Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Swiss-Prot release 30.0

Published October 1, 1994


                    SWISS-PROT RELEASE 30.0 RELEASE NOTES


                               1. INTRODUCTION

   1.1  Evolution

   Release 30.0  of SWISS-PROT  contains 40292 sequence entries, comprising
   14'147'368 amino acids abstracted from 37887 references. This represents
   an increase  of 5.1% over release 29. The recent growth of the data bank
   is summarized below.

   Release    Date   Number of entries     Nb of amino acids

   2.0        09/86               3939               900 163
   3.0        11/86               4160               969 641
   4.0        04/87               4387             1 036 010
   5.0        09/87               5205             1 327 683
   6.0        01/88               6102             1 653 982
   7.0        04/88               6821             1 885 771
   8.0        08/88               7724             2 224 465
   9.0        11/88               8702             2 498 140
   10.0       03/89              10008             2 952 613
   11.0       07/89              10856             3 265 966
   12.0       10/89              12305             3 797 482
   13.0       01/90              13837             4 347 336
   14.0       04/90              15409             4 914 264
   15.0       08/90              16941             5 486 399
   16.0       11/90              18364             5 986 949
   17.0       02/91              20024             6 524 504
   18.0       05/91              20772             6 792 034
   19.0       08/91              21795             7 173 785
   20.0       11/91              22654             7 500 130
   21.0       03/92              23742             7 866 596
   22.0       05/92              25044             8 375 696
   23.0       08/92              26706             9 011 391
   24.0       12/92              28154             9 545 427
   25.0       04/93              29955            10 214 020
   26.0       07/93              31808            10 875 091
   27.0       10/93              33329            11 484 420
   28.0       02/94              36000            12 496 420
   29.0       06/94              38303            13 464 008
   30.0       10/94              40292            14 147 368



      2. DESCRIPTION OF THE CHANGES MADE TO SWISS-PROT SINCE RELEASE 29

   2.1  Sequences and annotations

   About 2005 sequences have been added since release 29, the sequence data
   of 296  existing entries  has been  updated and  the annotations of 5260
   entries have been revised.






<PAGE>



   We are  continuing the process to 'clean-up' the various representations
   of domains  in the  feature lines  (especially the  usage of the feature
   keys "DOMAIN", "REPEAT", "DNA_BIND", and "SITE"). We also have undertook
   an overall  revision of  the CC  topics "SUBCELLULAR LOCATION", "SUBUNIT
   and "CAUTION".


   2.2  What's happening with the model organisms

   As we  announced in the last three releases we have selected a number of
   organisms that  are the  target  of  genome  sequencing  and/or  mapping
   projects and for which we intend to:

   -  Be as  complete as  possible. All sequences available at a given time
      should be  immediately included  in SWISS-PROT.  This  also  includes
      sequence corrections and updates.
   -  Provide a high level of annotations.
   -  Cross-references to specialized database(s) that contain, among other
      data, some  genetic information  about the  genes that code for these
      proteins.
   -  Provide specific indices or documents.

   What was  done since  the last  release or  in preparation  for the next
   release:

   -  We have  added Bacillus  subtilis as  a model  organism. We will soon
      link SWISS-PROT to the SubtiList database currently being designed by
      Ivan Moszer of the Pasteur Institute in Paris.
   -  The next  release of  LISTA will  include accession  numbers for each
      gene entry;  we will  therefore be able to cross-reference SWISS-PROT
      to LISTA.

   Here is the current status of the model organisms:

   Organism        Database                    Index file       Number of
                   cross-referenced                             sequences
   --------------  --------------------------  --------------   ---------
   B.subtilis      SubtiList (in preparation)  In preparation         777
   C.elegans       WormPep                     CELEGANS.TXT           688
   D.discoideum    DictyDB                     DICTY.TXT              198
   D.melanogaster  FlyBase                     In preparation         647
   E.coli          EcoGene                     ECOLI.TXT             2901
   H.sapiens       MIM                         MIMTOSP.TXT           2914
   S.cerevisiae    LISTA (in preparation)      YEAST.TXT             2287


   2.3  Changes in the CC line

   We have  introduced in  this release a new 'topic' for the comments (CC)
   line-type: DOMAIN.  This topic  is used  to describe  the general domain
   structure of a protein. It is intended to be used for general statements
   on the domain organization of specific protein and supplement the domain
   information available in the feature table.




