backtranseq.txt

emboss的linux版本的源代码

DT   01-NOV-1997 (REL. 35, LAST ANNOTATION UPDATE)
DE   ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-LIKE CHAIN 2 PRECURSOR.
GN   ACRE OR SAD OR ACR96AB.
OS   DROSOPHILA MELANOGASTER (FRUIT FLY).
OC   EUKARYOTA; METAZOA; ARTHROPODA; TRACHEATA; HEXAPODA; INSECTA;
OC   PTERYGOTA; DIPTERA; BRACHYCERA; MUSCOMORPHA; EPHYDROIDEA;
OC   DROSOPHILIDAE; DROSOPHILA.
RN   [1]
RP   SEQUENCE FROM N.A.
RC   TISSUE=HEAD;
RX   MEDLINE; 90301489.
RA   BAUMANN A., JONAS P., GUNDELFINGER E.D.;
RT   "Sequence of D alpha 2, a novel alpha-like subunit of Drosophila
RT   nicotinic acetylcholine receptors.";
RL   NUCLEIC ACIDS RES. 18:3640-3640(1990).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   TISSUE=HEAD;
RX   MEDLINE; 90353591.
RA   JONAS P., BAUMANN A., MERZ B., GUNDELFINGER E.D.;
RT   "Structure and developmental expression of the D alpha 2 gene
RT   encoding a novel nicotinic acetylcholine receptor protein of
RT   Drosophila melanogaster.";
RL   FEBS LETT. 269:264-268(1990).
RN   [3]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 90360975.
RA   SAWRUK E., SCHLOSS P., BETZ H., SCHMITT B.;
RT   "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD,
RT   a novel developmentally regulated alpha-subunit.";
RL   EMBO J. 9:2671-2677(1990).
CC   -!- FUNCTION: AFTER BINDING ACETYLCHOLINE, THE ACHR RESPONDS BY AN
CC       EXTENSIVE CHANGE IN CONFORMATION THAT AFFECTS ALL SUBUNITS AND
CC       LEADS TO OPENING OF AN ION-CONDUCTING CHANNEL ACROSS THE PLASMA
CC       MEMBRANE.
CC   -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN.
CC   -!- TISSUE SPECIFICITY: CNS IN EMBRYOS.
CC   -!- DEVELOPMENTAL STAGE: LATE EMBRYONIC AND LATE PUPAL STAGES.
CC   -!- SIMILARITY: BELONGS TO THE LIGAND-GATED IONIC CHANNELS FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
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; X52274; G7803; -.
DR   EMBL; X53583; G8533; -.
DR   PIR; S11679; ACFFA2.
DR   FLYBASE; FBgn0000039; nAcR-alpha-96Ab.
DR   PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
DR   PFAM; PF00065; neur_chan; 1.
KW   RECEPTOR; POSTSYNAPTIC MEMBRANE; IONIC CHANNEL; GLYCOPROTEIN; SIGNAL;
KW   TRANSMEMBRANE; MULTIGENE FAMILY.
FT   SIGNAL        1     41       PROBABLE.
FT   CHAIN        42    576       ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2.
FT   DOMAIN       42    261       EXTRACELLULAR (POTENTIAL).
FT   TRANSMEM    262    285       POTENTIAL.
FT   TRANSMEM    293    311       POTENTIAL.
FT   TRANSMEM    327    346       POTENTIAL.
FT   DOMAIN      347    526       CYTOPLASMIC (POTENTIAL).
FT   TRANSMEM    527    545       POTENTIAL.
FT   DISULFID    169    183       BY SIMILARITY.
FT   DISULFID    243    244       ASSOCIATED WITH RECEPTOR ACTIVATION
FT                                (BY SIMILARITY).
FT   CARBOHYD     65     65       POTENTIAL.
FT   CARBOHYD    254    254       POTENTIAL.
FT   CARBOHYD    570    570       POTENTIAL.
SQ   SEQUENCE   576 AA;  65506 MW;  7B795689 CRC32;
     MAPGCCTTRP RPIALLAHIW RHCKPLCLLL VLLLLCETVQ ANPDAKRLYD DLLSNYNRLI
     RPVSNNTDTV LVKLGLRLSQ LIDLNLKDQI LTTNVWLEHE WQDHKFKWDP SEYGGVTELY
     VPSEHIWLPD IVLYNNADGE YVVTTMTKAI LHYTGKVVWT PPAIFKSSCE IDVRYFPFDQ
     QTCFMKFGSW TYDGDQIDLK HISQKNDKDN KVEIGIDLRE YYPSVEWDIL GVPAERHEKY
     YPCCAEPYPD IFFNITLRRK TLFYTVNLII PCVGISYLSV LVFYLPADSG EKIALCISIL
     LSQTMFFLLI SEIIPSTSLA LPLLGKYLLF TMLLVGLSVV ITIIILNIHY RKPSTHKMRP
     WIRSFFIKRL PKLLLMRVPK DLLRDLAANK INYGLKFSKT KFGQALMDEM QMNSGGSSPD
     SLRRMQGRVG AGGCNGMHVT TATNRFSGLV GALGGGLSTL SGYNGLPSVL SGLDDSLSDV
     AARKKYPFEL EKAIHNVMFI QHHMQRQDEF NAEDQDWGFV AMVMDRLFLW LFMIASLVGT
     FVILGEAPSL YDDTKAIDVQ LSDVAKQIYN LTEKKN
//

