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, 43 (Database issue), D204-12

UniProt: A Hub for Protein Information

Collaborators

UniProt: A Hub for Protein Information

UniProt Consortium. Nucleic Acids Res.

Abstract

UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.

Figures

Figure 1.
Figure 1.
Growth of UniProt and UniRef databases.
Figure 2.
Figure 2.
The distribution of proteomes and reference proteomes across the tree of life.
Figure 3.
Figure 3.
(A) Screenshot of the sequence annotation section of human ENOSF1 entry (UniProt Q7L5Y1, http://www.uniprot.org/uniprot/Q7L5Y1). (B) Image of magnesium-binding sites of human ENOSF1 X-ray structure in complex with magnesium (blue) using PyMol (PDB accession 4A35). (C) Image of active site of X. campestris fuconate dehydratase X-ray structure in complex with magnesium (blue) and substrate (green) using PyMol (PDB accession 2HXT).
Figure 4.
Figure 4.
Representation of rule based on HAMAP entry MF_ 01864.
Figure 5.
Figure 5.
Growth of coverage of UniProtKB/TrEMBL by manually curated UniRules. The Y-axis shows the percentage coverage of UniProtKB/TrEMBL by UniRule as a whole as well as by the individual sources. PIR represents the combination of both PIR Site Rules (PIRSR) and PIR Name Rules (PIRNR).
Figure 6.
Figure 6.
Customizable UniProt search results for ‘insulin’, with search term filters and breakdown by popular organism, and an additional column showing the annotation score for each entry.
Figure 7.
Figure 7.
UniProt entry view for human coiled-coil and C2 domain-containing protein 2A (UniProt Q9P2K1).
Figure 8.
Figure 8.
Reference proteome page for Bacillus subtilis (strain 168).
Figure 9.
Figure 9.
Distribution of citations to UniProt Publications by year.
Figure 10.
Figure 10.
Distribution of number of publications citing UniProt, according to research categories. Note a publication may be classified in more than one category.

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