Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr‐B‐Phos, Pfr‐C‐Phos and Pfr‐GAP, to describe the three groups of acid phosphatases. These sequence‐based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.

中文翻译：

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开发可靠的蛋白质分析图谱，以鉴定基因组和宏基因组文库中的细菌酸性磷酸酶。

进行了4000多种带注释的细菌酸性磷酸酶的系统进化分析。我们的分析使我们能够将这些酶分为以下三种类型：（1）与其他类型远相关的B类酸性磷酸酶；（2）C类酸性磷酸酶和（3）通用酸性磷酸酶（GAP）。尽管在包括已知病原体在内的有限细菌家族中发现了B类磷酸酶，但在居住于土壤，淡水和海洋环境的各种微生物中发现了C类酸性磷酸酶和GAP蛋白。作为分析的一部分，我们开发了三个配置文件，分别称为Pfr-B-Phos，Pfr-C-Phos和Pfr-GAP，以描述三组酸性磷酸酶。然后，将这些基于序列的配置文件用于扫描基因组和元基因组，以鉴定大量以前未知的酸性磷酸酶。这些配置文件还将数据库中标注为假设蛋白质的许多蛋白质鉴定为推定的酸性磷酸酶。验证这些在计算机模拟结果中，我们从基因组DNA克隆了编码候选酸性磷酸酶的基因，或者从宏基因组文库中回收了这些基因，或者从宏基因组数据中回收了基于蛋白质序列的体外合成基因。表达这些基因中的许多基因，然后对蛋白质进行酶促分析，进一步证实了使用我们的谱图进行序列相似性搜索可以成功鉴定出以前未知的酸性磷酸酶。