Output file format

   The output is a nucleotide sequence containing the most favoured back
   translation of the specified protein, and using the specified
   translation table (which defaults to human).

  Output files for usage example

  File: opsd_human.fasta

>OPSD_HUMAN P08100 RHODOPSIN.
ATGAACGGCACCGAGGGCCCCAACTTCTACGTGCCCTTCAGCAACGCCACCGGCGTGGTG
AGGAGCCCCTTCGAGTACCCCCAGTACTACCTGGCCGAGCCCTGGCAGTTCAGCATGCTG
GCCGCCTACATGTTCCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTGACCCTGTAC
GTGACCGTGCAGCACAAGAAGCTGAGGACCCCCCTGAACTACATCCTGCTGAACCTGGCC
GTGGCCGACCTGTTCATGGTGCTGGGCGGCTTCACCAGCACCCTGTACACCAGCCTGCAC
GGCTACTTCGTGTTCGGCCCCACCGGCTGCAACCTGGAGGGCTTCTTCGCCACCCTGGGC
GGCGAGATCGCCCTGTGGAGCCTGGTGGTGCTGGCCATCGAGAGGTACGTGGTGGTGTGC
AAGCCCATGAGCAACTTCAGGTTCGGCGAGAACCACGCCATCATGGGCGTGGCCTTCACC
TGGGTGATGGCCCTGGCCTGCGCCGCCCCCCCCCTGGCCGGCTGGAGCAGGTACATCCCC
GAGGGCCTGCAGTGCAGCTGCGGCATCGACTACTACACCCTGAAGCCCGAGGTGAACAAC
GAGAGCTTCGTGATCTACATGTTCGTGGTGCACTTCACCATCCCCATGATCATCATCTTC
TTCTGCTACGGCCAGCTGGTGTTCACCGTGAAGGAGGCCGCCGCCCAGCAGCAGGAGAGC
GCCACCACCCAGAAGGCCGAGAAGGAGGTGACCAGGATGGTGATCATCATGGTGATCGCC
TTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCCTTCTACATCTTCACCCACCAGGGC
AGCAACTTCGGCCCCATCTTCATGACCATCCCCGCCTTCTTCGCCAAGAGCGCCGCCATC
TACAACCCCGTGATCTACATCATGATGAACAAGCAGTTCAGGAACTGCATGCTGACCACC
ATCTGCTGCGGCAAGAACCCCCTGGGCGACGACGAGGCCAGCGCCACCGTGAGCAAGACC
GAGACCAGCCAGGTGGCCCCCGCC

  Output files for usage example 2

  File: ach2_drome.fasta

>ACH2_DROME P17644 ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-LIKE CHAIN 2 PRECURSOR
.
ATGGCCCCCGGCTGCTGCACCACCCGCCCCCGCCCCATCGCCCTGCTGGCCCACATCTGG
CGCCACTGCAAGCCCCTGTGCCTGCTGCTGGTGCTGCTGCTGCTGTGCGAGACCGTGCAG
GCCAACCCCGATGCCAAGCGCCTGTACGATGATCTGCTGAGCAACTACAACCGCCTGATC
CGCCCCGTGAGCAACAACACCGATACCGTGCTGGTGAAGCTGGGCCTGCGCCTGAGCCAG
CTGATCGATCTGAACCTGAAGGATCAGATCCTGACCACCAACGTGTGGCTGGAGCACGAG
TGGCAGGATCACAAGTTCAAGTGGGATCCCAGCGAGTACGGCGGCGTGACCGAGCTGTAC
GTGCCCAGCGAGCACATCTGGCTGCCCGATATCGTGCTGTACAACAACGCCGATGGCGAG
TACGTGGTGACCACCATGACCAAGGCCATCCTGCACTACACCGGCAAGGTGGTGTGGACC
CCCCCCGCCATCTTCAAGAGCAGCTGCGAGATCGATGTGCGCTACTTCCCCTTCGATCAG
CAGACCTGCTTCATGAAGTTCGGCAGCTGGACCTACGATGGCGATCAGATCGATCTGAAG
CACATCAGCCAGAAGAACGATAAGGATAACAAGGTGGAGATCGGCATCGATCTGCGCGAG
TACTACCCCAGCGTGGAGTGGGATATCCTGGGCGTGCCCGCCGAGCGCCACGAGAAGTAC
TACCCCTGCTGCGCCGAGCCCTACCCCGATATCTTCTTCAACATCACCCTGCGCCGCAAG
ACCCTGTTCTACACCGTGAACCTGATCATCCCCTGCGTGGGCATCAGCTACCTGAGCGTG
CTGGTGTTCTACCTGCCCGCCGATAGCGGCGAGAAGATCGCCCTGTGCATCAGCATCCTG
CTGAGCCAGACCATGTTCTTCCTGCTGATCAGCGAGATCATCCCCAGCACCAGCCTGGCC
CTGCCCCTGCTGGGCAAGTACCTGCTGTTCACCATGCTGCTGGTGGGCCTGAGCGTGGTG
ATCACCATCATCATCCTGAACATCCACTACCGCAAGCCCAGCACCCACAAGATGCGCCCC
TGGATCCGCAGCTTCTTCATCAAGCGCCTGCCCAAGCTGCTGCTGATGCGCGTGCCCAAG
GATCTGCTGCGCGATCTGGCCGCCAACAAGATCAACTACGGCCTGAAGTTCAGCAAGACC
AAGTTCGGCCAGGCCCTGATGGATGAGATGCAGATGAACAGCGGCGGCAGCAGCCCCGAT
AGCCTGCGCCGCATGCAGGGCCGCGTGGGCGCCGGCGGCTGCAACGGCATGCACGTGACC
ACCGCCACCAACCGCTTCAGCGGCCTGGTGGGCGCCCTGGGCGGCGGCCTGAGCACCCTG
AGCGGCTACAACGGCCTGCCCAGCGTGCTGAGCGGCCTGGATGATAGCCTGAGCGATGTG
GCCGCCCGCAAGAAGTACCCCTTCGAGCTGGAGAAGGCCATCCACAACGTGATGTTCATC
CAGCACCACATGCAGCGCCAGGATGAGTTCAACGCCGAGGATCAGGATTGGGGCTTCGTG
GCCATGGTGATGGATCGCCTGTTCCTGTGGCTGTTCATGATCGCCAGCCTGGTGGGCACC
TTCGTGATCCTGGGCGAGGCCCCCAGCCTGTACGATGATACCAAGGCCATCGATGTGCAG
CTGAGCGATGTGGCCAAGCAGATCTACAACCTGACCGAGAAGAAGAAC

Data files

   The codon usage table is read by default from "Ehum.cut" in the
   'data/CODONS' directory of the EMBOSS distribution. If the name of a
   codon usage file is specified on the command line, then this file will
   first be searched for in the current directory and then in the
   'data/CODONS' directory of the EMBOSS distribution.

   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

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   "Corrupt codon index file" - the codon usage file is incomplete or
   empty.

   "The file 'drosoph.cut' does not exist" - the codon usage file cannot
   be opened.

Exit status

   This program always exits with a status of 0, unless the codon usage
   table cannot be opened.

Known bugs

   None.

See also

   Program name                         Description
   backtranambig Back translate a protein sequence to ambiguous codons
   charge        Protein charge plot
   checktrans    Reports STOP codons and ORF statistics of a protein
   coderet       Extract CDS, mRNA and translations from feature tables
   compseq       Count composition of dimer/trimer/etc words in a sequence
   emowse        Protein identification by mass spectrometry
   freak         Residue/base frequency table or plot
   iep           Calculates the isoelectric point of a protein
   mwcontam      Shows molwts that match across a set of files
   mwfilter      Filter noisy molwts from mass spec output
   octanol       Displays protein hydropathy
   pepinfo       Plots simple amino acid properties in parallel
   pepstats      Protein statistics
   pepwindow     Displays protein hydropathy
   pepwindowall  Displays protein hydropathy of a set of sequences
   plotorf       Plot potential open reading frames
   prettyseq     Output sequence with translated ranges
   remap         Display sequence with restriction sites, translation etc
   showorf       Pretty output of DNA translations
   showseq       Display a sequence with features, translation etc
   sixpack       Display a DNA sequence with 6-frame translation and ORFs
   transeq       Translate nucleic acid sequences

Author(s)

   Alan Bleasby (ajb