Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins

Table 4 Search comparisons PPTdb and several general purpose genomic databases

Items	PPTdb	Entrez Gene	Uniprot	EuPathDB
Search term	nucleotide	nucleotide AND transporter AND Acanthamoeba castellanii str. Neff.	nucleotide transporter Acanthamoeba castellanii str. Neff.	nucleotide
^a Pre-search settings	Click A. castellanii str. Neff
	Set number of transmembrane domain: 1	–	–	Click AmoebaDB
	One-click potential transporters: checked			1135 genes for keyword search
Number of searched items	12 GO terms			76 genes with 1 transmembrane domain
	3 Prosite Patterns	No number of transmembrane domain filter	No number of transmembrane domain filter
	5 Pfams			^c0 genes for annotation with “transporter” as keyword
Number of Genes after searching	105	^b303	^b290	^c0/76

^aThere are several search combinations of each database, it is reasonable that different search combinations may lead to different search results. This demo demonstrates one search strategy of each database
^bNo transmembrane domain filter
^cThere is no specific column for putative transporter genes of EuPathDB. Using “transporter” as keyword is the most possible search action used by most users

ISSN: 1471-2105