UniProt release 1.11

Published June 7, 2004

Headlines

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