% pepnet -sask 
Draw a helical net for a protein sequence
Input protein sequence: tsw:gcn4_yeast
     Begin at position [start]: 253
       End at position [end]: 274
Graph type [x11]: cps

Created pepnet.ps

Draw a helical net for a protein sequence
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Protein sequence filename and optional
                                  format, or reference (input USA)
   -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)

   Additional (Optional) qualifiers (* if not always prompted):
*  -squares            string     [ILVM] By default the aliphatic residues
                                  ILVM are marked with squares. (Any string)
*  -diamonds           string     [DENQST] By default the residues DENQST are
                                  marked with diamonds. (Any string)
*  -octags             string     [HKR] By default the positively charged
                                  residues HKR are marked with octagons. (Any
                                  string)

   Advanced (Unprompted) qualifiers:
   -amphipathic        toggle     If this is true then the residues ACFGILMVWY
                                  are marked as squares and all other
                                  residues are unmarked. This overrides any
                                  other markup that you may have specified
                                  using the qualifiers '-squares', '-diamonds'
                                  and '-octags'.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   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

ID   GCN4_YEAST              Reviewed;         281 AA.
AC   P03069; D3DLN9; P03068; Q70D88; Q70D91; Q70D96; Q70D99; Q70DA0;
AC   Q96UT3;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   13-JUN-2012, entry version 139.
DE   RecName: Full=General control protein GCN4;
DE   AltName: Full=Amino acid biosynthesis regulatory protein;
GN   Name=GCN4; Synonyms=AAS3, ARG9; OrderedLocusNames=YEL009C;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
OC   Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=85038531; PubMed=6387704; DOI=10.1073/pnas.81.20.6442;
RA   Hinnebusch A.G.;
RT   "Evidence for translational regulation of the activator of general
RT   amino acid control in yeast.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:6442-6446(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=84298088; PubMed=6433345; DOI=10.1073/pnas.81.16.5096;
RA   Thireos G., Penn M.D., Greer H.;
RT   "5' untranslated sequences are required for the translational control
RT   of a yeast regulatory gene.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:5096-5100(1984).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS PRO-24; SER-62;
RP   ALA-82; ALA-91; ALA-125 AND GLU-196.
RC   STRAIN=CLIB 219, CLIB 382, CLIB 388, CLIB 410, CLIB 413, CLIB 556,
RC   CLIB 630, CLIB 95, K1, R12, R13, Sigma 1278B, YIIc12, and YIIc17;
RX   PubMed=15087486; DOI=10.1093/nar/gkh529;
RA   Leh-Louis V., Wirth B., Despons L., Wain-Hobson S., Potier S.,
RA   Souciet J.-L.;
RT   "Differential evolution of the Saccharomyces cerevisiae DUP240
RT   paralogs and implication of recombination in phylogeny.";
RL   Nucleic Acids Res. 32:2069-2078(2004).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204511 / S288c / AB972;
RX   MEDLINE=97313264; PubMed=9169868;
RA   Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA   Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA   Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G.,
RA   Hunicke-Smith S., Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H.,
RA   Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P.,
RA   Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T.,
RA   Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";


  [Part of this file has been deleted for brevity]

FT                                /FTId=PRO_0000076490.
FT   DOMAIN      253    274       Leucine-zipper.
FT   DNA_BIND    231    249       Basic motif.
FT   REGION       89    100       Required for transcriptional activation.
FT   REGION      106    125       Required for transcriptional activation.
FT   MOD_RES      17     17       Phosphoserine.
FT   MOD_RES     165    165       Phosphothreonine; by PHO85.
FT   MOD_RES     218    218       Phosphoserine.
FT   VARIANT      24     24       S -> P (in strain: CLIB 219).
FT   VARIANT      62     62       P -> S (in strain: CLIB 630 haplotype
FT                                Ha2).
FT   VARIANT      82     82       T -> A (in strain: CLIB 556 haplotype
FT                                Ha1).
FT   VARIANT      91     91       D -> A (in strain: CLIB 95, CLIB 219,
FT                                CLIB 382, CLIB 388, CLIB 410, CLIB 413,
FT                                CLIB 556, CLIB 630, K1, R12, R13
FT                                haplotype Ha2, Sigma 1278B haplotype Ha1,
FT                                YIIc12 and YIIc17).
FT   VARIANT     125    125       D -> A (in strain: CLIB 556 haplotype
FT                                Ha1).
FT   VARIANT     196    196       D -> E (in strain: CLIB 388, CLIB 410,
FT                                CLIB 413, CLIB 630 haplotype Ha1, K1,
FT                                YIIc12 haplotype Ha2 and YIIc17 haplotype
FT                                Ha1).
FT   MUTAGEN      97     98       FF->AA: Reduces transcriptional
FT                                activation activity; when associated with
FT                                A-107; A-110; A-113; A-120; A-123 and A-
FT                                124.
FT   MUTAGEN     107    107       M->A: Reduces transcriptional activation
FT                                activity; when associated with A-97; A-
FT                                98; A-110; A-113; A-120; A-123 and A-124.
FT   MUTAGEN     110    110       Y->A: Reduces transcriptional activation
FT                                activity; when associated with A-97; A-
FT                                98; A-107; A-113; A-120; A-123 and A-124.
FT   MUTAGEN     113    113       L->A: Reduces transcriptional activation
FT                                activity; when associated with A-97; A-
FT                                98; A-107; A-110; A-120; A-123 and A-124.
FT   MUTAGEN     120    124       WTSLF->ATSAA: Reduces transcriptional
FT                                activation activity; when associated with
FT                                A-97; A-98; A-107; A-110 and A-113.
FT   CONFLICT    239    281       ARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG
FT                                ER -> PGVLVRESCKE (in Ref. 2; AAA65521).
FT   HELIX       230    248
FT   HELIX       251    280
SQ   SEQUENCE   281 AA;  31310 MW;  2ED1B8E35D509578 CRC64;
     MSEYQPSLFA LNPMGFSPLD GSKSTNENVS ASTSTAKPMV GQLIFDKFIK TEEDPIIKQD
     TPSNLDFDFA LPQTATAPDA KTVLPIPELD DAVVESFFSS STDSTPMFEY ENLEDNSKEW
     TSLFDNDIPV TTDDVSLADK AIESTEEVSL VPSNLEVSTT SFLPTPVLED AKLTQTRKVK
     KPNSVVKKSH HVGKDDESRL DHLGVVAYNR KQRSIPLSPI VPESSDPAAL KRARNTEAAR
     RSRARKLQRM KQLEDKVEEL LSKNYHLENE VARLKKLVGE R
//