Table 1.

Proteins with poor annotation are abundant among plant-specific proteins

	Plant-specific proteins	Arabidopsis proteins found in all protein sets	Whole Arabidopsis protein set*
Hypothetical protein	557 (14%)	12 (0.5%)	4,363 (15%)
Unknown proteins	3 (0.1%)	0 (0.0%)	26 (0.1%)
Expressed protein	1,457 (38%)	50 (2.0%)	6,683 (23%)
Total	2,017 (52%)	62 (2.5%)	11,072 (38%)
Total in class	3,848	2,436	28,581

Comparison of the number of proteins annotated as 'expressed protein', 'hypothetical protein' or 'unknown protein' in the list of plant-specific proteins, proteins conserved throughout the phylogeny and in the whole Arabidopsis proteome. Total number of protein sequences per category (percentage relative to the total in the class) are shown. *Although the Arabidopsis TIGR genome release v3.0 (2002) was used to make the classification (plant-specific or other groups) and for all the other data analysis in this study, the numbers in this table reflect the latest protein annotation available from TIGR (genome release v4.0, April 2003).