Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

UUCD (ubiquitin and ubiquitin-like conjugation database)

General information

Description: a family-based database of ubiquitin and ubiquitin-like conjugation
Year founded: 2012
Last update: 2014-6-30
Version: v2.0
Accessibility:
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Accessible
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Country/Region: China
Data type:
Data object:
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Contact information

University/Institution: Huazhong University of Science and Technology
Address: Department of Biomedical Engineering,College of Life Science and Technology,Huazhong University of Science and Technology,Luoyu Road 1037,Wuhan,Hubei 430074
City: Wuhan
Province/State: Hubei
Country/Region: China
Contact name (PI/Team): Yu Xue
Contact email (PI/Helpdesk): xueyu@mail.hust.edu.cn

Record metadata

Created on: 2015-06-20
Curated by:
Hongyan Yin [2015-12-06]
Jian SA [2015-07-01]
Hongyan Yin [2015-06-26]

Ranking

All databases:
1147/4549 (74.808%)
Expression:
211/800 (73.75%)
1147
Total Rank
39
Citations
5.571
z-index

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Publications

23172288
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. [PMID: 23172288]
Gao T, Liu Z, Wang Y, Cheng H, Yang Q, Guo A, Ren J, Xue Y.

In this work, we developed a family-based database of UUCD (http://uucd.biocuckoo.org) for ubiquitin and ubiquitin-like conjugation, which is one of the most important post-translational modifications responsible for regulating a variety of cellular processes, through a similar E1 (ubiquitin-activating enzyme)-E2 (ubiquitin-conjugating enzyme)-E3 (ubiquitin-protein ligase) enzyme thioester cascade. Although extensive experimental efforts have been taken, an integrative data resource is still not available. From the scientific literature, 26 E1s, 105 E2s, 1003 E3s and 148 deubiquitination enzymes (DUBs) were collected and classified into 1, 3, 19 and 7 families, respectively. To computationally characterize potential enzymes in eukaryotes, we constructed 1, 1, 15 and 6 hidden Markov model (HMM) profiles for E1s, E2s, E3s and DUBs at the family level, separately. Moreover, the ortholog searches were conducted for E3 and DUB families without HMM profiles. Then the UUCD database was developed with 738 E1s, 2937 E2s, 46 631 E3s and 6647 DUBs of 70 eukaryotic species. The detailed annotations and classifications were also provided. The online service of UUCD was implemented in PHP + MySQL + JavaScript + Perl.

Nucleic Acids Res. 2013:41(Database issue) | 39 Citations (from Europe PMC, 2020-02-15)