Keyword Box

The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions of words, including vitamins, aldolase, and pyrophosphokinase. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene fig|171101.1.peg.269, a dual-role protein encoding gene for Streptococcus pneumoniae r6 that has 40 keywords.

FIG gene identifier	171101.1.peg.269
The aliases	15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8
All words in the functional role	Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine
The genome ID	171101.1
All words in the taxonomy	bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6
The subsystem names and classifications	folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
The EC number	2.7.6.3, 4.1.2.25
The subsystem role	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
Special Keywords	essential

Notes

• Some keywords appear twice.
• In the functional role, hyphenated words are stored in their full form (2-amino-4-hydroxy-6-hydroxymethyldihydropteridine) as well as broken up on the hyphen boundaries (amino hydroxy hydroxymethyldihydropteridine).
• Keywords are case-insensitive.
• Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data.
  • virulence, which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete.
  • essential, which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete.
  • iedb, which indicates that the gene is listed in the Immune Epitope Database

Advanced Keyword Searching

Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior using the following control characters.

char	Meaning	Example	Explanation of Example
-	negation	2.7.6.3 -firmicutes	search for all genes with EC number 2.7.6.3 that are not in firmicutes
()	optional	(2.7.6.3 4.1.2.25)	search for any gene with EC number 2.7.6.3 or 4.1.2.25
""	phrase	"folate biosynthesis"	search for all genes that participate in folate biosynthesis

Using Negation

It is illegal to use negation on all the keywords. For example, you can't do

   -hypothetical

to get all non-hypothetical proteins. You can trick the the keyword search a little by including a positive keyword for a broad category

   bacteria -hypothetical

which will return all non-hypothetical proteins for bacteria. This is not recommended, however, because you will get over a million results.

Queries that rely primarily on negation make the most sense when your result set is already restricted.