DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters

被引：74

作者：

Ichikawa, Natsuko ^{[1
]}

Sasagawa, Machi ^{[1
]}

Yamamoto, Mika ^{[1
]}

Komaki, Hisayuki ^{[1
]}

Yoshida, Yumi ^{[1
]}

Yamazaki, Shuji ^{[1
]}

Fujita, Nobuyuki ^{[1
]}

机构：

[1] Natl Inst Technol & Evaluat NBRC, Biol Resource Ctr, Shibuya Ku, Tokyo 1510006, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / D1期

关键词：

DRAFT GENOME SEQUENCE; POLYKETIDE SYNTHASE; IDENTIFICATION; ANTIBIOTICS; ANNOTATION; PROTEIN;

D O I：

10.1093/nar/gks1177

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

This article introduces DoBISCUIT (Database of BIoSynthesis clusters CUrated and InTegrated, http://www.bio.nite.go.jp/pks/), a literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. Bacterial secondary metabolites often show pharmacologically important activities and can serve as lead compounds and/or candidates for drug development. Biosynthesis of each secondary metabolite is catalyzed by a number of enzymes, usually encoded by a gene cluster. Although many scientific papers describe such gene clusters, the gene information is not always described in a comprehensive manner and the related information is rarely integrated. DoBISCUIT integrates the latest literature information and provides standardized gene/module/domain descriptions related to the gene clusters.

引用

页码：D408 / D414

页数：7

共 33 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2] SBSPKS: structure based sequence analysis of polyketide synthases [J].

Anand, Swadha ;

Prasad, M. V. R. ;

Yadav, Gitanjali ;

Kumar, Narendra ;

Shehara, Jyoti ;

Ansari, Md. Zeeshan ;

Mohanty, Debasisa .

NUCLEIC ACIDS RESEARCH, 2010, 38 :W487-W496

[3]

[Anonymous], NUCLEIC ACIDS RES S2

[4] Reorganizing the protein space at the Universal Protein Resource (UniProt) [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Casanova, Elisabet Barrera ;

Bely, Benoit ;

Bingley, Mark ;

Bower, Lawrence ;

Bursteinas, Borisas ;

Chan, Wei Mun ;

Chavali, Gayatri ;

Da Silva, Alan ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fazzini, Francesco ;

Fedotov, Alexander ;

Garavelli, John ;

Castro, Leyla Garcia ;

Gardner, Michael ;

Hieta, Reija ;

Huntley, Rachael ;

Jacobsen, Julius ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Pichler, Klemens ;

Poggioli, Diego ;

Pontikos, Nikolas ;

Pundir, Sangya ;

Rosanoff, Steven ;

Sawford, Tony ;

Sehra, Harminder ;

Turner, Edward ;

Wardell, Tony ;

Watkins, Xavier ;

Corbett, Matt ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Goujon, Mickael ;

McWilliam, Hamish ;

Lopez, Rodrigo ;

Xenarios, Ioannis ;

Bougueleret, Lydie ;

Bridge, Alan ;

Poux, Sylvain ;

Redaschi, Nicole .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D71-D75

[5] GenBank [J].

Benson, Dennis A. ;

Karsch-Mizrachi, Ilene ;

Clark, Karen ;

Lipman, David J. ;

Ostell, James ;

Sayers, Eric W. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D48-D53

[6] AN UNUSUALLY LARGE MULTIFUNCTIONAL POLYPEPTIDE IN THE ERYTHROMYCIN-PRODUCING POLYKETIDE SYNTHASE OF SACCHAROPOLYSPORA-ERYTHRAEA [J].

CORTES, J ;

HAYDOCK, SF ;

ROBERTS, GA ;

BEVITT, DJ ;

LEADLAY, PF .

NATURE, 1990, 348 (6297) :176-178

[7] Active-site residue, domain and module swaps in modular polyketide synthases [J].

Del Vecchio, F ;

Petkovic, H ;

Kendrew, SG ;

Low, L ;

Wilkinson, B ;

Lill, R ;

Cortés, J ;

Rudd, BAM ;

Staunton, J ;

Leadlay, PF .

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, 2003, 30 (08) :489-494

[8] MODULAR ORGANIZATION OF GENES REQUIRED FOR COMPLEX POLYKETIDE BIOSYNTHESIS [J].

DONADIO, S ;

STAVER, MJ ;

MCALPINE, JB ;

SWANSON, SJ ;

KATZ, L .

SCIENCE, 1991, 252 (5006) :675-679

[9] Genome Sequences of Three Tunicamycin-Producing Streptomyces Strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus ATCC 31396 [J].

Doroghazi, James R. ;

Ju, Kou-San ;

Brown, Daren W. ;

Labeda, David P. ;

Deng, Zixin ;

Metcalf, William W. ;

Chen, Wenqing ;

Price, Neil P. J. .

JOURNAL OF BACTERIOLOGY, 2011, 193 (24) :7021-7022

[10] PRODUCTION OF HYBRID ANTIBIOTICS BY GENETIC-ENGINEERING [J].

HOPWOOD, DA ;

MALPARTIDA, F ;

KIESER, HM ;

IKEDA, H ;

DUNCAN, J ;

FUJII, I ;

RUDD, BAM ;

FLOSS, HG ;

OMURA, S .

NATURE, 1985, 314 (6012) :642-644

← 1 2 3 4 →