Two examples of yeast complexes with predicted domain-domain interactions and MIPS physical protein interactions. The black arrows are predicted DDIs, the grey arrows are DDIs in iPfam, and the red arrows are PPIs from DIP. (a) SCF (Skp1-Cdc53-F-box protein) complexes. Cdc53 controls G1/S transition. Cdc34 is E2 ubiquitin-conjugating enzyme. Skp1 is kinetochore protein complex Cbf3, subunit D. Cdc4, Met30, and Grr1 are the F-box proteins. (b) Pyruvate dehydrogenase complexes. Pdb1 is pyruvate dehydrogenase (lipoamide) beta chain precursor, Pda1 is pyruvate dehydrogenase (lipoamide) alpha chain precursor, Lpd1 is dihydrolipoamide dehydrogenase precursor, Pdx1 is pyruvate dehydrogenase complex protein X, and Lat1 is dihydrolipoamide S-acetyltransferase. For details, see the main text.