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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >PREDICTION OF CELL WALL SORTING SIGNALS IN GRAM-POSITIVE BACTERIA WITH A HIDDEN MARKOV MODEL: APPLICATION TO COMPLETE GENOMES
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PREDICTION OF CELL WALL SORTING SIGNALS IN GRAM-POSITIVE BACTERIA WITH A HIDDEN MARKOV MODEL: APPLICATION TO COMPLETE GENOMES

机译：隐马尔可夫模型在革兰氏阳性菌中预测细胞壁排序信号：在完整基因组中的应用

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摘要

Surface proteins in Gram-positive bacteria are frequently implicated in virulence. We have focused on a group of extracellular cell wall-attached proteins (CWPs), containing an LPXTG motif for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A hidden Markov model (HMM) approach for predicting the LPXTG-anchored cell wall proteins of Gram-positive bacteria was developed and compared against existing methods. The HMM model is parsimonious in terms of the number of freely estimated parameters, and it has proved to be very sensitive and specific in a training set of 55 experimentally verified LPXTG-anchored cell wall proteins as well as in reliable data sets of globular and transmembrane proteins. In order to identify such proteins in Gram-positive bacteria, a comprehensive analysis of 94 completely sequenced genomes has been performed. We identified, in total, 860 LPXTG-anchored cell wall proteins, a number that is significantly higher compared to those obtained by other availablemethods. Of these proteins, 237 are hypothetical proteins according to the annotation of SwissProt, and 88 had no homologs in the SwissProt database — this might be evidence that they are members of newly identified families of CWPs. The prediction tool, the database with the proteins identified in the genomes, and supplementary material are available online at.
机译：革兰氏阳性细菌中的表面蛋白经常与毒力有关。我们专注于一组细胞外壁附着蛋白（CWP），其中包含LPXTG母题，用于裂解和通过分选酶与肽聚糖的共价偶联。一种隐马尔可夫模型（HMM）方法用于预测革兰氏阳性细菌的LPXTG锚定的细胞壁蛋白，并与现有方法进行了比较。 HMM模型在可自由估计的参数数量上是简约的，并且在55个经过实验验证的LPXTG锚定的细胞壁蛋白训练集以及球状和跨膜可靠数据集中已证明是非常灵敏和特异的蛋白质。为了鉴定革兰氏阳性细菌中的此类蛋白质，已对94个完全测序的基因组进行了全面分析。我们总共鉴定出860个LPXTG锚定的细胞壁蛋白，该数量明显高于其他可用方法获得的蛋白。根据SwissProt的注释，在这些蛋白质中，有237种是假设蛋白质，在SwissProt数据库中没有88种同源物-这可能证明它们是新发现的CWP家族的成员。预测工具，具有在基因组中鉴定出的蛋白质的数据库以及补充材料可在线获得。

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