Q.64 The amino acid substitution matrices in decreasing order of stringency for comparing protein
sequences are
(A) PAM250, PAM120, PAM100
(B) PAM100, PAM120, PAM250
(C) PAM250, PAM100, PAM120
(D) PAM120, PAM250, PAM100
PAM (Point Accepted Mutation) matrices rank amino acid substitutions by evolutionary distance, with stringency decreasing as the number increases. The correct order from highest to lowest stringency is PAM100, PAM120, PAM250.
Correct Answer
The correct option is (B) PAM100, PAM120, PAM250. Lower PAM numbers indicate higher stringency for closely related sequences, as they penalize substitutions more harshly based on observed mutation frequencies extrapolated to shorter evolutionary times.
PAM Matrices Overview
PAM matrices derive from Margaret Dayhoff’s model, where 1 PAM unit equals 1% accepted amino acid change. Matrices like PAM100 (100 PAMs, ~100% changes but ~20% identity remaining) suit close homologs, while PAM250 handles distant ones (~80% changes).
Higher numbers allow more substitutions, reducing stringency for database searches with divergent proteins.
Options Explained
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(A) PAM250, PAM120, PAM100: Incorrect; starts with lowest stringency (PAM250 for distant sequences) instead of highest.
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(B) PAM100, PAM120, PAM250: Correct; progresses from high stringency (close relatives, PAM100) to low (distant, PAM250).
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(C) PAM250, PAM100, PAM120: Incorrect; mixes distant-first order, ignoring PAM100 > PAM120 progression.
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(D) PAM120, PAM250, PAM100: Incorrect; skips to low stringency mid-way and ends with highest, disrupting decreasing order.
| Option | Order | Stringency | Use Case | Correct? |
|---|---|---|---|---|
| A | PAM250 > PAM120 > PAM100 | Low to High | Distant to close | No |
| B | PAM100 > PAM120 > PAM250 | High to Low | Close to distant | Yes |
| C | PAM250 > PAM100 > PAM120 | Mixed | Inconsistent | No |
| D | PAM120 > PAM250 > PAM100 | Medium to Low to High | Inconsistent | No |
