Vibrio sp. 菌株 EJY3 的基因组序列，该菌株是一种能够分解琼脂的海洋细菌，能够以 3,6-脱水-L-半乳糖作为唯一碳源进行代谢。
Genome sequence of Vibrio sp. strain EJY3, an agarolytic marine bacterium metabolizing 3,6-anhydro-L-galactose as a sole carbon source.
机构信息
Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.
出版信息
J Bacteriol. 2012 May;194(10):2773-4. doi: 10.1128/JB.00303-12.
Abstract
The metabolic fate of 3,6-anhydro-L-galactose (L-AHG) is unknown in the global marine carbon cycle. Vibrio sp. strain EJY3 is an agarolytic marine bacterium that can utilize L-AHG as a sole carbon source. To elucidate the metabolic pathways of L-AHG, we have sequenced the complete genome of Vibrio sp. strain EJY3.
摘要
3,6-脱水-L-半乳糖（L-AHG）在全球海洋碳循环中的代谢命运尚不清楚。Vibrio sp. 菌株 EJY3 是一种能分解琼脂的海洋细菌，可以将 L-AHG 作为唯一碳源加以利用。为了阐明 L-AHG 的代谢途径，我们对 Vibrio sp. 菌株 EJY3 的全基因组进行了测序。
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本文引用的文献
1
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2
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Nat Biotechnol. 2011 Jan;29(1):24-6. doi: 10.1038/nbt.1754.
3
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N Biotechnol. 2010 May 31;27(2):156-68. doi: 10.1016/j.nbt.2010.02.023. Epub 2010 Mar 6.
4
Agarase: review of major sources, categories, purification method, enzyme characteristics and applications.琼胶酶：主要来源、种类、纯化方法、酶特性和应用综述。
Mar Drugs. 2010 Jan 26;8(1):200-18. doi: 10.3390/md8010200.
5
Vibrio atypicus sp. nov., isolated from the digestive tract of the Chinese prawn (Penaeus chinensis O'sbeck).新种弧菌属，从中国对虾（斑节对虾 O'sbeck）的消化道中分离得到。
Int J Syst Evol Microbiol. 2010 Nov;60(Pt 11):2517-2523. doi: 10.1099/ijs.0.016915-0. Epub 2009 Dec 4.
6
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Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.
7
Fast and accurate short read alignment with Burrows-Wheeler transform.使用Burrows-Wheeler变换进行快速准确的短读比对。
Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.
8
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.碳水化合物活性酶数据库（CAZy）：糖原组学的专业资源。
Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8. doi: 10.1093/nar/gkn663. Epub 2008 Oct 5.
9
The RAST Server: rapid annotations using subsystems technology.RAST服务器：使用子系统技术进行快速注释。
BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.
10
Microbial structuring of marine ecosystems.海洋生态系统的微生物结构
Nat Rev Microbiol. 2007 Oct;5(10):782-91. doi: 10.1038/nrmicro1747.
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