<PAGE>



   Examples of its usage:

   CC   -!- DOMAIN: CONTAINS A COILED-COIL DOMAIN ESSENTIAL FOR VESICULAR
   CC       TRANSPORT AND A DISPENSABLE C-TERMINAL REGION.

   CC   -!- DOMAIN: THE B CHAIN IS COMPOSED OF TWO DOMAINS, EACH DOMAIN
   CC       CONSISTS OF 3 HOMOLOGOUS SUBDOMAINS (ALPHA, BETA, GAMMA).


   The topic  "ALTERNATIVE  SPLICING"  has  been  renamed  to  "ALTERNATIVE
   PRODUCTS" as  it used  for describing  the existence  of related protein
   sequence(s) produced  by either alternative splicing of the same gene(s)
   or by the use of alternative initiation codons.

   Examples of its usage:

   CC   -!- ALTERNATIVE PRODUCTS: SKELETAL MUSCLE AND FIBROBLAST
   CC       TROPOMYOSINS ARE OBTAINED BY ALTERNATIVE MRNA SPLICING.

   CC   -!- ALTERNATIVE PRODUCTS: USING ALTERNATIVE INITIATION CODONS IN
   CC       THE SAME READING FRAME, THE GENE TRANSLATES INTO THREE
   CC       ISOZYMES: ALPHA, BETA AND BETA'.


   2.4  Changes in the DR line

   We  have   added  cross-references   from  SWISS-PROT   to   the   Yeast
   Electrophoresis Protein  Database (YEPD) from the Quest Protein Database
   Center of  Cold Spring  Harbor Laboratory.  These  cross-references  are
   present in the DR lines:

   Data bank identifier:    YEPD
   Primary identifier  :    Protein spot alphanumeric designation.
   Secondary identifier:    None; a dash '-' is stored in that field
   Example             :    DR   YEPD; 4270; -.


   2.5  Status of the documentation files

   SWISS-PROT is  distributed with  a large  number of documentation files.
   Some of  these files  have been  available for  a long  time  (the  user
   manual, release  notes, the  various  indices  for  authors,  citations,
   keywords, etc.),  but  many  have  been  created  recently  and  we  are
   continuously  adding  new  files.  The  following  table  list  all  the
   documents that are currently available or that will be added in the next
   few months.

   USERMAN .TXT   User manual
   RELNOTES.TXT   Release notes
   SHORTDES.TXT   Short description of entries in SWISS-PROT
   JOURLIST.TXT   List of abbreviations for journals cited
   KEYWLIST.TXT   List of keywords in use
   SPECLIST.TXT   List of organism identification codes
   EXPERTS .TXT   List of on-line experts for PROSITE and SWISS-PROT



<PAGE>



   ACINDEX .TXT   Accession number index
   AUTINDEX.TXT   Author index
   CITINDEX.TXT   Citation index
   KEYINDEX.TXT   Keyword index
   SPEINDEX.TXT   Species index

