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，负责病原体和肿瘤中的多药耐药性，以及， 当有缺陷时，会导致数十种重要的人类遗传疾病。我们的实验室维护、更新 并改进了运输机分类数据库TCDB，该数据库包含运输机 国际生物化学和分子生物学联合会正式采用的分类（TC）系统 生物学（IUBMB）。TCDB是国际公认的、经过仔细注释的通用标准， 分类和提供有关转运蛋白和转运相关蛋白在所有主要 生活的领域。它提供了序列，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。它使用一个成功的 基于运输工具类、子类、族、亚科、个体运输工具的分类系统 系统和组成蛋白质。它还包括一个超家族超链接。 在GM 0077402的竞争性更新中，我们建议继续扩展、更新和 半自动TCDB。我们的具体目标是（1）通过特征化和分类来升级TCDB 蛋白质结构域及其拓扑结构，基序，重复单元，功能相互作用，选择性剪接 和翻译后修饰，（2）通过实现新的数据输入管道来扩展TCDB 这将增加TCDB中传输分集的覆盖范围，同时更有效地描述 多组分转运系统的复杂性，（3）进入TCDB转运蛋白调节剂，如 激活剂、抑制剂、药物和外源性物质以及影响 转运活动，同时生成一个本体来描述化学调节剂的作用， 将补充我们的基质本体，（4）纳入TCDB合成孔/通道（TC 子类1.D）和载波（TC子类2.B），（5）引入到传输之间的TCDB连接中 和新陈代谢，以及（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.