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Evolution of respiratory complex I: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.呼吸复合物 I 的进化:“多余”的亚基存在于α-变形菌的酶中。
J Biol Chem. 2011 Feb 18;286(7):5023-33. doi: 10.1074/jbc.M110.194993. Epub 2010 Nov 29.
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progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.渐进紫:具有基因增益、缺失和重排的多基因组比对。
PLoS One. 2010 Jun 25;5(6):e11147. doi: 10.1371/journal.pone.0011147.
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Velvet: algorithms for de novo short read assembly using de Bruijn graphs.《天鹅绒:使用德布鲁因图进行从头短读长拼接的算法》
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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.
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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.将BioCyc通路/基因组数据库集合扩展至160个基因组。
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Complete mineralisation of dimethylformamide by Ochrobactrum sp. DGVK1 isolated from the soil samples collected from the coalmine leftovers.从煤矿废弃物收集的土壤样品中分离出的苍白杆菌属菌株DGVK1对二甲基甲酰胺的完全矿化作用
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The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.用于检测tRNA和snoRNA的tRNAscan-SE、snoscan和snoGPS网络服务器。
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W686-9. doi: 10.1093/nar/gki366.
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GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.基因标记:用于在原核生物、真核生物和病毒中寻找基因的网络软件。
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Mauve: multiple alignment of conserved genomic sequence with rearrangements.Mauve:带重排的保守基因组序列多重比对。
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Versatile and open software for comparing large genomes.用于比较大型基因组的通用且开放的软件。
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一种新型 Paracoccus denitrificans 菌株的基因组,该菌株能够降解 N,N-二甲基甲酰胺。

Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide.

机构信息

Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Professor CR Rao Road, Gachibowli, Hyderabad 500 046, India.

出版信息

J Bacteriol. 2011 Oct;193(19):5598-9. doi: 10.1128/JB.05667-11.

DOI:10.1128/JB.05667-11
PMID:21914898
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3187436/
Abstract

The bacterial genus Paracoccus is comprised of metabolically versatile organisms having diverse degradative capabilities and potential industrial and environmental applications for bioremediation in particular. We report a de novo-assembled sequence and annotation of the genome of a novel isolate of Paracoccus denitrificans originally sourced from coal mine tailings in India. The isolate was capable of utilizing N,N-dimethylformamide (DMF) as a source of carbon and nitrogen and therefore holds potential for bioremediation and mineralization of industrial pollutants. The genome sequence and biological circuitry revealed thereupon will be invaluable in understanding the metabolic capabilities, functioning, and evolution of this important bacterial organism.

摘要

副球菌属是一个代谢多样的细菌属,具有多种降解能力,在生物修复,特别是在工业和环境应用方面具有潜在的应用价值。我们报告了一种新型副球菌(Paracoccus denitrificans)的从头组装序列和基因组注释,该菌最初来源于印度的煤矿尾矿。该菌能够利用 N,N-二甲基甲酰胺(DMF)作为碳源和氮源,因此具有生物修复和工业污染物矿化的潜力。由此揭示的基因组序列和生物电路将对理解这种重要细菌的代谢能力、功能和进化具有不可估量的价值。