   7TMRLIST.TXT   List of 7-transmembrane G-linked receptors entries
   CDLIST  .TXT   CD nomenclature for surface proteins of human leucocytes
   CELEGANS.TXT   Index  of   Caenorhabditis  elegans   entries  and  their
                  corresponding  gene   designations  and   WormPep  cross-
   DICTY   .TXT   Index  of  Dictyostelium  discoideum  entries  and  their
                  corresponding   gene   designations  and  DictyDB  cross-
                  references
   EC2DTOSP.TXT   Index of  Escherichia coli  Gene-protein database entries
                  referenced in SWISS-PROT
   ECOLI   .TXT   Index of  Escherichia coli  K12 chromosomal  entries  and
                  their corresponding EcoGene cross-reference [4]
   EMBLTOSP.TXT   Index of EMBL Database entries referenced in SWISS-PROT
   EXTRADOM.TXT   Nomenclature of extracellular domains [1]
   GLYCOSYL.TXT   Index of  glycosyl hydrolases  classified by  families on
                  the basis of sequence similarities [2]
   HOXLIST .TXT   Vertebrate homeobox proteins: nomenclature and index
   MIMTOSP .TXT   Index of MIM entries referenced in SWISS-PROT
   NOMLIST .TXT   List of nomenclature related references for proteins
   PDBTOSP .TXT   Index of Brookhaven PDB entries referenced in SWISS-PROT
   PLASTID .TXT   List of chloroplast and cyanelle encoded proteins
   RESTRIC .TXT   List of restriction enzymes and methylases entries
   RIBOSOMP.TXT   Index of ribosomal proteins classified by families on the
                  basis of sequence similarities [2]
   YEAST   .TXT   Index  of  Saccharomyces  cerevisiae  entries  and  their
                  corresponding gene designations
   YEAST2 .TXT    Yeast Chromosome II entries [1]
   YEAST3 .TXT    Yeast Chromosome III entries [1]
   YEAST8 .TXT    Yeast Chromosome VIII entries [2]
   YEAST11 .TXT   Yeast Chromosome XI entries

   Notes:

   [1]  New in release 30.
   [2]  Will be available starting with release 31 in February 1995.


   2.6  The Expasy World-Wide Web server

   The World-Wide Web (WWW), which originated at CERN, is a powerful global
   information  system   merging  networked   information   retrieval   and
   hypertext. It  gives access, using hypertext links, to the documents and
   information contained  in all the existing WWW servers around the world,
   as well  as to  the data  obtainable through other information retrieval
   systems like WAIS, Gopher, X500, etc. To access a WWW server, one has to
   run on a local computer a client program (a WWW browser), which displays
   hypertext documents.  The user  can then either request a keyword search
   or jump  to another  document by following a hypertext link. WWW has the




<PAGE>



   outstanding advantage  of extending  the hypertext  model to  the  whole
   world (by allowing hypertext jumps to documents anywhere on the internet
   network) and  by being  device and  user-interface independent (browsers
   exist for  a variety  of computers  and user-interfaces,  including Unix
   workstations  running  XWindows,  MacIntoshes  and  PCs  with  Microsoft
   Windows).

   The ExPASy  WWW server  allows access, using the user-friendly hypertext
   model,  to  the  SWISS-PROT,  PROSITE,  SWISS-2DPAGE  and  SWISS-3DIMAGE
   databases and,  through any  SWISS-PROT protein sequence entry, to other
   databases such  as EMBL, PROSITE, REBASE, FlyBase, GCRDb, MaizeDB, OMIM,
   PDB and Medline. Using a browser which is able to display images one can
   also remotely access 2D gels image data from SWISS-2DPAGE.

   A WWW  server can  be accessed  on  the  internet  through  its  Uniform
   Resource Locator  (URL), the addressing system defined by the WWW model.
   The URL for the ExPASy WWW server is:

                           http://expasy.hcuge.ch/
   or
                            http://129.195.254.61/

   To access a WWW server, you need to run a browser (or client) program on
   your local computer. Browsers exist for a variety of machines and may be
   obtained by  anonymous ftp. ExPASy can be used with any WWW browser, but
   we recommend  NCSA Mosaic.  It is  a very  flexible and powerful browser
   with  a  graphical  user  interface;  available  for  Unix  boxes  using
   X11/Motif; for  Apple McIntoshes  and for Microsoft Windows. You can get
   it from the FTP site: ftp.ncsa.uiuc.edu.

   To access  all the  data available  from SWISS-2DPAGE,  the user's local
   computer needs  to run  an image  viewing program.  For most browsers on
   Unix workstations  the default  program is  xv, a shareware application.
   Similar Windows  or Apple  shareware or  public domain  applications are
   also available.

   For more  information on  the  ExPASy  WWW  server,  you  can  read  the
   following article:

      Appel R.D., Bairoch A., Hochstrasser D.F.
      A new  generation of  information retrieval tools for biologists: the
      example of the ExPASy WWW server.
      Trends Biochem. Sci. 19:258-260(1994).


