Kihara Daisuke, Skolnick Jeffrey
UB Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14215, USA.
Proteins. 2004 May 1;55(2):464-73. doi: 10.1002/prot.20044.
The genome scale threading of five complete microbial genomes is revisited using our state-of-the-art threading algorithm, PROSPECTOR_Q. Considering that structure assignment to an ORF could be useful for predicting biochemical function as well as for analyzing pathways, it is important to assess the current status of genome scale threading. The fraction of ORFs to which we could assign protein structures with a reasonably good confidence level to each genome sequences is over 72%, which is significantly higher than earlier studies. Using the assigned structures, we have predicted the function of several ORFs through "single-function" template structures, obtained from an analysis of the relationship between protein fold and function. The fold distribution of the genomes and the effect of the number of homologous sequences on structure assignment are also discussed.
使用我们最先进的穿线算法PROSPECTOR_Q重新审视了五个完整微生物基因组的基因组规模穿线。考虑到将结构分配给一个开放阅读框（ORF）对于预测生化功能以及分析代谢途径可能有用，评估基因组规模穿线的当前状态很重要。我们能够以合理良好的置信水平为每个基因组序列分配蛋白质结构的ORF比例超过72%，这显著高于早期研究。利用分配的结构，我们通过从蛋白质折叠与功能关系分析中获得的“单功能”模板结构预测了几个ORF的功能。还讨论了基因组的折叠分布以及同源序列数量对结构分配的影响。
