Rychlewski L, Zhang B, Godzik A
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
Fold Des. 1998;3(4):229-38. doi: 10.1016/S1359-0278(98)00034-0.
Uncharacterized proteins from newly sequenced genomes provide perfect targets for fold and function prediction.
For 38% of the entire genome of Mycoplasma genitalium, sequence similarity to a protein with a known structure can be recognized using a new sequence alignment algorithm. When comparing genomes of M. genitalium and Escherichia coli, > 80% of M. genitalium proteins have a significant sequence similarity to a protein in E. coli and there are > 40 examples that have not been recognized before. For all cases of proteins with significant profile similarities, there are strong analogies in their functions, if the functions of both proteins are known. The results presented here and other recent results strongly support the argument that such proteins are actually homologous. Assuming this homology allows one to make tentative functional assignments for > 50 previously uncharacterized proteins, including such intriguing cases as the putative beta-lactam antibiotic resistance protein in M. gentalium.
Using a new profile-to-profile alignment algorithm, the three-dimensional fold can be predicted for almost 40% of proteins from a genome of the small bacterium M. genitalium, and tentative function can be assigned to almost 80% of the entire genome. Some predictions lead to new insights about known functions or point to hitherto unexpected features of M. genitalium.
新测序基因组中的未表征蛋白质为折叠和功能预测提供了理想靶点。
利用一种新的序列比对算法，可以识别出生殖道支原体整个基因组中38%的序列与具有已知结构的蛋白质具有相似性。在比较生殖道支原体和大肠杆菌的基因组时，超过80%的生殖道支原体蛋白质与大肠杆菌中的蛋白质具有显著的序列相似性，并且有40多个此前未被识别的例子。对于所有具有显著轮廓相似性的蛋白质情况，如果两种蛋白质的功能已知，它们在功能上有很强的相似性。此处呈现的结果以及其他近期结果有力地支持了这样一种观点，即这些蛋白质实际上是同源的。假设这种同源性，能够对50多个此前未表征的蛋白质进行初步功能分配，包括生殖道支原体中假定的β-内酰胺抗生素抗性蛋白等有趣例子。
使用一种新的轮廓到轮廓比对算法，可以预测小细菌生殖道支原体基因组中近40%的蛋白质的三维折叠，并能为几乎80%的整个基因组分配初步功能。一些预测为已知功能带来了新见解，或指出了生殖道支原体迄今未被发现的特征。
