Tutorial: The TCDB homepage
About:
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Here you will find a description of the organization and functionality of the different components of the main TCDB homepage.
Anatomy of the homepage:
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The TCDB homepage consists mainly of 4 sections that warrant descriptions. The other three sections are self-explanatory. Figure 1 shows the different sections of the TCDB homepage with their respective components.
Figure 1. Components of the TCDB homepage. The page is organized in 4 main sections: A. Top menu bar. B. Software/tools. C. Quick access to data. D. References to TCDB publications.
Each section is described separately below.
A: The top menu bar section.
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This section (Figure 1A) covers the top menu bar, which includes the following five tabs:
The HOME tab This tab provides a quick shortcut link to the main TDCB homepage. The same happens if you click on the TCDB logo on the top left of the screen.
The CONTENTS tab
By clicking on this tab, a query is submitted to TCDB that returns the total number of systems, clusters (subfamilies), Families, Superfamilies, 3D structures and references in TCDB (see Figure 2). Each link in the table of contents shown in Figure 2 returns full lists of all the associated data.
Figure 2. TCDB contents table.The SUPERFAMILIES tab
This tab returns the list of all the superfamilies currently recognized in TCDB, their descriptions and their complete lists of member families (see Figure 3).
Figure 3. Current list of TC Superfamilies.The TC-SYSTEM tab
This tab links to a page describing the TC system and provides a complete fully-interactive map of the TC hierarchy with descriptions at the level of class, subclass and family (see Figure 4).
Figure 4. Description of the TC System. An interactive interface to navigate the TC system hierarchy is available (red dashed box).
The HELP tab
This tab links to the main TCDB help page, which provides links to our list of frequently asked questions (FAQ) and to a number of tutorials designed to maximize the benefit you get from TCDB.
Figure 5. The main TCDB help page.
B: The SOFTWARE/TOOLS section.
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This section (Figure 1B) provides links to (1) software tools that allow the extraction of homologous proteins and systems transporting specific substrates from TCDB, and perform different types of analysis on transport-related proteins; (2) links to downloadable relevant data, such as sequences and mappings among different types of identifiers that cover the entire content of the database. The links in this section are described below:
The BLAST and PSIBLAST links
These links lead to two html forms where users can submit a query sequence to search for homologous proteins in TCDB. The functionality of both pages is very similar and you can follow our TC-BLAST tutorial for step-by-step instructions to submit an example sequence.The SUBSTRATE SEARCH TOOL link
This link points to an html form where users can query TCDB for all systems involved in the transport of specific substrates. The search is based on the ChEBI ontology, which was adopted by TCDB. For a detailed step-by-step example on how to use this tool, follow our Substrate Search Tool tutorial.The TMS STATISTICS TOOL link
This link points to an html form where users can analyze full families for their characteristic distributions of protein lengths and numbers of TMSs. The results present frequencies and histograms, as well as the identity of each TC system that was counted.The BIO-TOOLS link
This link points to our biotools server, where we provide additional bioinformatic web services. The services we provide are divided into two categories: in-house tools created in the Saier lab and external tools relevant to the study of transport biology (Figure 6). All in-house tools have their own descriptions and help. We are not responsible for the maintenance, documentation and functionality of the external resource linked in our page, but we have tested them and find them useful.
Figure 6. The BIO-TOOLS server.The MAPPING FILES link
This link points to the page where users can download multiple files and tables from TCDB (Figure 7). For example, it is possible to download (1) all sequences in fasta format; (2) tab-delimited mapping tables between TCIDs and transporter substrates; (3) mappings between family TCIDs and their family definitions; (4) mappings of TCIDs of systems, subfamilies and families to their superfamilies; (5) mappings of TC systems to PDB accessions; and much more. Each link has a description of the information available for download. These links always provide the more current information because they execute scripts that directly extract the information from TCDB.
Figure 7. The BIO-TOOLS server.The TC-DOMS link
This link points to our collection of Hidden Markov Model profiles of the characteristic domains of each family (tcDoms) in TCDB (Figure 8). These domain profiles can be used to test the membership of a query protein to a family or to infer their functions. Visit the tcDoms page for a full description. All tcDoms profiles can be downloaded from this page and our MAPPING FILES page.
Figure 8. The tcDoms page.
C: The QUICK ACCESS section.
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This section (Figure 1C) contains several links to frequently requested data:
The STRUCTURE DATA link
This link points to a table listing all structures available in TCDB for each transport system. The table lists the TCID, the description of the system and the organism, and it provides links to the corresponding PDB and CATH entries for each PDB accession.The HUMAN TRANSPORTERS link
This link points to a page (Figure 9) with links to several types of transport related proteins in humans (i.e., annexins, ABC transporters, ATPases, calcium channels, potassium channels, sodium channels and solute carriers). Each link in this page generates tables listing all the human transporters of that particular type.
Figure 9. Human transporters.The TRANSPORTERS & DISEASES link
This link points to an html form where the user can query TCDB for all transport systems involved in a particular human disease, or alternatively, all transporters within a (sub)class or (sub)family involved in human diseases. For step-by-step instructions and and example on how to use this tool, follow our tutorial on transporters and human diseases.The PREDICTED EVOLUTIONARY PATHWAYS link
This link downloads a document with a description of how the transmembrane topology of transporter families evolved from a basic repeat unit. This information, known for a limited number of families, is updated with new families as more knowledge becomes available.
D: The references section.
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This section (Figure 1D) provides references to all the papers about TCDB published in the database issue of the journal Nucleic Acides Research. These papers provide the latest updates to TCDB contents, software tools, and published research. If you use TCDB for your research, please cite the most recent paper in this list.