The Transporter Classification Database (TCDB): 2021 update
Open accessAbstract
The Transporter Classification Database (TCDB; tcdb.org) is a freely accessible reference resource, which provides functional, structural, mechanistic, medical and biotechnological information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB) and now (October 1, 2020) consists of 20 653 proteins classified in 15 528 non-redundant transport systems with 1567 tabulated 3D structures, 18 336 reference citations describing 1536 transporter families, of which 26% are members of 82 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. This comprehensive update of the database contents and features include (i) adoption of a chemical ontology for substrates of transporters, (ii) inclusion of new superfamilies, (iii) a domain-based characterization of transporter families for the identification of new members as well as functional and evolutionary relationships between families, (iv) development of novel software to facilitate curation and use of the database, (v) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators and (vi) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers.
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Operon 36 encodes a 4.A.3 family PTS, a GH1 6-phospho-beta-glucosidase (bglA), and a gntR/yydK-like regulator.
“Likewise, operon 36 encodes a 4.A.3 family PTS [90] , a GH1 6-phospho-beta-glucosidase ( bgl A), and a gnt R/ yyd K-like regulator [Figure 6B].”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [90]
The citation is attached to the identification of the operon’s PTS as family 4.A.3, not to the later gene descriptions. The Introduction describes TCDB’s transporter-classification system, but searches for “4.A.3” and “phosphotransferase system PTS” found no passage in our copy identifying that family or discussing operon 36. (LLM, conf=0.72)
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- Authors
- Saier, M. H., Reddy, V. S., Moreno-Hagelsieb, G., Hendargo, K. J., Zhang, Y., Iddamsetty, V., Lam, K. J. K., Tian, N., Russum, S., Wang, J., & Medrano-Soto, A.
- Affiliations
- University of California San Diego (US)
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
- Corresponding author
- Saier, Milton H
- Medrano-Soto, Arturo
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-11-10
- Volume
- 49
- Issue
- D1
- Pages
- D461-D467
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC7778945
- OpenAlex
- W3099496190
- Cited by
- 467
- References
- 52
- Citations by year
- 2026: 72 · 2025: 112 · 2024: 118 · 2023: 81 · 2022: 61 · 2021: 23
- FWCI
- 14.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (GM077402)
- Topics
- Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- transporter classification, membrane transporters, transporter families, transport channels
- MeSH terms
- Protein Domains, Software, Substrate Specificity, Membrane Transport Proteins, Databases, Protein, Metagenomics
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