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UniProt release 1.11

Published June 7, 2004

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Fungi and Swiss-Prot

As we are reaching the 10'000 entries mark for fungi in Swiss-Prot, we believe it is useful to inform our users that we are actively working in speeding up the annotation and re-annotation of fungal protein sequences and most notably those originating from the two model organisms Saccharomyces cerevisiae and Schizosaccharomyces pombe. We are currently building up a fungal annotation group which will soon consist of four annotators, three in Geneva and one in Hinxton.

UniProt news

Changes concerning keywords

New keywords:


Changes concerning the controlled vocabulary for PTMs

We are continuously overhauling the annotation of post-translational modifications (PTMs). For the feature key MOD_RES, the new initially introduced controlled vocabularies for PTMs are:

  • Bromination: All entries with annotated bromination sites have the keyword Bromination.

     Bromohistidine
     6'-bromotryptophan
    
  • Deamidation

     Deamidated asparagine
     Deamidated glutamine
    
  • Formylation: All entries with annotated formylation sites have the keyword Formylation.

     N-formylmethionine
     N-formylglycine
    
  • Hydroxylation: All entries with annotated hydroxylation sites have the keyword Hydroxylation.

     Hydroxyproline
     3-hydroxyasparagine
     3-hydroxyaspartate
     5-hydroxylysine
     3-hydroxytryptophan
    
  • Iodination: All entries with annotated iodination sites have the keyword Iodination.

     Thyroxine
     Triiodothyronine
    
  • Other new controlled vocabularies for PTMs that are annotated with the feature key MOD_RES:

     3',4'-dihydroxyphenylalanine
     3-methylthioaspartic acid
     3-oxoalanine (Cys)
     3-oxoalanine (Ser)
     4-carboxyglutamate (Keyword: Gamma-carboxyglutamic acid)
     ADP-ribosylarginine
     ADP-ribosylcysteine
     Allysine
     Aspartyl isopeptide (Asn)
     Cysteine persulfide
     Pentaglycyl murein peptidoglycan amidated threonine
     PolyADP-ribosyl glutamic acid
     Pyruvic acid (Ser)
     Pyruvic acid (Cys)
     S-nitrosocysteine (Keyword: S-nitrosylation)
    
  • Unidentified modifications

     Alanine derivative
     Arginine derivative
     Cysteine derivative
     Glutamine derivative
     Isoleucine derivative
     Lysine derivative
     Methionine derivative
     Tryptophan derivative