Database

db={"MSP_Prosper":[{"Protein_ID":"P62258","Cleavage_score":1},{"Protein_ID":"P77124","Cleavage_score":1},{"Protein_ID":"P33111","Cleavage_score":0.2}],"Uniprot_New_Entries":[{"Uniprot_AC":"P11234P33245P62258P71993","Min_Max_Of_the_Ft_chain":"sometime","Uniprot_ID":"test"}]}

Query

db.MSP_Prosper.aggregate([{$match:{Cleavage_score:{$gte:0.7}}},{$lookup:{from:"Uniprot_New_Entries",let:{"order_item":"$Protein_ID"},pipeline:[{$match:{$expr:{$regexMatch:{input:"$Uniprot_AC",regex:"$$order_item"}}}},{$project:{_id:0,test:"$$order_item",date:{name:"$Uniprot_ID",date:"$Min_Max_Of_the_Ft_chain"}}},],as:"cleavage_sites"}}])

Result