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UniProt release 5.4

Published July 5, 2005

UniProtKB News

Modified wording of reldate.txt in UniProt Knowledgebase ftp directories

The official names for the manually and automatically annotated sections of the UniProt Knowledgebase are UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.

To reflect this, we have changed the wording of the reldate.txt file in UniProt Knowledgebase ftp directories:

from

UniProt Release 5.4 consists of:
Swiss-Prot Release 47.4 of 05-Jul-2005
TrEMBL Release 30.4 of 05-Jul-2005

to

UniProt Knowledgebase Release 5.4 consists of:
UniProtKB/Swiss-Prot Release 47.4 of 05-Jul-2005
UniProtKB/TrEMBL Release 30.4 of 05-Jul-2005

Format change in the dbxref.txt document file

The dbxref.txt file lists the names and abbreviations and URLs of all databases cross-referenced in the UniProt Knowledgebase. We have added a new field, "Note", which is optional. This field will be used, among others, to list obsolete abbreviations for the cross-referenced databases.

Example:

Abbrev: MGI
Name  : Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
LinkTp: Explicit
Server: http://www.informatics.jax.org/
Db_URL: www.informatics.jax.org/searches/accession_report.cgi?id=%s
Note  : Obsolete abbreviation: MGD

Multiple comment line (CC) topics COFACTOR

From now on, the CC line topic COFACTOR can occur more than once per entry. When an enzyme can bind several cofactors, each of them is indicated in a separate topic.

Example:

CC   -!- COFACTOR: Binds 1 2Fe-2S cluster per subunit (By similarity).
CC   -!- COFACTOR: Binds 1 Fe(2+) ion per subunit (By similarity).

CC   -!- COFACTOR: Binds 5 heme groups covalently per monomer.
CC   -!- COFACTOR: Binds 1 calcium ion per monomer.

Changes concerning keywords

New keyword:

Deleted keywords:

  • Testosterone
  • Submandibular gland

Changes concerning the controlled vocabulary for PTMs

New term for the feature key 'CROSSLNK':

  • 2-tetrahydro-2-pyridyl-5-imidazolinone (Lys-Gly)