The transporter classification database

Abstract

The Transporter Classification Database (TCDB; http://www.tcdb.org) serves as a common reference point for transport protein research. The database contains more than 10,000 non-redundant proteins that represent all currently recognized families of transmembrane molecular transport systems. Proteins in TCDB are organized in a five level hierarchical system, where the first two levels are the class and subclass, the second two are the family and subfamily, and the last one is the transport system. Superfamilies that contain multiple families are included as hyperlinks to the five tier TC hierarchy. TCDB includes proteins from all types of living organisms and is the only transporter classification system that is both universal and recognized by the International Union of Biochemistry and Molecular Biology. It has been expanded by manual curation, contains extensive text descriptions providing structural, functional, mechanistic and evolutionary information, is supported by unique software and is interconnected to many other relevant databases. TCDB is of increasing usefulness to the international scientific community and can serve as a model for the expansion of database technologies. This manuscript describes an update of the database descriptions previously featured in NAR database issues.

Figure 1.

Current MySQL schema, displayed using Workbench 6.0 CE and showing the tables currently in TCDB’s database architecture. Each line in a table represents a column and displays which datatype (such as int, varchar, text, etc.) can be stored. Ten tables, which are not being used directly by TCDB but that have been used for maintenance tasks are not shown in the diagram: test, lang error, proteinold, tc2acc broke, tc2acc 1, flags, cflags, temp_tms, temp_preds and misc. A table that has a trifork (entity relationships) pointing toward it contains a column with explicit IDs from another table. The tables having no entity relationships are grouped on the left. The diagram contains four layers (left to right, and from top to bottom): the protein layer (green), the family layer (yellow), the ontology layer (blue) and the compounds layer (red).

Figure 2.

Growth of TCDB since August 2010. (A) Number of thousands of proteins (solid line); (B) number of hundreds of families (broken line); (C) number of superfamilies (dashed line). Numbers of proteins, families and superfamilies in TCDB as of 19 August 2013 were 9853, 778 and 49, respectively.