The transport protein annotations listed in TransportDB 2.0 were generated using the Transporter Automated Annotation Pipeline (TransAAP), this annotation engine is predominately intended for prokaryotic organisms as eukaryotes require significantly more manual curation, however a number of eukaryotes are included in the database. These eukaryotes have been extensively manually curated. This pipeline predicts the complete complement of transport proteins in an organism from its genome by running a variety of searches including: Blastp searches (against the NCBI non-redundant database, the transporter classification database (TCDB) and TransportDB 2.0), HMMER3 searches (using Pfam HMMs and TIGRFAM HMMs relevant to membrane transport proteins) and COG searches, as well as other analyses such as hydropathy predictions using TMHMM. The results of these analyses are used to identify complete sets of putative transport proteins in each genome, classify them into protein families according to the TC classification system (tcdb.org), and provide predictions of their function/substrates.
Complete lists of the transporters for each organism are accessible from the autocompleting pull down search bar on the front page. Selecting an organism will open the organism’s transporter summary page, detailing the numbers of transport proteins of each transporter type and each transporter family encoded by the organism’s genome. Selecting the individual transporter family tabs will provide a detailed list of transporters with their predicted substrate(s) and links to individual protein pages, which contain protein sequences and annotation information. A search engine is set up under the “Search” button to search TransportDB 2.0 by transporter type, transporter family, specific individual protein or by substrate. Blastp searches for a protein sequence of interest can be performed against the TransportDB 2.0 database by selecting the “Blast” tab. The complete transporter complements of two or more different organisms can be compared by selecting the “Compare organisms” tab. This enables users to select any number of organisms of interest, or compare all bacteria/archaea/eukarya within the database.
TransportDB 2.0 is the latest iteration of the very popular TransportDB. The transporter annotations listed in both databases were generated using the Transporter Automated Annotation Pipeline (TransAAP). In TransportDB the annotations were subject to manual curation prior to entry. However, to keep pace with the exponentially increasing number of genome sequences in public databases, the TransAAP pipeline feeding TransportDB 2.0 is fully automated but integrates a combination of PHP and Perl scripts to drive a rigorous filtering of the candidates, using empirically-derived rules to more accurately predict membrane transport proteins and their substrates without the need for human intervention.
We will keep updating this site with the newly published genomes. If you have any suggestions, corrections, or comments on our site, please contact us.
When using the data listed in TransportDB or TransportDB2 please cite:
- Ren Q, Chen K, Paulsen IT. 2007. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 35:D274-279.
- Ren Q, Kang KH, Paulsen IT. 2004. TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res 32:D284-288.