TCDB: the Transporter Classification Database for membrane transport protein analyses and information

By Milton H. Saier Jr., Can V. Tran, Ravi D. Barabote. Nucleic Acids Res., 2005

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The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10 000 references, encompassing ∼3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at . The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.

Subfields: Biochemistry, Molecular Biology, Oncology

View Paper: https://www.semanticscholar.org/paper/6eff868c9d023597cbf73c33fa39e2a4f540e672

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Citations in the corpus

Prediction of the human membrane proteome (2010, background): “A set of membrane-related protein classes were obtained from web-based sources with classiﬁcations for potential G-protein-coupled receptors (GPCRs) [30], CD markers [30], transporters [32], and voltage-gated ion channels [33].”
The Transporter Classification Database: recent advances (2008, background): “Since our last description of TCDB (3), this database has expanded with the introduction of six new subclasses (increase of 33%), 143 novel families (increase of 34%), 2009 novel proteins (increase of 67%) and 167 novel subfamilies in the five largest superfamilies (increase of 30%).”
EcoCyc: fusing model organism databases with systems biology (2012, methodology): “In doing so, we have taken into account the prokaryotic protein naming guidelines developed by UniProt and also the International Union of Biochemistry and Molecular Biology (IUBMB)-approved classiﬁcation system for membrane transport proteins known as the Transporter Classiﬁcation system (18).”
The Transporter Classification Database (TCDB): 2021 update (2020, background): “In June 2001, the International Union of Biochemistry and Molecular Biology (IUBMB) formally adopted the Transporter Classification (TC) system as the only internationally recognized system for the organization of transport protein information derived from all organisms in the Earth’s biosphere (6,7”
Siderophore-Based Iron Acquisition and Pathogen Control (2007, background): “The cellular import of Fe(II) that is reductively released from iron-siderophore complexes is mediated mainly by the high-affinity uptake system Fet3p-Ftr1p (306, 310), which is the prototype of the newly classified oxidase-dependent Fe(II) transporter family as part of the iron/lead transporter sup”
A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies* (2008, neutral): “TCDB, Transporter Classification Database; DBD, DNA-binding domain.”
The Transporter Classification Database (TCDB): recent advances (2015, methodology): “Earlier versions of the TC database (TCDB) have been described in previous publications in Nucleic Acids Research (7,9,10).”
Network-based prediction of human tissue-specific metabolism (2008, neutral): “(HMTD) and from the Transport Classification Databas”
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels (2006, background): “A total of 71 659 transport proteins and 4790 outer membrane channels have been annotated and assigned to 183 families according to the TC classification system (1,6).”
Learning classifiers from only positive and unlabeled data (2008, background): “Consider the database that we are associated with, which is called TCDB [15].”
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea (2011, background): “ABC-transporters utilizing ATP hydrolysis to provide energy for transport [123] have a conserved architecture of one nucleotide binding fold (NBF) and six transmembrane-spanning helices (TMD) in different arrangements (Table 5).”