   Or you can contact Dr. Ron Appel:

      Email: appel@cih.hcuge.ch
      Fax: +41-22-372 61 98








<PAGE>



   2.7  Weekly updates of SWISS-PROT

   Weekly updates of SWISS-PROT are available by anonymous FTP. Three files
   are updated at each update:

   new_seq.dat    Contains all the new entries since the last full release.
   upd_seq.dat    Contains the entries for which the sequence data has been
                  updated since the last release.
   upd_ann.dat    Contains the  entries for  which one  or more  annotation
                  fields have been updated since the last release.

   Currently these  files are  available on  the  following  anonymous  ftp
   servers:

   Organization   ExPASy (Geneva University Expert Protein Analysis System)
   Address        expasy.hcuge.ch  (or 129.195.254.61)
   Directory      /databases/swiss-prot/updates

   Organization   National Center for Biotechnology Information (NCBI)
   Address        ncbi.nlm.nih.gov (or 130.14.20.1)
   Directory      /repository/swiss-prot/updates

   Organization   EBI ftp server
   Address        ftp.ebi.ac.uk (193.62.196.6)
   Directory      /pub/databases/swissprot/new

   !! Important notes !!!

   Although we  try to  follow a  regular schedule,  we do  not promise  to
   update these  files every  week. In some cases two weeks will elapse in-
   between two updates.

   Due to  the current  mechanism used  to build a release the entries that
   are provided in these updates are not guaranteed to be error free. Also,
   for the  same reason,  new  entries  do  not  contain  an  OC  (Organism
   Classification) line.



                            3. ENZYME AND PROSITE

   3.1  The ENZYME data bank

   Release 17.0  of the  ENZYME data bank is distributed with release 30 of
   SWISS-PROT. ENZYME  release 17.0  contains information  relative to 3546
   enzymes.

   3.2  The PROSITE data bank

   Release 12.1  of the PROSITE data bank is distributed with release 30 of
   SWISS-PROT.  Release  12.1  contains  785  documentation  chapters  that
   describes 1029  different patterns, rules and profiles/matrices. Release
   12.1 does  not really  represent a new release; the only changes between




<PAGE>



   releases 12.0  and 12.1  are updating  of the pointers to the SWISS-PROT
   entries whose  name have  been modified between  releases 29 and 30. The
   next release  of PROSITE  (13.0) will  be distributed with release 31 of
   SWISS-PROT.

                             WE NEED YOUR HELP !

   We welcome  feedback from our users. We would especially appreciate that
   you notify  us if  you find  that sequences  belonging to  your field of
   expertise are  missing from  the data  bank. We  also would  like to  be
   notified about  annotations to be updated, if, for example, the function
   of a protein has been clarified or if new post-translational information
   has become available.












































<PAGE>

                         APPENDIX A: SOME STATISTICS



   A.1  Amino acid composition

        A.1.1  Composition in percent for the complete data bank

   Ala (A) 7.60   Gln (Q) 4.03   Leu (L) 9.22   Ser (S) 7.15
   Arg (R) 5.23   Glu (E) 6.28   Lys (K) 5.84   Thr (T) 5.81
   Asn (N) 4.48   Gly (G) 6.95   Met (M) 2.36   Trp (W) 1.28
   Asp (D) 5.29   His (H) 2.24   Phe (F) 4.01   Tyr (Y) 3.21
   Cys (C) 1.76   Ile (I) 5.61   Pro (P) 5.00   Val (V) 6.52

   Asx (B) 0.005  Glx (Z) 0.005  Xaa (X) 0.02


        A.1.2  Classification of the amino acids by their frequency

   Leu, Ala, Ser, Gly, Val, Glu, Lys, Thr, Ile, Asp, Arg, Pro, Asn, Gln,
   Phe, Tyr, Met, His, Cys, Trp



