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UniProt release 9.7

Published February 20, 2007

Headlines

Complete human kinome in UniProtKB/Swiss-Prot!

Phosphorylation by protein kinases is a universal and fundamental cell-signalling process in eukaryotic cells. A comprehensive catalog of predicted human kinases has been published in 2002 (Manning et al.).

We have annotated the 518 protein kinases predicted to exist, and when necessary revised their sequences. The human kinome as defined by Manning et al., is now complete in UniProtKB/Swiss-Prot !

These protein kinases are subdivided in 10 groups

  • AGC (containing PKA, PKG and PKC families)
  • CAMK (Calcium/Calmodulin-dependent protein kinase)
  • CK1 (Casein kinase 1)
  • CMGC (containing CDK, MAPK, GSK3 and CLK families)
  • RGC (Receptor guanylate cyclases)
  • STE (homologs of yeast Sterile 7, 11 and 20 kinases)
  • TK (Tyrosine kinase)
  • TKL (Tyrosine kinase-like)
  • Atypical
  • Other

In addition to these 518 protein kinases, there is currently one family of lipid kinases which is being fully characterized: the phosphatidyl 3-kinase (PI3 kinase) family (PI3 kinome). This emerging family appears to also include phosphatidyl 4-kinase (PI4 kinases). PI4 kinases as well as PI3 kinases share the same catalytic kinase domain. However, they are distantly related to the catalytic domain of the protein kinases and as a consequence belong to a separate family. This lipid kinase family will be soon integrated into UniProtKB/Swiss-Prot.

Mouse kinase orthologs are in the process of being all integrated into UniProtKB/Swiss-Prot. By providing annotated and up-to-date human and mouse kinomes to the scientific community, our knowledgebase becomes a central and reference portal for kinases.

UniProtKB News

Cross-references to CYGD

Cross-references have been added to the MIPS Comprehensive Yeast Genome Database. This database aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.

The CYGD is available at http://mips.gsf.de/genre/proj/yeast.

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

Resource abbreviation CYGD
Resource identifier Ordered locus name.
Example
P35688:
DR   CYGD; YDL240w; -.

Cross-references to EMBL: new molecule type

We added the value Viral_cRNA to the controlled vocabulary of the field MoleculeType of the cross-references to the EMBL nucleotide sequence database. The format of the DR EMBL line is:

DR   EMBL; AccessionNumber; ProteinID; StatusIdentifier; MoleculeType.

The controlled vocabulary of the field MoleculeType is:

  • Genomic_DNA
  • Genomic_RNA
  • pre-RNA
  • mRNA
  • Unassigned_DNA
  • Unassigned_RNA
  • Other_DNA
  • Other_RNA
  • Viral_cRNA
  • -

Changes concerning keywords

New keywords: