在氨基酸水平上，蒙古黄芪异黄酮合成酶与大豆、鹰嘴豆、豌豆、刺甘草异黄酮合成酶的氨基酸序列分别有80％、83％、79％、83％的相同性和88％、89％、87％、88％的相似性。
Hsiao had 80%, 83%, 79%, 83% identity and 88%, 89%, 87%, 88% similarity with Glycin max, Cicer arietinum, Pisum sativum and Glycyrrhiza echinata respectively.
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