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UniProt release 13.0

Published February 26, 2008

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UniProtKB major release (13.0)

UniProt Knowledgebase release 13.0 includes Swiss-Prot release 55.0 and TrEMBL release 38.0.

Release 55.0 of 26-Feb-08 of UniProtKB/Swiss-Prot contains 356'194 sequence entries, comprising 127'836'513 amino acids abstracted from 165776 references. 80'183 sequences have been added since release 54.0, the sequence data of 1'411 existing entries has been updated and the annotations of 262'009 entries have been revised.

The following improvements were carried out in the last 7 months:

UniProtKB News

New representation of non-standard amino acids (selenocysteine and pyrrolysine)

The non-standard amino acids selenocysteine and pyrrolysine used to be annotated in the 'Sequence annotation' section, 'Amino acid modifications' subsection, under the feature keys 'Selenocysteine' and 'Modified residue', respectively. In the sequence, selenocysteine was represented by the one-letter code 'C' and pyrrolysine by 'K'. In order to annotate these and future non-standard amino acids more adequately, we created a new key 'Non- standard residue'. The type of non-standard residue involved is indicated in the 'description' of the feature key. Sequences will accomodate the IUPAC/IUBMB recommended one-letter codes 'U' for selenocysteine and 'O' for pyrrolysine.

In the flat file, selenocysteine used to be described with the feature key SE_CYS and pyrrolysine with the more generic feature key MOD_RES. We have replaced these keys with the new feature key NON_STD (non-standard). The type of non-standard residue involved is indicated in the 'description' of the NON_STD key.

Former annotation in the flat file:

     ID   BTHD_DROME              Reviewed;         249 AA.
     ..
     FT   SE_CYS       37     37
     ..
     MPPKRNKKAE APIAERDAGE ELDPNAPVLY VEHCRSCRVF RRRAEELHSA LRERGLQQLQ
     *
    
     ID   MTBB1_METAC             Reviewed;         467 AA.
     ..
     FT   MOD_RES     356    356       Pyrrolysine (Probable).
     ..
     RAVNFMKAAV QASPIPCHVD MGMGVGGIPM LETPPVDAVT RASKAMVEVA GVDGIKIGVG
     *
    

Current annotation:

     ID   BTHD_DROME              Reviewed;         249 AA.
     ..
     FT   NON_STD      37     37       Selenocysteine.
     ..
     MPPKRNKKAE APIAERDAGE ELDPNAPVLY VEHCRSURVF RRRAEELHSA LRERGLQQLQ
     *
    
     ID   MTBB1_METAC             Reviewed;         467 AA.
     ..
     FT   NON_STD     356    356       Pyrrolysine (Probable).
     ..
     RAVNFMKAAV QASPIPCHVD MGMGVGGIPM LETPPVDAVT RASKAMVEVA GVDGIOIGVG
     *
    

UniProtKB/Swiss-Prot entries describing a selenocysteine- and pyrrolysine- containing sequences can be retrieved with the 'Selenocysteine' and 'Pyrrolysine' keywords, respectively.

Cross-references to PhosphoSite

Cross-references have been added to PhosphoSite, an expert-curated knowledgebase of information focused on protein phosphorylation mainly in vertebrates. In addition to phosphorylation sites curated from the literature, large numbers of new unpublished sites discovered by MS/MS analyses are being added regularly.

The Phosphorylation site database is available at http://phosphosite.cellsignal.com/.

The format of the explicit links in the flat file is:

Resource abbreviation PhosphoSite
Resource identifier UniProtKB accession number.
Examples
P01266:
DR   PhosphoSite; P01266; -.

Q9JMH6:
DR   PhosphoSite; Q9JMH6; -.

Cross-references to 2DBase-Ecoli

Cross-references have been added to 2DBase-Ecoli, the 2D-PAGE database of Escherichia coli. The 2DBase-Ecoli database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on various functional categories enabling quick and subsequent analysis.

The 2D-PAGE Database of Escherichia coli is available at http://2dbase.techfak.uni-bielefeld.de/.

The format of the explicit links in the flat file is:

Resource abbreviation 2DBase-Ecoli
Resource identifier UniProtKB accession number.
Examples
P02930:
DR   2DBase-Ecoli; P02930; -.

P04816:
DR   2DBase-Ecoli; P04816; -.

Changes concerning keywords

New keywords:

Changes in subcellular location controlled vocabulary

New subcellular locations:

  • Extravirionic side
  • Intravirionic side

Changes in PTM controlled vocabulary

New terms in the 'Amino acid modifications' subsection (feature key 'MOD_RES' in the flat file):

  • 2'-methylsulfonyltryptophan
  • 4,5-dihydroxyleucine
  • (3R,4S)-3,4-dihydroxyproline
  • Cyclopeptide (Ala-Pro)
  • D-serine (Cys)
  • D-serine (Ser)
  • D-threonine
  • N,N-dimethylalanine
  • N-acetylisoleucine
  • O-(5'-phospho-DNA)-serine
  • O-(5'-phospho-DNA)-tyrosine
  • O-(5'-phospho-RNA)-serine
  • O-(5'-phospho-RNA)-tyrosine
  • S-glutathionyl cysteine