Searching databases of conserved sequence regions by aligning protein multiple-alignments
Searching databases of conserved sequence regions by aligning protein multiple-alignments
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DOI：
10.1093/nar/24.19.3836
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发表时间：
1996-10-01
影响因子：
14.9
通讯作者：
Pietrokovski, S
中科院分区：
文献类型：
--
作者：
Pietrokovski, S
提出了一种比较多序列比对的通用搜索方法，用于检测保守蛋白区域之间的序列关系，将多序列比对作为氨基酸分布序列，通过比对氨基酸分布对进行比对，采用4种不同的比较方法进行检验，并选择Pearson相关系数，该方法灵敏度高，可检测蛋白质家族之间的弱序列关系。两个氧化还原酶家族的黄蛋白亚基之间先前未被发现的关系指向其中一个家族的潜在活性位点，细菌RecA， DnaA和Rad51蛋白家族之间的相似性揭示了DnaA和Rad51蛋白中可能结合和解开单链DNA的区域。来自不同蛋白质的螺旋-转-螺旋DNA结合域很容易被检测到，并且彼此相似，糖基天冬酰胺酶和γ -谷氨酰转移酶在其蛋白水解裂解位点上被发现相似。该方法已在万维网上完全实现：http://blocks.fhcrc.org/blocks-bin/LAMA_search
A general searching method for comparing multiple sequence alignments was developed to detect sequence relationships between conserved protein regions, Multiple alignments are treated as sequences of amino acid distributions and aligned by comparing pairs of such distributions, Four different comparison measures were tested and the Pearson correlation coefficient chosen, The method is sensitive, detecting weak sequence relationships between protein families, Relationships are detected beyond the range of conventional sequence database searches, illustrating the potential usefulness of the method, The previously undetected relation between flavoprotein subunits of two oxidoreductase families points to the potential active site in one of the families, The similarity between the bacterial RecA, DnaA and Rad51 protein families reveals a region in DnaA and Rad51 proteins likely to bind and unstack single-stranded DNA, Helix-turn-helix DNA binding domains from diverse proteins are readily detected and shown to be similar to each other, Glycosylasparaginase and gamma-glutamyltransferase enzymes are found to be similar in their proteolytic cleavage sites, The method has been fully implemented on the World Wide Web at URL: http://blocks.fhcrc.org/blocks-bin/LAMA_search