Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models
Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models
复制标题
DOI：
10.1111/j.1742-4658.2010.07656.x
复制
发表时间：
2010-05-01
期刊：
影响因子：
5.4
通讯作者：
Persson, Bengt
中科院分区：
文献类型：
--
作者：
Kallberg, Yvonne;Oppermann, Udo;Persson, Bengt
短链脱氢酶/还原酶（SDR）超家族现在有超过47000个成员，其中大多数是远亲，在成对比较中通常具有20-30%的残基同一性，使得难以获得该超家族的概述。因此，我们已经开发了一个家庭分类系统，基于隐马尔可夫模型（HALGORY）。为此，我们确定了314个特别提款权家族，包括约31 900名成员。此外，约有9 700份特别提款权表格属于目前成员太少而无法建立有效障碍的家庭。在人类基因组中，我们发现了47个SDR家族，对应于82个基因。十三个家族存在于所有三个域中（真核生物、细菌和微生物），因此预期催化基本代谢过程。这些酶中的大多数是“扩展”类型，与早期的研究结果一致。大约一半的SDR家族仅在细菌中发现，其中“经典”SDR类型最为突出。基于HMM的分类被用作可持续和可扩展的命名系统的基础。
The short-chain dehydrogenase/reductase (SDR) superfamily now has over 47 000 members, most of which are distantly related, with typically 20-30% residue identity in pairwise comparisons, making it difficult to obtain an overview of this superfamily. We have therefore developed a family classification system, based upon hidden Markov models (HMMs). To this end, we have identified 314 SDR families, encompassing about 31 900 members. In addition, about 9700 SDR forms belong to families with too few members at present to establish valid HMMs. In the human genome, we find 47 SDR families, corresponding to 82 genes. Thirteen families are present in all three domains (Eukaryota, Bacteria, and Archaea), and are hence expected to catalyze fundamental metabolic processes. The majority of these enzymes are of the 'extended' type, in agreement with earlier findings. About half of the SDR families are only found among bacteria, where the 'classical' SDR type is most prominent. The HMM-based classification is used as a basis for a sustainable and expandable nomenclature system.