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TCDB specifications


Unique identifier OMICS_07177
Alternative name The Transporter Classification Database
Restrictions to use None
Data access File download, Browse
Maintained Yes


  • person_outline Milton H. Saier Jr

Publications for The Transporter Classification Database

TCDB citations


Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino Oligosaccharide Utilization

Front Microbiol
PMCID: 5928203
PMID: 29740413
DOI: 10.3389/fmicb.2018.00776

[…] ns with information from literature accessed via the PaperBLAST tool () and reference databases including SwissProt for characterized protein annotations (), KEGG for reference metabolic pathways (), TCDB for transporter classification () and CAZy for classification of Glycosyde Hydrolases (GHs) (). Orthologs were identified using BLAST-based protein similarity searches and gene neighborhood analy […]


Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia

Front Microbiol
PMCID: 5911502
PMID: 29713316
DOI: 10.3389/fmicb.2018.00738

[…] ted PFAM domains. AntiSMASH () was used to predict biosynthesis of secondary metabolites. Transmembrane helices in proteins were predicted with TMHMM. Transporter protein specificity was predicted by TCDB (). SignalP and SecretomeP were used to predict signal peptides and secreted proteins, respectively (; ). To predict the twin-arginine motif we utilized TatP server (). Autotransporter proteins w […]


Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi

Sci Rep
PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] parative genomics approach enabled us to annotate these genes as TPP transporters. We first carried out the BLASTP search of all those hypothetical proteins versus all the transporter proteins in the TCDB (Transporter Classification Database) to identify the homologs to known and predicted transporters in the TCDB. The parameters set to consider homologous genes were as follows: E-value ≤10−5, sim […]


Bioinformatic characterization of the Anoctamin Superfamily of Ca2+ activated ion channels and lipid scramblases

PLoS One
PMCID: 5868767
PMID: 29579047
DOI: 10.1371/journal.pone.0192851
call_split See protocol

[…] All sequences from a reference family in TCDB were automatically extracted with the program extractFamily, which connects to TCDB, downloads the sequences and returns them in one of several formats (i.e. fasta, column or blast database). The […]


A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

Front Microbiol
PMCID: 5876298
PMID: 29628913
DOI: 10.3389/fmicb.2018.00520

[…] , DB; Cantarel et al., ), Clusters of Orthologous Groups of proteins (COGs, DB; Tatusov et al., ), MetaCyc (DB; Caspi et al., ), and RefSeq (DB; Pruitt et al., ), Transporter Classification Database (TCDB, DB; Saier et al., ), MetaPathways (ST; Konwar et al., ), RAxML version 8 (ST; Stamatakis, ), and Circos (ST; Krzywinski et al., ) for analyzing metagenomics, metatranscriptomics, and single geno […]


Genome analysis reveals evolutionary mechanisms of adaptation in systemic dimorphic fungi

Sci Rep
PMCID: 5852033
PMID: 29540755
DOI: 10.1038/s41598-018-22816-6

[…] FunK1 kinases were further identified using HMMER3. We further annotated carbohydrate active enzymes, peptidases, and transporter families using the CAZY version 07-15-2016, MEROPS version 9.12, and TCDB version 01-05-2017 databases, respectively. Proteins were searched against their corresponding databases using BLAST, with minimum e-values of 1 × 10−80 for CAZY, 1 × 10−20 for MEROPS, and 1 × 10 […]

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TCDB institution(s)
Department of Molecular Biology, University of California, San Diego, CA, USA; Department of Medical Sciences, Boston University School of Medicine, Boston, MA, USA; Department of Biological Engineering, School of Life Sciences, Beijing Institute of Technology, Beijing, China; Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
TCDB funding source(s)
National Institutes of Health [GM 077402]

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