For example, REACTOME cross-references UniProt, ChEBI, and Gene Ontology (GO); the PRIDE database cross-references UniProt and many other protein databases; and the Expression Atlas cross-references Ensembl genes, UniProt, and GO.
As a result, many annotations retrieved from protein databases are only textual (as in UniProtKB) or ontology based [as in Gene Ontology (Ashburner et al., 2000)] and do not provide the required metabolic information directly.
A search of the protein databases uncovered many additional putative phosphite dehydrogenases.
(Since protein databases contain many similar and almost identical proteins, the number of functionally different proteins with GO terms is obviously smaller).
Forty-seven and 43% of contig consensus sequences had BLAST matches to known proteins in the Uniref50 and TAIR9 annotated protein databases, respectively; many contigs fully represented orthologous proteins in TAIR9.
This finding suggests that database searches that are based on proximity to GGDP synthase genes can be used to find novel diterpene cyclases in public protein databases, and that many currently unrecognized diterpene cyclases might be buried in public protein databases.
4. The "nucleotide collection (nr/nt)" database contains all Genbank, RefSeq, EMBL (Europe's primary nucleotide database), DNA Database of Japan (DDJB), and many Protein Databank (PDB) sequences.
During this update of the database and analysis many protein kinases have come into light which are splice variants of previously identified protein kinases listed in various kinome datasets such as the one in http://www.itb.cnr.it/kinweb[ 11].
While many other contigs had significant BLAST matches in protein databases, these were to genes that have no GO annotation.
Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores.