   A.2  Repartition of the sequences by their organism of origin

   Total number of species represented in this release of SWISS-PROT: 4550

        A.2.1 Table of the frequency of occurrence of species

        Species represented 1x: 2045
                            2x:  740
                            3x:  414
                            4x:  255
                            5x:  187
                            6x:  192
                            7x:  115
                            8x:   80
                            9x:   95
                           10x:   44
                       11- 20x:  175
                       21- 50x:  122
                       51-100x:   42
                         >100x:   44















<PAGE>



        A.2.2  Table of the most represented species

    Number   Frequency          Species
         1        2914          Human
         2        2901          Escherichia coli
         3        2287          Baker's yeast (Saccharomyces cerevisiae)
         4        1748          Mouse
         5        1610          Rat
         6         777          Bacillus subtilis
         7         723          Bovine
         8         688          Caenorhabditis elegans
         9         647          Fruit fly (Drosophila melanogaster)
        10         551          Chicken
        11         493          Salmonella typhimurium
        12         432          African clawed frog (Xenopus laevis)
        13         393          Rabbit
        14         347          Pig
        15         251          Arabidopsis thaliana (Mouse-ear cress)
                   251          Vaccinia virus (strain Copenhagen)
        17         246          Maize
        18         224          Fission yeast (Schizosaccharomyces pombe)
        19         210          Rice
        20         200          Bacteriophage T4
        21         199          Pseudomonas aeruginosa
        22         198          Slime mold (Dictyostelium discoideum)
        23         193          Human cytomegalovirus (strain AD169)
        24         184          Tobacco
        25         183          Vaccinia virus (strain WR)
        26         176          Pea
        27         170          Wheat
        28         163          Barley
        29         151          Marchantia polymorpha (Liverwort)
        30         147          Dog
        31         146          Variola virus
        32         141          Staphylococcus aureus
                   141          Sheep
        34         139          Soybean
        35         137          Pseudomonas putida
                   137          Rhodobacter capsulatus
        37         133          Spinach
        38         130          Neurospora crassa
        39         128          Klebsiella pneumoniae
        40         117          Bacillus stearothermophilus
                   117          Tomato
        42         113          Agrobacterium tumefaciens
        43         108          Potato
        44         103          Rhizobium meliloti










<PAGE>



   A.3  Repartition of the sequences by size

               From   To  Number             From   To   Number
                  1-  50    2250             1001-1100      378
                 51- 100    3939             1101-1200      267
                101- 150    5433             1201-1300      198
                151- 200    3898             1301-1400      120
                201- 250    3409             1401-1500      115
                251- 300    3036             1501-1600       58
                301- 350    2862             1601-1700       55
                351- 400    2914             1701-1800       48
                401- 450    2171             1801-1900       57
                451- 500    2291             1901-2000       37
                501- 550    1656             2001-2100       20
                551- 600    1149             2101-2200       48
                601- 650     813             2201-2300       54
                651- 700     617             2301-2400       21
                701- 750     586             2401-2500       26
                751- 800     445             >2500          122
                801- 850     346
                851- 900     373
                901- 950     246
                951-1000     234


   A.4  Longest sequences

   The longest sequences (>=4000 residues) are listed here:

                               HTS1_COCCA  5217
                               FAT_DROME   5147
                               RYNR_RABIT  5037
                               RYNR_HUMAN  5032
                               RYNC_RABIT  4969
                               DYHC_DICDI  4725
                               DYHC_DROME  4639
                               APB_HUMAN   4563
                               APOA_HUMAN  4548
                               RRPA_CVMJH  4488
                               DYHC_TRIGR  4466
                               GRSB_BACBR  4451
                               PLEC_RAT    4140
                               DYHC_YEAST  4092
                               RRPA_CVH22  4085













