Search the NMPDR Database
BLAST or ScanGenesSubsystemsOrganisms
- Keyword search: Type one or more keywords into the box and click go. Keywords can include gene IDs (
gi|14247351), gene names (dnaK), EC numbers (2.7.6.3), genus (Vibrio), species (vulnificus), and words contained in subsystem names (transport), functional assignments (phosphoglycerate), and subsystem classes (membrane). You may also use attributes like iedb, virulence, and essential. A list of protein encoding genes that match all of the keywords will be returned. (more help >>)
To search for genes matching only some of the keywords, surround the optional words with parentheses. For example, 2.7.6.3 4.1.2.25 would match all bifunctional genes associated with both EC numbers 2.7.6.3 and 4.1.2.25, while (2.7.6.3) (4.1.2.25) would match the bifunctional genes as well as all single function genes with either of those EC numbers. Use a minus sign to exclude genes matching a particular keyword. For example, Vibrio -hypothetical would match all Vibrio genes except those marked hypothetical.
Finally, you can use quotes to ensure the keywords appear in the proper order. For example, a search of Campylobacter coli RM2228 for membrane protein will match all genes with the words membrane and protein anywhere in the annotation. In particular, it will match fig|306254.1.peg.1000 Ferric uptake regulation protein FUR, which is small transcription factor that belongs to a subsystem in the membrane transport group. To exclude this gene and others like it, you would instead search for "membrane protein", which will only match genes that encode actual membrane proteins.
- Sequence search: Choose the BLAST or Scan link to search using a DNA or amino acid sequence as the query term. The sequence may be an exact gene or protein sequence (BLAST) or a degenerate motif (Scan).
- Advanced query form: Choose the Genes link to compose an advanced query with limits on genomes or subsystems.
- Subsystem search: Choose the Subsystems link to select a subsystem for browsing from a hierarchical list or to search for a gene within a chosen subsystem.
- Organism search: Choose the Organisms link to see the annotation status of any organism in the database and to search for a gene within the chosen genome.
