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Consistency analysis of similarity between multiple alignments: Predictionof protein function and fold structure from analysis of local sequencemotifs

机译:多个比对之间相似性的一致性分析:通过局部序列基序分析预测蛋白质功能和折叠结构

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摘要

A new method to analyze the similarity between multiply aligned protein motifs (blocks) was developed. It identifies sets of consistently aligned blocks. These are found to be protein regions of similar function and structure that appear in different contexts. For example, the Rossmann fold ligand-binding region is found similar to TIM barrel and methylase regions, various protein families are predicted to have a TIM-barrel fold and the structural relation between the ClpP protease and crotonase folds is identified from their sequence. Besides identifying local structure features, sequence similarity across short sequence-regions (less than 20 amino acid regions) also predicts structure similarity of whole domains (folds) a few hundred amino acid reidues long. Most of these relations could not be identified by other advanced sequence-to-sequence or sequence-to-multiple alignments comparisons. We describe the method (termed CYRCA), present examples of our findings, and discuss their implications.
机译:开发了一种分析多重比对的蛋白质基序(嵌段)之间相似性的新方法。它标识一致对齐的块集。发现这些是在不同情况下出现的具有相似功能和结构的蛋白质区域。例如,发现罗斯曼折叠配体结合区与TIM桶和甲基化酶区域相似,各种蛋白质家族预计具有TIM桶形折叠,并从其序列确定ClpP蛋白酶和巴豆酶折叠之间的结构关系。除了确定局部结构特征外,跨短序列区域(少于20个氨基酸区域)的序列相似性还预测整个结构域(折叠)的结构相似性长数百个氨基酸残基。这些关系中的大多数不能通过其他高级序列间比较或序列间多重比对比较来识别。我们描述了该方法(称为CYRCA),介绍了我们的发现的示例,并讨论了其含义。

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