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Tutorial: The Search TCDB Box


  • The TCDB search box supports multiple types of queries. For example, you can type in a family name, a species name, a TCID number (TC#) or functional keyword(s) to retrieve all transport systems whose annotations matched the query. TCDB organizes the search results in different categories, including Systems, Families, PDB structures, and References.

    In this tutorial, we shall submit 3 different queries to TCDB using keywords that indicate: 1) a family name, 2) a species name, and 3) a protein accession.

1. Submitting a family name as keyword:

  • In this example we will search TCDB for all systems related to the family name "SWEET". Type the keyword in the search box as shown below in Figure 1. For a description of the different sections in the TCDB homepage, please follow our tutorial The TCDB homepage.

    Search SWEET
    Figure 1. Search TCDB for all entries whose annotations match the keyword "SWEET". The input box is located on the upper right corner. If you can click on the question mark ("?"), you will be redirected to the appropriate question in our list of FAQ that includes a link to this tutorial.

    The results of the search are presented in Figure 2 below.

    Search results
    Figure 2. Search results after typing "SWEET" into the search box (Figure 1). We are interested in the link "Families" (red dashed box).

    The results page shows the number of systems, families, 3D structures and references associated with the keyword "SWEET". Note that this search is performed on the annotated information for families and systems, so the search will not only return systems within the SWEET family, but any other system where the word "SWEET" is found. For example, it will include systems whose annotations contain strings such us "sweet-tasting" or "sweeter than" (TC# 1.C.45.4.2) or "... architecture similar to that observed for SWEET family members ..." (TC# 9.B.191.1.8).

    In this example, we are interested in systems that belong to the SWEET family, so click on the "Families" link (dashed red box in Figure 2) to get the desired information. The result is shown in Figure 3.

    Family result
    Figure 3. Families associated with the keyword SWEET. The TCID of the family "Sweet" is enclosed in the red dashed box.

    By clicking on the TCID 2.A.123, you will be taken to the page with the definition of the family including all curated annotations, a link to access all systems available in the family, and the corresponding references to the scientific literature.

2. Submitting a species name as query:

  • Before we start, please note that currently this is not a formal taxonomic browser implemented in TCDB. Instead, TCDB scans the annotations of all families and systems in TCDB for that particular species name, which may not be the functionality you are expecting. However, we are working on implementing a taxonomic browser for TCDB based on the NCBI taxonomy database.

    Now, continuing with our example, we will query TCDB for all systems associated with the keyword "Salmonella". First, we type this keyword in the TCDB search box as illustrated in Figure 4.

    Keyword Salmonella

    Figure 4. Searching TCDB for all entries related to "Salmonella".

    The results are shown in Figure 5. Currently, there are 126 systems (dashed red box) that include the word "Salmonella" in their annotations, one cluster (subfamily), 23 structures and 156 references.

    Table of Contents
    Figure 5. Results after querying TCDB with the keyword "Salmonella". We are interested in the systems matching the query keyword (red dashed box).

    However, please note that these results would include systems that mention Salmonella indirectly, but actually belong to a different organism. For example, the system 1.A.16.2.1 is from the archaeon Thermofilum pendens but its annotation includes the sentence: "... Structure/function studies including the x-ray structure of the Salmonella orthologue have been reported ..." As previously mentioned, we are working on implementing an organismal navigator for TCDB based on the NCBI taxonomy databse; we shall update this tutorial when it is ready.

    Click on the Systems link (dashed red box in Figure 5) to see the results and browse through the systems that include "Salmonella" in their annotations (Figure 6).

    Systems from Salmonella
    Figure 6. Systems associated with the keyword "Salmonella". Red dashed boxes indicate where the keyword was found.

    To determine which systems in the results page are of interest to you, you can search for the keyword "Salmonella" in the results page (red dashed boxes in Figure 6) and then click on the specific systems you are interested in to get more details.

3. Submitting a protein accession number as query:

  • In this example, we will query TCDB using the UniProt protein accession F7IWF6 as keyword. The corresponding UniProt entry for this protein is shown in Figure 7.

    UniProt page

    Figure 7. Uniprot entry for accession F7IWF6 (red dashed box).

    Enter the accession in the TCDB search box as illustrated in Figures 1 and 4, and press enter. The results are shown in Figure 8.

    TC system entry page

    Figure 8. Results of querying TCDB with the protein accession: F7IWF6 (red dashed box).

    If the protein exists in TCDB, the query will directly return the page with all the annotations in TCDB for that protein. In this case, the query accession belongs to system 1.B.38.1.4. For a detailed explanation of the organization and functionality of the page in Figure 8, please follow our tutorial: The system component entry page.

    Oftentimes, the particular accession you are interested in may not be available in TCDB. This is expected because TCDB is, by design, a database of representative transport systems, and was never meant to contain all transporters that have been sequenced to date. However, you can find the closest homolog in TCDB by blasting the sequence of your transporter against all proteins in TCDB. TCDB has a specific blast page for this purpose, and you can also check the corresponding tutorial to learn how to use it.

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