Table 1.

Examples of previously uncharacterized yeast proteins with reliable models

ORF	residues	PDB code	residues	name	Percent sequence identity	Model accuracy	Conserved features
YDL117W	13–64	1lckA	65A–115A	P56-LCK SH3 domain	30 (24.5)	0.97	W31 conserved; other binding residues conserved or similar.
YCR033W	885–935	1idz	140–190	c-MYB DNA binding domain	21 (22.3)	0.99	N interacting with DNA is conserved; K’s replaced by R’s.
YNL181W	44–341	1fmcA	2A–215A	7-α-hydroxysteroid dehydrogenase	14 (25.5)	0.98	K163 conserved; Y159F.
YOR221C	124–368	1mla	87–296	malonyl-COA ACP transacylase	17 (23.7)	0.95	Active site residues S92, R117, and H201 are conserved.
YPL217C	63–182	1etu	5–145	elongation factor Tu (domain I)	22 (22.7)	0.86	GTP binding loops are similar. Conserved GKTTL motif.

These ORFs do not have clear similarity to any protein of known function according to the following sources (October 31, 1997): MIPS (http://www.mips.biochem.mpg.de/mips/yeast/index.html), Yeast Protein Database (http://quest7.proteome.com/YPDhome.html), genequiz (http://www.sander.ebi.ac.uk/genequiz), sacch3d (http://genome-www.stanford.edu/Sacch3D), pedant (http://pedant.mips.biochem.mpg.de/frishman/pedant.html), and pfam (27). The examples were selected partly by considering conservation of the functionally important residues (Conserved features). Thus, they have higher sequence similarity to known protein structures than most of the other previously uncharacterized yeast proteins. For each ORF and its corresponding template, the starting and ending residues of the matching regions are indicated. The number in parenthesis in the percent sequence identity column is the alignment significance score in nats (13). The overall model accuracy is given by p(GOOD/Q_SCORE). The complete list of 236 previously uncharacterized yeast proteins with reliable models is available at http://guitar.rockefeller.edu.