Uniprot/Swiss-Prot Data Base

A Uniprot/Swiss-Prot Data Base is a broad-coverage curated biomedical knowledge base of protein data in the form of annotated Swiss-Prot records.

AKA: SwissProt KB.
Context:
- It can (typically) be a Disambiguated Database.
- It can (typically) provide a high level of Integration with other Databases.
- It can be a part of the Universal Protein Resource (UniProt). The other component being TrEMBL.
- It can be distributed by European Molecular Biology Laboratory (EMBL)
- It can be updated regularly the PSC
- It can be published in Swiss-Prot Accession Format [1]
- It can include a Controlled Vocabulary for Biological Entities, such as the Swiss-Prot SCL Controlled Vocabulary.
Example(s):
- Release 52.3 of 17-Apr-2007 of UniProtKB/Swiss-Prot contains 264,492 sequence entries, comprising 96,880,444 amino acids abstracted from 154,049 references.
- Release 49.0 of 07-Feb-2006 of UniProtKB/Swiss-Prot contains 207,132 sequence entries, comprising 75,438,310 amino acids abstracted from 139,151 references. From more than 9,731 different species;
Counter-Example(s):
- NeuronDB.
- GenBank Database.
- a Uniprot/Trembl Data Base.
See: PPLRE Swiss-Prot Table, Protein Sequence.

References

2017

(Wikipedia, 2017) ⇒ https://en.wikipedia.org/wiki/UniProt#UniProtKB Retrieved:2017-6-8.
- UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. It combines information extracted from scientific literature and biocurator-evaluated computational analysis. The aim of UniProtKB/Swiss-Prot is to provide all known relevant information about a particular protein. Annotation is regularly reviewed to keep up with current scientific findings. The manual annotation of an entry involves detailed analysis of the protein sequence and of the scientific literature.^[1]
  Sequences from the same gene and the same species are merged into the same database entry. Differences between sequences are identified, and their cause documented (for example alternative splicing, natural variation, incorrect initiation sites, incorrect exon boundaries, frameshifts, unidentified conflicts). A range of sequence analysis tools is used in the annotation of UniProtKB/Swiss-Prot entries. Computer-predictions are manually evaluated, and relevant results selected for inclusion in the entry. These predictions include post-translational modifications, transmembrane domains and topology, signal peptides, domain identification, and protein family classification.
  Relevant publications are identified by searching databases such as PubMed. The full text of each paper is read, and information is extracted and added to the entry. Annotation arising from the scientific literature includes, but is not limited to:
  - Protein and gene names
  - Function
  - Enzyme-specific information such as catalytic activity, cofactors and catalytic residues.
  - Subcellular location.
  - Protein-protein interactions.
  - Pattern of expression
  - Locations and roles of significant domains and sites
  - Ion-, substrate- and cofactor-binding sites
  - Protein variant forms produced by natural genetic variation, RNA editing, alternative splicing, proteolytic processing, and post-translational modification
- Annotated entries undergo quality assurance before inclusion into UniProtKB/Swiss-Prot. When new data becomes available, entries are updated.

2009

(Wikipedia, 2009) ⇒ http://en.wikipedia.org/wiki/Swiss-Prot
- … From the March and April 2007 releases

 3.2  Table of the most represented species

 ------  ---------  --------------------------------------------
 Number  Frequency  Species
 ------  ---------  --------------------------------------------
      1      15803  Homo sapiens (Human)
      2      12577  Mus musculus (Mouse)
      6       4931  Escherichia coli
     10       2848  Bacillus subtilis
     12       1882  Escherichia coli O157:H7
     13       1782  Methanococcus jannaschii
     14       1774  Haemophilus influenzae
     17       1624  Salmonella typhimurium
     19       1550  Escherichia coli O6
     20       1521  Shigella flexneri
     21       1416  Mycobacterium tuberculosis
     22       1220  Salmonella typhi
     23       1158  Mycobacterium bovis
     26       1106  Pseudomonas aeruginosa
     28        976  Synechocystis sp. (strain PCC 6803)
     29        971  Archaeoglobus fulgidus
     31        886  Vibrio cholerae

                                  Total    Number of  Average

Line type / subtype                number   entries    per entry

-------- --------- ---------

References (RL)                     511783              1.97

  Journal                          446039    233211    1.71
  Submitted to EMBL/GenBank/DDBJ    61712     54310    0.24
  Submitted to Swiss-Prot            1137      1119   <0.01

...
Comments (CC)                      1051386              4.04

  SIMILARITY                       295447    237694    1.14
  FUNCTION                         183661    177123    0.71
  SUBCELLULAR LOCATION             142311    142311    0.55

...

  5.2  List of the most cited journals in UniProtKB/Swiss-Prot

  Nb    Citations   Journal name
  --    ---------   -------------------------------------------------------------
   1        14709   Journal of Biological Chemistry
   2         7044   Proceedings of the National Academy of Sciences of the U.S.A.
   3         4488   Journal of Bacteriology
   4         4199   Gene
   5         4063   Nucleic Acids Research
   6         3794   Biochemical and Biophysical Research Communications
   7         3524   FEBS Letters
   8         3274   Biochemistry
   9         3238   The EMBO Journal
  10         2931   European Journal of Biochemistry
  11         2801   Nature

User Interfaces

Basic UniProtKB Entry Viewer

http://www.uniprot.org/entry/P23189

ExPASy:

PIR

↑ Annotation of UniProtKB

[faq45-1] Annotation of UniProtKB

[1]

Uniprot/Swiss-Prot Data Base

References

2017

2009

User Interfaces

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