<PAGE>



   A.5  List of the most cited journals in SWISS-PROT

   Citations            Journal abbreviation

   4345                 J. BIOL. CHEM.
   3050                 NUCLEIC ACIDS RES.
   2777                 PROC. NATL. ACAD. SCI. U.S.A.
   1755                 J. BACTERIOL.
   1528                 FEBS LETT.
   1452                 GENE
   1407                 EUR. J. BIOCHEM.
   1243                 EMBO J.
   1227                 NATURE
   1171                 BIOCHEM. BIOPHYS. RES. COMMUN.
   1134                 BIOCHEMISTRY
    896                 J. MOL. BIOL.
    879                 BIOCHIM. BIOPHYS. ACTA
    869                 CELL
    800                 MOL. CELL. BIOL.
    715                 MOL. GEN. GENET.
    683                 VIROLOGY
    641                 BIOCHEM. J.
    620                 PLANT MOL. BIOL.
    535                 SCIENCE
    521                 J. BIOCHEM.
    475                 MOL. MICROBIOL.
    436                 J. VIROL.
    382                 J. GEN. VIROL.
    268                 J. CELL BIOL.
    247                 BIOL. CHEM. HOPPE-SEYLER
    242                 GENOMICS
    232                 GENES DEV.
    213                 HOPPE-SEYLER'S Z. PHYSIOL. CHEM.
    212                 ARCH. BIOCHEM. BIOPHYS.
    210                 CURR. GENET.
    201                 J. IMMUNOL.
    174                 MOL. BIOCHEM. PARASITOL.
    171                 MOL. ENDOCRINOL.
    169                 YEAST
    164                 J. GEN. MICROBIOL.
    154                 INFECT. IMMUN.
    150                 J. CLIN. INVEST.
    142                 DNA
    138                 ONCOGENE
    123                 PLANT PHYSIOL.
    122                 J. EXP. MED.
    122                 FEMS MICROBIOL. LETT.
    114                 J. MOL. EVOL.
    111                 AM. J. HUM. GENET.
    101                 HUM. MOL. GENET.






<PAGE>

           APPENDIX B: RELATIONSHIPS BETWEEN BIOMOLECULAR DATABASES

   The current  status of the relationships (cross-references) between some
   biomolecular databases is shown in the following schematic:

                                                       **********************
                        ***********************        * EPD [Euk. Promot.] *
                        *  EMBL Nucleotide    * <----> **********************
                        *  Sequence Data      *
******************      *  Library            *        **********************
* FLYBASE        * <--> *********************** <----- * ECD [E. coli map]  *
* [Drosophila    *                ^   ^  ^             **********************
* genomic d.b.]  * <---------+    |   |  |
******************           |    |   |  +------------ **********************
                             |    |   |                * TFD [Trans. fact.] *
                             |    |   |                **********************
******************           |    |   |
* MaizeDb        * <------+  |    |   |                **********************
******************        |  |    |   +--------------> * GCRDb [7TM recep.] *
                          |  |    |   |                **********************
******************        |  |    |   |
* WormPep        *        |  |    |   |                **********************
* [C.elegans]    * <----+ |  |    |   |       +------> * DictyDB [D.disco.] *
******************      | |  |    |   |       |        **********************
                        | |  |    |   |       |
******************      | v  v    v   v       v        **********************
* REBASE         *      ***********************        * ENZYME [Nomencl.]  *
* [Restriction   * <--- *  SWISS-PROT         * <----- **********************
*  enzymes]      *      *  Protein Sequence   *            |
******************      *  Data Bank          *            v
                        ***********************        **********************
******************       ^  ^  ^  | |  ^ ^  |          * OMIM   [Diseases]  *
* EcoGene/EcoSeq *       |  |  |  | |  | |  +--------> **********************
* [E. coli]      * <-----+  |  |  | |  | |
******************          |  |  | |  | +-----------> **********************
                            |  |  | |  |               * ECO2DBASE     [2D] *
                            |  |  | |  |               **********************
******************          |  |  | |  |
* PROSITE        * <--------+  |  | |  +-------------> **********************
* [Patterns]     *             |  | |                  * SWISS-2DPAGE  [2D] *
******************             |  | |                  **********************
             |                 |  | |
             |                 |  | +----------------> **********************
             |                 |  |                    * Aarhus/Ghent  [2D] *
             |                 |  +---------------+    **********************
             |                 v                  |
             |          ***********************   |    **********************
             +--------> * PDB [3D structures] *   +--> * YEPD (yeast)  [2D] *
                        ***********************        **********************










<PAGE>