UniProt: A hub for protein information

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/.

María Martín | Peter B. McGarvey | Y Wang | Cathy H. Wu | Rachael P. Huntley | Tony Sawford | Claire O'Donovan | Rolf Apweiler | Michel Schneider | Anne Morgat | Elisabeth Coudert | Kristian B. Axelsen | Alan Bridge | Lydie Bougueleret | Ioannis Xenarios | Baris E. Suzek | Damien Lieberherr | Darren A. Natale | Cecilia N. Arighi | Hongzhan Huang | Alex Bateman | Christian J. A. Sigrist | Elisabeth Gasteiger | Hamish McWilliam | Sandra Orchard | Chuming Chen | Aleksandra Shypitsyna | Lara | Rabie Saidi | Michele Magrane | Anne Estreicher | Lionel Breuza | Nicole Redaschi | Thierry Lombardot | Lucila Aimo | Borisas Bursteinas | Jerven T. Bolleman | Sebastien Gehant | Brigitte Boeckmann | Tunca Doğan | Sylvain Poux | Michael Tognolli | Delphine Baratin | Chantal Hulo | John S. Garavelli | Ghislaine Argoud-Puy | Benoit Bely | Emmanuel Boutet | L Famiglietti | Marc Feuermann | Arnaud Gos | N Gruaz-Gumowski | Ursula Hinz | F Jungo | G Keller | K Laiho | D Legge | P Lemercier | Patrick Masson | Ivo Pedruzzi | Klemens Pichler | D Poggioli | Catherine Rivoire | Bernd Roechert | A Stutz | S Sundaram | Andrew Peter Cowley | Sangya Pundir | Andrew Nightingale | Andrea H. Auchincloss | Béatrice A. Cuche | Rodrigo Lopez | C. R. Vinayaka | Leslie Arminski | Xavier Watkins | Monica Pozzato | Ramona Britto | Emanuele Alpi | Alistair MacDougall | Severine Duvaud | Manuela Pruess | Penelope Garmiri | R Antunes | J Arganiska | M Bingley | C Bonilla | G Chavali | Elena Cibrian-Uhalte | A Da Silva | M De Giorgi | F Fazzini | P Gane | Lg Castro | E Hatton-Ellis | Reija Hieta | W Liu | J Luo | P Mutowo | L Pureza | G Qi | S. Rosanoff | Edd Turner | Volynkin | T Wardell | H Zellner | Parit Bansal | M. C. Blatter | C Casal-Casas | E. de Castro | M Doche | D Dornevil | Gerritsen | T Neto | S Paesano | S Pilbout | K Sonesson | S Staehli | L Verbregue | A-L Veuthey | Youhai H. Chen | C. R. Vinayaka | Q Wang | L-S Yeh | Yerramalla | J Zhang | L Figueira | Weizhong Li | X Martin | N Nouspikel | C. Arighi | D. Natale | A. Bateman | I. Xenarios | J. Garavelli | M. Magrane | R. Apweiler | R. Huntley | T. Sawford | M. Martin | C. O’Donovan | S. Orchard | B. Roechert | S. Poux | B. Boeckmann | R. Lopez | C. Sigrist | E. D. Castro | A. Bridge | L. Bougueleret | Weizhong Li | H. McWilliam | L. Breuza | M. Feuermann | U. Hinz | P. Masson | I. Pedruzzi | E. Gasteiger | Hongzhan Huang | N. Redaschi | L. Yeh | P. Gane | A. Auchincloss | K. Axelsen | B. Bely | M. Blatter | E. Boutet | R. Britto | E. Coudert | A. Estreicher | L. Famiglietti | P. Garmiri | A. Gos | N. Gruaz-Gumowski | E. Hatton-Ellis | C. Hulo | F. Jungo | G. Keller | K. Laiho | D. Lieberherr | K. Pichler | C. Rivoire | A. Shypitsyna | A. Stutz | S. Sundaram | M. Tognolli | Ghislaine Argoud-Puy | P. McGarvey | H. Zellner | S. Paesano | P. Mutowo | E. Alpi | B. Bursteinas | Michel Schneider | J. Luo | A. Morgat | A. Veuthey | M. Bingley | Manuela Pruess | Parit Bansal | Chuming Chen | G. Chavali | Rabie Saidi | T. Lombardot | L. Aimo | Monica Pozzato | S. Rosanoff | R. Antunes | T. Neto | Elena Cibrián-Uhalte | S. Gehant | Andrew Nightingale | P. Lemercier | Lara | Youhai H. Chen | L. Arminski | A. Cowley | Delphine Baratin | D. Legge | W. Liu | D. Poggioli | M. Doche | D. Dornevil | X. Martin | S. Pilbout | K. Sonesson | S. Staehli | L. Verbregue | J. Zhang | R. Hieta | C. Bonilla | M. D. Giorgi | F. Fazzini | L. Figueira | Alistair MacDougall | S. Pundir | L. Pureza | G. Qi | T. Wardell | X. Watkins | C. Casal-Casas | N. Nouspikel | A. D. Silva | Tunca Dogan | Severine Duvaud | Q. Wang | J. Arganiska | Lg Castro | E. Turner | Y. Wang | Borisas Bursteinas | Nicole Redaschi | Hamish McWilliam | S. Duvaud | Penelope Garmiri | Sangya Pundir | Xavier Watkins | Aleksandra Shypitsyna

[1]  Christoph Steinbeck,et al.  The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 , 2012, Nucleic Acids Res..

[2]  Christoph Steinbeck,et al.  Rhea—a manually curated resource of biochemical reactions , 2011, Nucleic Acids Res..

[3]  C. Médigue,et al.  Profiling the orphan enzymes , 2014, Biology Direct.

[4]  Cathy H. Wu,et al.  Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase. , 2011, Methods in molecular biology.

[5]  Rachael P. Huntley,et al.  The UniProt-GO Annotation database in 2011 , 2011, Nucleic Acids Res..

[6]  B. Dolnick,et al.  Cloning and characterization of a naturally occurring antisense RNA to human thymidylate synthase mRNA. , 1993, Nucleic acids research.

[7]  Chris P. Ponting,et al.  A Code for RanGDP Binding in Ankyrin Repeats Defines a Nuclear Import Pathway , 2014, Cell.

[8]  Tomer Altman,et al.  Finding Sequences for over 270 Orphan Enzymes , 2014, PloS one.

[9]  Wyatt W. Yue,et al.  Enzymatic and Structural Characterization of rTSγ Provides Insights into the Function of rTSβ , 2014, Biochemistry.

[10]  Claire O'Donovan,et al.  Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data , 2014, Database J. Biol. Databases Curation.

[11]  Rolf Apweiler,et al.  UniProt archive , 2004, Bioinform..

[12]  A. Black,et al.  rTS gene expression is associated with altered cell sensitivity to thymidylate synthase inhibitors. , 1996, Advances in enzyme regulation.

[13]  Robert D. Finn,et al.  InterPro in 2011: new developments in the family and domain prediction database , 2011, Nucleic acids research.

[14]  Robert D. Finn,et al.  Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation , 2011, PloS one.

[15]  Steven C Almo,et al.  Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris. , 2006, Biochemistry.

[16]  Elisabeth Coudert,et al.  HAMAP in 2015: updates to the protein family classification and annotation system , 2014, Nucleic Acids Res..

[17]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[18]  Peter B. McGarvey,et al.  UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..