TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available. One can also compare the transporter system from different organisms or perform a blast search of a protein sequence against the transporter database.
Type of Material:
Database.
Recommended Uses:
This material could be used as a reference material for an in-class or homework assignment.
Technical Requirements:
Web access and browser.
Identify Major Learning Goals:
None stated. Using this database, students will be able to identify and compare the membrane proteins found in 365 different organisms, including bacteria, archaea, and eukaryota. Students will also be able to view 3D illustrations of membrane protein structures.
Target Student Population:
Upper level undergraduate or graduate students or intro genetics and biochem classes.
Prerequisite Knowledge or Skills:
Students should have a basic understanding of the roles and type of transmembrane proteins, as well as familiarity with transcription/translation. Basic background in biochemistry or cell biology would be helpful.
Content Quality
Rating:
Strengths:
The database contains a wealth of information in a condensed format
Students can quickly select an organism and view the types of membrane proteins present, broken down by category (e.g. ATP-dependent, ion channels, etc.)
For each transmembrane protein, students can access the protein and DNA sequences as well as any known protein substrates
Material is current and accurate--a very complete source for multiple organisms
Concerns:
The database does not provide any guidance as to what one can learn or do with this information, so the instructor would need to provide context.
The material was last updated in 2013 as of this review, therefore, may not be up-to-date
It is also not entirely clear how to get started--there are no obvious instructions for students when they first arrive at the site
Potential Effectiveness as a Teaching Tool
Rating:
Strengths:
Very complete set of data with multiple links to external sites
The database content is clearly categorized and easy to locate
After students search for membrane proteins in a particular organism, they can easily dive deeper in order to learn more about a specific protein
Concerns:
It would be difficult to develop assignments that students could interpret easily
There are no assignments already designed for this site
The database doens't provide any information about how students might be able to use, interpret or apply the information found here
It would need significant contextualization within an assignment or lecture
Ease of Use for Both Students and Faculty
Rating:
Strengths:
Searchable with many internal links
A good reference site
Easu to navigate
The database is easy to search and extensively linked for ease of use
Concerns:
The front page could use some clearer instructions for use by undergraduates
The website appears somewhat dated, and was last updated in 2013
There is no "start here" or welcome page to introduce students to the database/website and the resources therein
Creative Commons:
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