A functional update of the Escherichia coli K-12 genome
A functional update of the Escherichia coli K-12 genome
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DOI：
10.1186/gb-2001-2-9-research0035
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发表时间：
2001-01-01
期刊：
影响因子：
12.3
通讯作者：
Riley, Monica
中科院分区：
文献类型：
--
作者：
Serres, Margrethe H.;Gopal, Shuba;Riley, Monica
背景资料：自1997年首次注释大肠杆菌K-12的基因组以来，基于序列相似蛋白的生物学特性和功能的其他功能信息已经变得可用。基于这些新的信息，一个更新版本的注释染色体已经产生。大肠杆菌K-12染色体目前由4,401个基因代表，编码116个RNA和4,285个蛋白质。使用GenBank登录号U 00096中鉴定的基因的边界。一些蛋白质编码序列是复合的并且编码多模块蛋白质。编码序列（CDS）由模块（具有生物活性和独立进化历史的至少100个氨基酸的蛋白质元件）表示。在4，285个蛋白质中有4，616个被鉴定的模块。其中，48.9%已被表征，29.5%具有插补功能，2.1%具有表型，19.5%没有功能分配。只有7%的模块是E.大肠杆菌，并且随着更多的基因组数据变得可用，这一数字预计将减少。通过BLAST和达尔文分析以及MAGPIE基因组注释系统对预测功能进行人工评估，并在此基础上对估算的功能进行了分配。coliK-12基因组自1997年注释发表以来，这些数据对分析E.大肠杆菌基因产物以及由其他基因组编码的基因产物。
Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated.Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system.Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.