▁needed ▁to ▁be ▁pick ▁to ▁produce ▁ 9 9 % ▁identity ▁after ▁mut ation ▁is ▁then ▁given ▁by ▁the ▁equation ▁ ▁This ▁ ▁value ▁can ▁then ▁be ▁used ▁in ▁the ▁mut ation ▁matrix ▁for ▁the ▁P AM 1 ▁matrix . ▁ ▁Const ruction ▁of ▁the ▁P AM n ▁matrices ▁ ▁The ▁Mark ov ▁chain ▁model ▁of ▁protein ▁mut ation ▁rel ates ▁the ▁mut ation ▁matrix ▁for ▁P AM n , ▁, ▁to ▁the ▁mut ation ▁matrix ▁for ▁the ▁P AM 1 ▁matrix , ▁ ▁by ▁the ▁simple ▁relationship ▁ ▁The ▁P AM n ▁matrix ▁is ▁constructed ▁from ▁the ▁ratio ▁of ▁the ▁probability ▁of ▁point ▁accepted ▁mut ations ▁replacing ▁the ▁th ▁am ino ▁acid ▁ ▁with ▁the ▁th ▁am ino ▁acid , ▁to ▁the ▁probability ▁of ▁these ▁am ino ▁ac ids ▁being ▁aligned ▁by ▁chance . ▁The ▁entries ▁of ▁the ▁P AM n ▁matrix ▁are ▁given ▁by ▁the ▁equation ▁ ▁Note ▁that ▁in ▁G us field ' s ▁book , ▁the ▁entries ▁ ▁and ▁ ▁are ▁related ▁to ▁the ▁probability ▁of ▁the ▁th ▁am ino ▁acid ▁mut ating ▁into ▁the ▁th ▁am ino ▁acid . ▁This ▁is ▁the ▁origin ▁of ▁the ▁different ▁equation ▁for ▁the ▁entries ▁of ▁the ▁P AM ▁matrices . ▁ ▁When ▁using ▁the ▁P AM n ▁matrix ▁to ▁score ▁an ▁alignment ▁of ▁two ▁prote ins , ▁the ▁following ▁assumption ▁is ▁made : ▁If ▁these ▁two ▁prote ins ▁are ▁related , ▁the ▁evolution ary ▁interval ▁separ ating ▁them ▁is ▁the ▁time ▁taken ▁for ▁ ▁point ▁accepted ▁mut ations ▁to ▁occur ▁per ▁