helixturnhelix.txt

emboss的linux版本的源代码

                              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 protein 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     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outfile]           report     [*.helixturnhelix] Output report file name

   Additional (Optional) qualifiers:
   -mean               float      [238.71] Mean value (Number from 1.000 to
                                  10000.000)
   -sd                 float      [293.61] Standard Deviation value (Number
                                  from 1.000 to 10000.000)
   -minsd              float      [2.5] Minimum SD (Number from 0.000 to
                                  100.000)
   -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
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   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 dying program messages

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 [e-mail]).
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: Sat 15 Jul 2006 12:00:00
# Commandline: helixturnhelix
#    -sequence tsw:laci_ecoli
# 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


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

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 1
#---------------------------------------

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      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
   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 (ajb