▁to ▁occur ▁per ▁ 1 0 0 ▁am ino ▁ac ids , ▁sometimes ▁called ▁' a ▁P AM ▁unit ' ▁or ▁' a ▁P AM ' ▁of ▁time . ▁This ▁is ▁precisely ▁the ▁duration ▁of ▁mut ation ▁assumed ▁by ▁the ▁P AM 1 ▁matrix . ▁ ▁The ▁constant ▁ ▁is ▁used ▁to ▁control ▁the ▁proportion ▁of ▁am ino ▁ac ids ▁that ▁are ▁un changed . ▁By ▁using ▁only ▁align ments ▁of ▁prote ins ▁that ▁had ▁at ▁least ▁ 8 5 % ▁similarity , ▁it ▁could ▁be ▁reason ably ▁assumed ▁that ▁the ▁mut ations ▁observed ▁were ▁direct , ▁without ▁any ▁intermediate ▁states . ▁This ▁means ▁that ▁scaling ▁down ▁these ▁counts ▁by ▁a ▁common ▁factor ▁would ▁provide ▁an ▁accurate ▁estimate ▁of ▁the ▁mut ation ▁counts ▁had ▁the ▁similarity ▁been ▁closer ▁to ▁ 1 0 0 %. ▁It ▁also ▁means ▁that ▁the ▁number ▁of ▁mut ations ▁per ▁ 1 0 0 ▁am ino ▁ac ids , ▁the ▁ ▁in ▁P AM n ▁is ▁equal ▁to ▁the ▁number ▁of ▁mut ated ▁am ino ▁ac ids ▁per ▁ 1 0 0 ▁am ino ▁ac ids . ▁ ▁To ▁find ▁the ▁mut ation ▁matrix ▁for ▁the ▁P AM 1 ▁matrix , ▁the ▁requirement ▁that ▁ 9 9 % ▁of ▁the ▁am ino ▁ac ids ▁in ▁a ▁sequence ▁are ▁conser ved ▁is ▁im posed . ▁The ▁quantity ▁ ▁is ▁equal ▁to ▁the ▁number ▁of ▁conser ved ▁am ino ▁acid ▁ ▁units , ▁and ▁so ▁the ▁total ▁number ▁of ▁conser ved ▁am ino ▁ac ids ▁is ▁ ▁The ▁value ▁of ▁