The Transporter Classification Database (TCDB)

摘要 转运蛋白催化分子进出细胞和细胞器。他们 实现细胞内稳态，对病原体和肿瘤的多药耐药性负责，以及， 当基因缺陷时，会导致数十种重要的人类遗传病。我们的实验室维护、更新 并改进了传送器分类数据库TcDB，其中存储了传送器 国际生物化学和分子联合会正式采用的分类(TC)系统 生物学(IUBMB)。Tcdb是国际上公认的、经过仔细注释的 分类并提供所有主要运输工具和运输相关蛋白的信息 生命的领域。它呈现了序列、生化、生理、病理、结构和 关于这些蛋白质及其组成的运输系统的进化数据。它使用了一个成功的 基于运输者类别、亚类、家族、亚家族、个体运输的分类系统 系统和组成蛋白。它还包括一个超级家族超链接。 在GM0077402的这次竞争性续订中，我们建议继续扩展、更新和 半自动Tcdb。我们的具体目标是：(1)通过特征和分类来提升Tcdb 蛋白质结构域及其拓扑结构、基序、重复单位、功能相互作用、选择性剪接 和翻译后修改，(2)通过实施用于数据输入的新管道来扩展TcdB 这将增加传输分集在Tcdb中的覆盖范围，同时更有效地描述 多分量传输系统的复杂性，(3)进入Tcdb传输器调制器，如 激活剂、抑制剂、药物和外源物质以及影响 转运体活动，同时生成一个本体来描述化学调节剂的影响， 将补充我们的底物本体，(4)结合到Tcdb合成孔/通道(TC 子类1.D)和载波(TC子类2.B)，(5)在传输之间引入Tcdb连接 和新陈代谢，(6)扩大我们的长期Tcdb可持续性计划。

ABSTRACT Transporters catalyze entry and exit of molecules into and out of cells and organelles. They achieve cellular homeostasis, are responsible for multidrug resistance in pathogens and tumors, and, when defective, cause dozens of important human genetic diseases. Our laboratory maintains, updates and improves the Transporter Classification Database, TCDB, which houses the Transporter Classification (TC) system, adopted officially by the International Union of Biochemistry and Molecular Biology (IUBMB). TCDB is the internationally acclaimed, carefully annotated, universal standard for classifying and providing information about transporters and transport-related proteins in all major domains of life. It presents sequence, biochemical, physiological, pathological, structural and evolutionary data about these proteins and the transport systems they comprise. It uses a successful system of classification based on transporter class, subclass, family, subfamily, individual transport system and constituent proteins. It also includes a superfamily hyperlink. In this competitive renewal of GM0077402, we propose to continue to expand, update, and semi-automate TCDB. Our specific aims are to (1) upgrade TCDB by characterizing and categorizing protein domains and their topologies, motifs, repeat units, functional interactions, alternative splicing and post-translational modifications, (2) expand TCDB by implementing novel pipelines for data entry that will increase the coverage of transport diversity in TCDB while describing more effectively the complexity of multicomponent transport systems, (3) enter into TCDB transporter modulators such as activators, inhibitors, drugs and xenobiotics as well as internal and external conditions that influence transporter activities, while generating an ontology to describe the effects of chemical modulators that will complement our substrate ontology, (4) incorporate into TCDB synthetic pores/channels (TC subclass 1.D), and carriers (TC subclass 2.B), (5) introduce into TCDB connections between transport and metabolism and (6) expand our plans for long-term TCDB sustainability.