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UniProt proteomes specifications


Unique identifier OMICS_05991
Name UniProt proteomes
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes



  • person_outline UniProt proteomes Team

Publication for UniProt proteomes

UniProt proteomes citations


The Apoplastic Secretome of Trichoderma virens During Interaction With Maize Roots Shows an Inhibition of Plant Defence and Scavenging Oxidative Stress Secreted Proteins

Front Plant Sci
PMCID: 5896443
PMID: 29675028
DOI: 10.3389/fpls.2018.00409

[…] ) for a total cycle time of 1.8 s. The mass spectrometer and HPLC system were under the control of Analyst TF 1.7 software (Sciex, USA).The MS data were searched against a database which combined the Uniprot proteomes from Z. mays (http://www.uniprot.org/proteomes/UP000007305) and T. virens Gv29.8 (http://www.uniprot.org/proteomes/UP000007115) along with common contaminant entries (141,930 entries […]


The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators

PMCID: 5768985
PMID: 29376036
DOI: 10.3389/fcimb.2017.00537

[…] n the most representative proteome for V. cholerae V52, a non-redundant database of 3756 proteins from two available proteomes was compiled. Proteomes UP000005193 and UP000178081 were downloaded from UniProt Proteomes database and CD-HIT with default settings was used to cluster proteins at sequence identity threshold of 1 (Fu et al., ). Acquired mass spectrometry spectra were processed using MaxQ […]


Systematic bacterialization of yeast genes identifies a near universally swappable pathway

PMCID: 5536947
PMID: 28661399
DOI: 10.7554/eLife.25093.026

[…] Protein sequence features were calculated using UniProt () proteomes from the respective species downloaded in March 2015. E. coli nucleotide sequence features were calculated using EcoGene () sequences downloaded April 2015.[Sc|Ec]_LengthThe numbe […]


Characterizing the Syphilis Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry

PLoS Negl Trop Dis
PMCID: 5015957
PMID: 27606673
DOI: 10.1371/journal.pntd.0004988

[…] Spectra from each sample were extracted by Peak Explorer and screened against a T. pallidum database UniProt proteomes IDs UP000014259 and UP000000811 using the MASCOT search engine (Matrix Science; version 2.1.03) based on the digestion enzyme trypsin. We chose to screen against the Nichols strain d […]


Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem

Front Microbiol
PMCID: 4933709
PMID: 27458440
DOI: 10.3389/fmicb.2016.01043

[…] UniProt proteomes (http://www.uniprot.org/help/proteome) were subjected to metacaspase and recA queries using the method described above. The identified caspase/metacaspase or recA sequences were alig […]


“Controlled, cross species dataset for exploring biases in genome annotation and modification profiles”

PMCID: 4660258
PMID: 26693519
DOI: 10.1016/j.dib.2015.10.042

[…] igned their respective groups and fractions. The most recent honey bee Official Gene Set (OGS) protein database was downloaded from www.beebase.org (OGSv3.2). All other databases were downloaded from Uniprot proteomes (www.uniprot.org) on Feb. 5th, 2014. […]


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UniProt proteomes institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Switzerland; Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA; Protein Information Resource, University of Delaware, Newark, DE, USA
UniProt proteomes funding source(s)
Supported by The National Institutes of Health (NIH) [UniProt 4U41HG006104-04; GO 5U41HG002273-13; 5R01GM 080646-08, 5G08LM010720-03 and 5P20GM103446-13]; British Heart Foundation [SP/07/007/23671]; Swiss Federal Government through the State Secretariat for Education, Research and Innovation; EC [GEN2PHEN (200754) and MICROME (222886)]; National Science Foundation (NSF) [DBI-1062520] and EMBL core funds.

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