helixturnhelix Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Identify nucleic acid-binding motifs in protein sequences Description helixturnhelix uses the method of Dodd and Egan to identify helix-turn-helix nucleic acid binding motifs in an input protein sequence. The output is a standard EMBOSS report file describing the location, size and score of any putative motifs. Usage Here is a sample session with helixturnhelix % helixturnhelix Identify nucleic acid-binding motifs in protein sequences 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 Identify nucleic acid-binding motifs in protein sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Protein sequence(s) filename and optional format, or reference (input USA) [-outfile] report [*.helixturnhelix] Output report file name (default -rformat motif) 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 -rstrandshow2 boolean Show the nucleotide strand 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 first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 -version boolean Report version number and exit Input file format helixturnhelix reads one or more protein sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. 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 Reviewed; 360 AA. AC P03023; O09196; P71309; Q2MC79; Q47338; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 19-JUL-2003, sequence version 3. DT 15-JUN-2010, entry version 117. DE RecName: Full=Lactose operon repressor; GN Name=lacI; OrderedLocusNames=b0345, JW0336; OS Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0; RA Farabaugh P.J.; RT "Sequence of the lacI gene."; RL Nature 274:765-769(1978). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Chen J., Matthews K.K.S.M.; RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases. RN [3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Marsh S.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.; RT "Sequence of minutes 4-25 of Escherichia coli."; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [5] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RX MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453; RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., RA Riley M., Collado-Vides J., Glasner J.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 [6] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=16738553; DOI=10.1038/msb4100049; RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.; RT "Highly accurate genome sequences of Escherichia coli K-12 strains [Part of this file has been deleted for brevity] FT CHAIN 1 360 Lactose operon repressor. FT /FTId=PRO_0000107963. FT DOMAIN 1 58 HTH lacI-type. FT DNA_BIND 6 25 H-T-H motif. FT VARIANT 282 282 Y -> D (in T41 mutant). FT MUTAGEN 17 17 Y->H: Broadening of specificity. FT MUTAGEN 22 22 R->N: Recognizes an operator variant. FT CONFLICT 286 286 L -> S (in Ref. 1, 4 and 7). FT HELIX 6 11 FT TURN 12 14 FT HELIX 17 24 FT HELIX 33 45 FT HELIX 51 56 FT STRAND 63 69 FT HELIX 74 89 FT STRAND 93 98 FT STRAND 101 103 FT HELIX 104 115 FT TURN 116 118 FT STRAND 122 126 FT HELIX 130 139 FT TURN 140 142 FT STRAND 145 150 FT STRAND 154 156 FT STRAND 158 161 FT HELIX 163 177 FT STRAND 181 186 FT HELIX 192 207 FT STRAND 213 217 FT HELIX 222 234 FT STRAND 240 246 FT HELIX 247 259 FT TURN 265 267 FT STRAND 268 271 FT HELIX 277 281 FT STRAND 282 284 FT STRAND 287 290 FT HELIX 293 308 FT STRAND 314 319 FT STRAND 322 324 FT STRAND 334 338 FT HELIX 343 353 FT HELIX 354 356 SQ SEQUENCE 360 AA; 38590 MW; 347A8DEE92D736CB CRC64; 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 CYIPPLTTIK 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, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, 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: Fri 15 Jul 2011 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 Maximum_score_at: 4 Standard_deviations: 6.54 #--------------------------------------- #--------------------------------------- #--------------------------------------- # Total_sequences: 1 # Total_length: 360 # Reported_sequences: 1 # Reported_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 The helix-turn-helix protein structural 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. The motif is commonly involved in binding DNA. The motif is of fundamental biological importance and is found in most proteins that regulate gene expression. It is formed by of two alpha-helices joined by a short turn. 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 garnier Predicts protein secondary structure using GOR method pepcoil Predicts coiled coil regions in protein sequences pepnet Draw a helical net for a protein sequence pepwheel Draw a helical wheel diagram for a protein sequence Author(s) Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. Original program "HELIXTURNHELIX" (EGCG 1990) by Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. 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