Clue: Well over 25% of yakitori is protein (4)
Answer: SOYA
Explanation: Definition: protein
 SO(well/extremely, as in "he was well/so out of it") **placed above**(over, in a down clue) **1st 2 out of 8 letters of**(25% of) "yakitori".
Defn: … derived from the beans of the same name.