.

## Diagnostic Error Messages

None.

## Exit status

It exits with status 0 unless an error is reported.

## 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
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

## Author(s)

Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Original program "HELIXTURNHELIX" (EGCG 1990) by Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

Completed 11th March 1999

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None