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.

Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon

“…These include a sodium-acetate symporter (HLASF_0396) of the 2.A.21 family (Saier et al, 2014), two ADP-forming acetyl-CoA synthases (operon HLASF_0398-0400), one putative succinyl-CoA:acetate CoA-transferase (HLASF_2086), one pyruvate ferredoxin oxidoreductase (PFOR, HLASF_0492-0493), all enzymes of the TCA cycle, and a complete set of glyoxylate bypass enzymes (Figure 3). …”

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

“…Proteases, peptidases and protease inhibitors were predicted using Blastp against the Merops database (Rawlings et al, 2014). Transporters were identified by querying the genome against the TCDB (transporter classification database) (Saier et al, 2014) using Blastp (Altschul et al, 1990). Gene duplications were identified by running local Blastp using the proteins as both the subject and the query, where non-self hits with a similarity cutoff of 490% are considered duplicates.…”

A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform

“…Plant transporters facilitating tetrahydroxy borate anion [B(OH) 4 ] 2 efflux are classified in the 2.A.31 anion exchanger (AE) family, together with distant orthologs of mammalian and yeast carriers (Saier et al, 2014). Plant members of the AE family play important roles in tolerance to both high and low boron concentrations in soils (Takano et al, 2002;Nakagawa et al, 2007;Sutton et al, 2007;Pallotta et al, 2014).…”