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.
Highlights
THE Transporter Classification (TC) SYSTEM: DESIGN AND RATIONALIZATIONIn 1995, Fleischmann et al [1] published the full genome sequence of a living organism, Haemophilus influenzae, the first time such a feat had been accomplished
Transporter Classification Database (TCDB) collaborates with many important databases, and shares cross-database links with them; these are available on the individual protein pages
Summarizing, we have developed and perfected novel tools suited for the analysis of transporters
Summary
THE TC SYSTEM: DESIGN AND RATIONALIZATIONIn 1995, Fleischmann et al [1] published the full genome sequence of a living organism, Haemophilus influenzae, the first time such a feat had been accomplished. Transporters in the TC Database (TCDB) are classified using a functional/phylogenetic five-tier system [4,5] as follows: N1.L1.N2.N3.N4, where N is a number and L is a letter: N1 is the class; L1 is the subclass; N2 is the family (sometimes a superfamily); N3 is the subfamily; (or family in the case of a superfamily) and N4 is the actual transport system. D252 Nucleic Acids Research, 2014, Vol 42, Database issue at the top levels for information about classes and families and descend to the deepest level about individual proteins.
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