title: UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation.
abstract: 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.
authors.affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan, Hubei 430074, China.
authors.forename: Tianshun
authors.initials: T
authors.lastname: Gao
authors.forename: Zexian
authors.initials: Z
authors.lastname: Liu
authors.forename: Yongbo
authors.initials: Y
authors.lastname: Wang
authors.forename: Han
authors.initials: H
authors.lastname: Cheng
authors.forename: Qing
authors.initials: Q
authors.lastname: Yang
authors.forename: Anyuan
authors.initials: A
authors.lastname: Guo
authors.forename: Jian
authors.initials: J
authors.lastname: Ren
authors.forename: Yu
authors.initials: Y
authors.lastname: Xue
mesh_terms: D030562:Databases, Protein; D010450:Endopeptidases / Q000737:chemistry / Q000145:classification*; D020407:Internet; D040901:Proteomics; D025801:Ubiquitin / Q000378:metabolism; D044764:Ubiquitin-Activating Enzymes / Q000737:chemistry / Q000145:classification*; D044763:Ubiquitin-Conjugating Enzymes / Q000737:chemistry / Q000145:classification*; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry / Q000145:classification*; D054875:Ubiquitination; D014452:Ubiquitins / Q000378:metabolism
chemical_list: D025801:Ubiquitin; D014452:Ubiquitins; D044763:Ubiquitin-Conjugating Enzymes; D044767:Ubiquitin-Protein Ligases; D010450:Endopeptidases; D044764:Ubiquitin-Activating Enzymes