Searching NMPDR for a specific gene or protein

The initial search option is a keyword search against the text of the data records. Thus, it suffers from the same limitations as all keyword searches, such as misspellings and presence or absence of synonyms. Most genes and gene products can be described by several text strings. In this example, we will try to find an enzyme in the folate biosynthesis pathway that has several common names, but one specific EC number. The name of the gene that encodes the target enzyme has been named by several groups working on different organisms. Any of the following terms may be used to describe the target enzyme:

• 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
• hydroxymethylpterin pyrophosphokinase
• HPPK
• pyrophosphokinase
• sulD
• folK
• folate biosynthesis
• EC 2.7.6.3
• 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

Use these terms to try a few different keyword searches in the box below. Some of these terms will result in no hits, while some result in hundreds. Neither option is useful. As with all keyword searches, there is an appropriate subset of the above terms that will return the record of interest. If more than one term is entered, they are joined with "AND" by default.

Search results are presented in tables that list a maximum of 50 proteins per page. This default limit may be reset on the advanced search page. If the query term matches records of proteins in NMPDR core organisms, these are returned at the top of the list. For each result, the name of the organism, the ID andfunctional assignment of the protein, and buttons to open the record are presented. There are two environments for viewing the data record. The GBrowse button will open the generic genome browser, and the NMPDR button will open the protein context page.