Table 2. The P. falciparum proteome.

Feature	Number	Per cent
Total predicted proteins	5,268
Hypothetical proteins	3,208	60.9
InterPro matches	2,650	52.8
Pfam matches	1,746	33.1
Gene Ontology
Process	1,301	24.7
Function	1,244	23.6
Component	2,412	45.8
Targeted to apicoplast	551	10.4
Targeted to mitochondrion	246	4.7
Structural features
Transmembrane domain(s)	1,631	31.0
Signal peptide	544	10.3
Signal anchor	367	7.0
Non-secretory protein	4,357	82.7

Of the apicoplast-targeted proteins, 126 were judged on the basis of experimental evidence or the predictions of multiple programs^61,158 to be localized to the apicoplast with high confidence. Predicted apicoplast localization for 425 other proteins is based on an analysis using only one method and is of lower confidence. Predicted mitochondrial localization was based upon BLASTP searches of S. cerevisiae mitochondrion-targeted proteins¹⁵⁹ and TargetP¹⁵⁸ and MitoProtll¹⁶⁰ predictions; 148 genes were judged to be targeted to the mitochondrion with a high or medium confidence level, and an additional 98 genes with a lower confidence of mitochondrial targeting. Other specialized searches used the following programs and databases: InterPro¹⁶¹; Pfam¹⁶²; Gene Ontology⁴²; transmembrane domains, TMHMM¹⁶³; signal peptides and signal anchors, SignalP-2.0¹⁶⁴.