The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families.
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families.
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DOI：
10.1186/1471-2105-10-273
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发表时间：
2009-09-01
影响因子：
3
通讯作者：
Peracchi A
中科院分区：
文献类型：
--
作者：
Percudani R;Peracchi A
依赖于维生素B6的酶（特别是其代谢活性形式pyridoxal 5'-phosphate， PLP）与生物学和医学有很大的相关性，因为它们催化了多种主要涉及氨基酸底物的生化反应。尽管依赖plp的酶属于少数独立的进化谱系，但它们包含超过160种不同的催化功能，因此代表了分化进化的一个显著例子。这些酶的重要性和显著的多功能性，以及它们在功能分类上的困难，创造了一个关于它们的综合信息来源的需要。B6数据库包含记录的B6依赖活性和相关蛋白家族，定义为具有相同酶功能的单系序列组。一个或多个家族与121个已知序列的plp依赖性活性相关。隐马尔可夫模型（hmm）从家族序列中建立并纳入数据库。这些hmm可用于预测蛋白质序列基因组集中plp依赖性酶的功能分类。这里提供了这种分析的一个例子（对plp依赖性酶的人类基因编码的普查），而更多的可以通过数据库本身访问。B6数据库是一个关于一组重要酶的生物化学和分子信息的管理库。这些信息具有一定的逻辑组织，可用于计算分析，为b6依赖性酶的鉴定、分类和比较分析提供了关键资源。
Enzymes that depend on vitamin B6 (and in particular on its metabolically active form, pyridoxal 5'-phosphate, PLP) are of great relevance to biology and medicine, as they catalyze a wide variety of biochemical reactions mainly involving amino acid substrates. Although PLP-dependent enzymes belong to a small number of independent evolutionary lineages, they encompass more than 160 distinct catalytic functions, thus representing a striking example of divergent evolution. The importance and remarkable versatility of these enzymes, as well as the difficulties in their functional classification, create a need for an integrated source of information about them. The B6 database contains documented B6-dependent activities and the relevant protein families, defined as monophyletic groups of sequences possessing the same enzymatic function. One or more families were associated to each of 121 PLP-dependent activities with known sequences. Hidden Markov models (HMMs) were built from family alignments and incorporated in the database. These HMMs can be used for the functional classification of PLP-dependent enzymes in genomic sets of predicted protein sequences. An example of such analyses (a census of human genes coding for PLP-dependent enzymes) is provided here, whereas many more are accessible through the database itself. The B6 database is a curated repository of biochemical and molecular information about an important group of enzymes. This information is logically organized and available for computational analyses, providing a key resource for the identification, classification and comparative analysis of B6-dependent enzymes.
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DOI：
10.1016/j.bbrc.2006.09.112
发表时间：
2006-12-01
影响因子：
3.1
作者：
Donini, Stefano;Percudani, Riccardo;Peracchi, Alessio
通讯作者：
Peracchi, Alessio
DOI：
10.1016/s0167-4781(97)00106-1
发表时间：
1997-09-12
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION
影响因子：
--
作者：
Koguchi, K;Kobayashi, S;Hayashi, S
通讯作者：
Hayashi, S
影响因子：
3.5
作者：
Koch, KA;Capitani, G;Kirsch, JF
通讯作者：
Kirsch, JF
影响因子：
5.8
作者：
Söding, J
通讯作者：
Söding, J
DOI：
10.1016/s0969-2126(00)00085-x
发表时间：
2000-01-15
期刊：
STRUCTURE WITH FOLDING & DESIGN
影响因子：
--
作者：
Schneider, G;Käck, H;Lindqvist, Y
通讯作者：
Lindqvist, Y