CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models.
CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models.
复制标题
DOI：
10.1016/j.ibmb.2014.06.004
复制
发表时间：
2014-09
影响因子：
3.8
通讯作者：
Hamodrakas, Stavros J.
中科院分区：
文献类型：
--
作者：
Ioannidou, Zoi S.;Theodoropoulou, Margarita C.;Papandreou, Nikos C.;Willis, Judith H.;Hamodrakas, Stavros J.
关键词：
节肢动物的角质层是一个复合的、二分的系统，由包埋在蛋白质基质中的几丁质细丝组成。角质层的物理性质是由其两个主要组成部分，角质层蛋白（CP）和几丁质的结构和相互作用决定的。蛋白质基质主要由结构表皮蛋白组成。迄今为止已经描述的大多数结构蛋白属于CPR家族，并且它们通过保守的R&R区域（Rebers和Riddiford Consensus）鉴定。CPR家族的两个主要亚家族RR-1和RR-2也已从序列水平的保守性和与角质层类型的一些相关性中鉴定出来。最近，一些新的家庭，也包含特征保守区，已被描述。包HMMER v3.0 [http：//hmmer.janelia.org/]用于基于这些家族中的8个家族（CPF、CPAP 3、CPAP 1、CPCFC、CPLCA、CPLCG、CPLCW、Tweedle）的特征区域构建特征谱隐马尔可夫模型。简而言之，这些家族可以被描述为具有：CPF（具有44个氨基酸的保守区）; CPAP 1和CPAP-3（类似于围肌肽，分别具有1个和3个几丁质结合结构域）; CPCFC（2或3个C-x（5）-C重复）;以及五个低复杂性（LC）家族中的四个，每个家族具有特征结构域。使用这些模型，以及先前为CPR家族的两个主要亚家族RR-1和RR-2创建的模型，我们开发了CutProtFam-Pred，这是一种在线工具（http：//bioinformatics.biol.uoa.gr/CutProtFam-Pred），允许从蛋白质组或翻译的转录组查询序列，用于准确检测和分类推定的结构表皮蛋白。该工具已成功地应用于不同的节肢动物蛋白质组，包括甲壳类动物（蚤状水蚤）和螯形动物（二斑叶螨），但在这个分类距离只有CPR和CPAPs恢复。
The arthropod cuticle is a composite, bipartite system, made of chitin filaments embedded in a proteinaceous matrix. The physical properties of cuticle are determined by the structure and the interactions of its two major components, cuticular proteins (CPs) and chitin. The proteinaceous matrix consists mainly of structural cuticular proteins. The majority of the structural proteins that have been described to date belong to the CPR family, and they are identified by the conserved R&R region (Rebers and Riddiford Consensus). Two major subfamilies of the CPR family RR-1 and RR-2, have also been identified from conservation at sequence level and some correlation with the cuticle type. Recently, several novel families, also containing characteristic conserved regions, have been described. The package HMMER v3.0 [http://hmmer.janelia.org/] was used to build characteristic profile Hidden Markov Models based on the characteristic regions for 8 of these families, (CPF, CPAP3, CPAP1, CPCFC, CPLCA, CPLCG, CPLCW, Tweedle). In brief, these families can be described as having: CPF (a conserved region with 44 amino acids); CPAP1 and CPAP-3 (analogous to peritrophins, with 1 and 3 chitin-binding domains, respectively); CPCFC (2 or 3 C-x(5)-C repeats); and four of five low complexity (LC) families, each with characteristic domains. Using these models, as well as the models previously created for the two major subfamilies of the CPR family, RR-1 and RR-2, we developed CutProtFam-Pred, an on-line tool (http://bioinformatics.biol.uoa.gr/CutProtFam-Pred) that allows one to query sequences from proteomes or translated transcriptomes, for the accurate detection and classification of putative structural cuticular proteins. The tool has been applied successfully to diverse arthropod proteomes including a crustacean (Daphnia pulex) and a chelicerate (Tetranychus urticae), but at this taxonomic distance only CPRs and CPAPs were recovered.
登录
查看更多内容
影响因子：
3.8
作者：
Jasrapuria, Sinu;Arakane, Yasuyuki;Muthukrishnan, Subbaratnam
通讯作者：
Muthukrishnan, Subbaratnam
影响因子：
5.6
作者：
KROGH, A;BROWN, M;HAUSSLER, D
通讯作者：
HAUSSLER, D
影响因子：
3.8
作者：
Kucharski, R.;Maleszka, J.;Maleszka, R.
通讯作者：
Maleszka, R.
影响因子：
3.8
作者：
Andersen, SO
通讯作者：
Andersen, SO
影响因子：
4.4
作者：
Dittmer, Neal T.;Hiromasa, Yasuaki;Kanost, Michael R.
通讯作者：
Kanost, Michael R.