A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana.
A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana.
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DOI：
10.1155/2009/820381
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发表时间：
2009
影响因子：
--
通讯作者：
Gayler KR
中科院分区：
文献类型：
--
作者：
Gunawardana D;Likic VA;Gayler KR
营养素酶是一个具有保守的共同反应机制的超家族，其提供了水解广谱代谢物的能力。我们使用隐马尔可夫模型的基础上，从PFAM和PROSITE数据库的NUCLEAR序列，以确定NUCLEAR水解酶编码的拟南芥基因组。共鉴定出25种核酸水解酶，通过序列比对将其分为11个家族。内含子相位在每个家庭中是惊人的保守。系统发育分析表明，所有的多成员家庭形成单系簇。用MEME基序分析算法鉴定保守的家族序列基序。一个基序（基序4）被发现在三个不同的家庭。所有含有基序4的蛋白质都对含有ADP部分的底物表现出一定程度的偏好。我们的结论是，HMM模型为基础的基因组扫描和MEME基序分析，分别可以显着提高识别和分配功能的新成员的这个机制多样的蛋白质超家族。
Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily.
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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
4.9
作者：
Munoz, Francisco Jose;Baroja-Fernandez, Edurne;Pozueta-Romero, Javier
通讯作者：
Pozueta-Romero, Javier
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2.9
作者：
ABEYGUNAWARDANA, C;WEBER, DJ;MILDVAN, AS
通讯作者：
MILDVAN, AS
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14.9
作者：
Huala, E;Dickerman, AW;Rhee, SY
通讯作者：
Rhee, SY
影响因子：
2.9
作者：
Harris, TK;Wu, G;Mildvan, AS
通讯作者：
Mildvan, AS