LectomeXplore,是 UniLectin 的更新版本,用于基于新的凝集素分类发现糖结合蛋白。

LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification.

机构信息

Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.

Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.

出版信息

Nucleic Acids Res. 2021 Jan 8;49(D1):D1548-D1554. doi: 10.1093/nar/gkaa1019.

Abstract

Lectins are non-covalent glycan-binding proteins mediating cellular interactions but their annotation in newly sequenced organisms is lacking. The limited size of functional domains and the low level of sequence similarity challenge usual bioinformatics tools. The identification of lectin domains in proteomes requires the manual curation of sequence alignments based on structural folds. A new lectin classification is proposed. It is built on three levels: (i) 35 lectin domain folds, (ii) 109 classes of lectins sharing at least 20% sequence similarity and (iii) 350 families of lectins sharing at least 70% sequence similarity. This information is compiled in the UniLectin platform that includes the previously described UniLectin3D database of curated lectin 3D structures. Since its first release, UniLectin3D has been updated with 485 additional 3D structures. The database is now complemented by two additional modules: PropLec containing predicted β-propeller lectins and LectomeXplore including predicted lectins from sequences of the NBCI-nr and UniProt for every curated lectin class. UniLectin is accessible at https://www.unilectin.eu/.

摘要

凝集素是非共价结合糖蛋白,介导细胞间相互作用,但在新测序的生物体中缺乏其注释。功能域的有限大小和序列相似性低挑战了常用的生物信息学工具。在蛋白质组中识别凝集素结构域需要基于结构折叠手动整理序列比对。提出了一种新的凝集素分类。它基于三个层次构建:(i)35 种凝集素结构域折叠,(ii)共享至少 20%序列相似性的 109 种凝集素类,(iii)共享至少 70%序列相似性的 350 种凝集素家族。该信息编排在 UniLectin 平台中,该平台包括之前描述的 UniLectin3D 经过精心整理的凝集素 3D 结构数据库。自首次发布以来,UniLectin3D 已更新了 485 个额外的 3D 结构。该数据库现在由两个附加模块补充:包含预测的β-螺旋桨凝集素的 PropLec 和包括从 NBCI-nr 和 UniProt 中每个经过精心整理的凝集素类的序列中预测的凝集素的 LectomeXplore。UniLectin 可在 https://www.unilectin.eu/ 访问。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7b93/7778903/303255280f8f/gkaa1019fig1.jpg

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