Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space
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DOI：
10.1093/nar/gkj494
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发表时间：
2006-01-01
影响因子：
14.9
通讯作者：
Orengo, CA
中科院分区：
文献类型：
--
作者：
Marsden, RL;Lee, D;Orengo, CA
我们对Gene3D资源中的203个完整基因组（包括17个真核生物）进行了分析，结果表明，随着时间的推移，蛋白质家族的数量不断扩大，单基因序列似乎是基因组的内在组成部分。相当大比例的蛋白质组可以被分配到不到6000个特征明确的结构域家族，其余的结构域样区域属于数量更多的小的未特征的家庭，这些家庭很大程度上是物种特异性的。我们对203个基因组进行了全面的结构域注释，使我们能够比以前的计算更准确地估计出在生命的三个王国中发现的多结构域蛋白质的数量。我们发现67%的真核生物序列是多结构域，而原核生物的这一比例为56%。通过测量基因组序列的结构域覆盖率，我们表明结构基因组学计划的目标应该是提供少于一千个结构未表征的Pfam家族的结构，以实现基因组的合理结构注释。然而，在大家庭中，应该确定额外的结构，因为这些将揭示更多关于家庭进化的信息，并使我们能够更好地了解功能是如何进化的。
We present an analysis of 203 completed genomes in the Gene3D resource (including 17 eukaryotes), which demonstrates that the number of protein families is continually expanding over time and that singleton-sequences appear to be an intrinsic part of the genomes. A significant proportion of the proteomes can be assigned to fewer than 6000 well-characterized domain families with the remaining domain-like regions belonging to a much larger number of small uncharacterized families that are largely species specific. Our comprehensive domain annotation of 203 genomes enables us to provide more accurate estimates of the number of multi-domain proteins found in the three kingdoms of life than previous calculations. We find that 67% of eukaryotic sequences are multi-domain compared with 56% of sequences in prokaryotes. By measuring the domain coverage of genome sequences, we show that the structural genomics initiatives should aim to provide structures for less than a thousand structurally uncharacterized Pfam families to achieve reasonable structural annotation of the genomes. However, in large families, additional structures should be determined as these would reveal more about the evolution of the family and enable a greater understanding of how function evolves.