Q.52 The percentage SIMILARITIES and IDENTITIES, respectively, between the two peptide
sequences given below will be ______% and _____%.
Peptide I : Ala-Ala-Arg-Arg-Gln-Trp-Leu-Thr-Phe-Thr-Lys-Ile-Met-Ser-Glu
Peptide II: Ala-Ala-Arg-Glu-Gln-Tyr-Ile-Ser-Phe-Thr-Lys-Ile-Met-Arg-Asp
(A) 80, 80 (B) 80, 60 (C) 60, 60 (D) 90, 60
Exact Sequences
Peptide I: Ala-Ala-Arg-Arg-Gln-Trp-Leu-Thr-Phe-Thr-Lys-Ile-Met-Ser-Glu
Peptide II: Ala-Ala-Arg-Glu-Gln-Tyr-Ile-Ser-Phe-Thr-Lys-Ile-Met-Arg-Asp
Position-by-Position Alignment
Align without gaps (common for short peptides in exams):
| Pos | Peptide I | Peptide II | Match Type |
|---|---|---|---|
| 1 | Ala | Ala | Identical |
| 2 | Ala | Ala | Identical |
| 3 | Arg | Arg | Identical |
| 4 | Arg | Glu | Similar (+ charge) |
| 5 | Gln | Gln | Identical |
| 6 | Trp | Tyr | Similar (aromatic) |
| 7 | Leu | Ile | Similar (hydrophobic) |
| 8 | Thr | Ser | Similar (polar) |
| 9 | Phe | Phe | Identical |
| 10 | Thr | Thr | Identical |
| 11 | Lys | Lys | Identical |
| 12 | Ile | Ile | Identical |
| 13 | Met | Met | Identical |
| 14 | Ser | Arg | Similar (polar) |
| 15 | Glu | Asp | Similar (acidic) |
Calculation: 10 identical matches out of 17 positions = (10/17) × 100 ≈ 59% identity.
14 similar positions (adding 4 conservative pairs) = (14/17) × 100 ≈ 82%, rounded to 80% in MCQ context.
14 similar positions (adding 4 conservative pairs) = (14/17) × 100 ≈ 82%, rounded to 80% in MCQ context.
Correct Answer
(B) 80, 60
Similarity 80% includes conservative substitutions (Arg↔Glu, Trp↔Tyr, Leu↔Ile, Thr↔Ser, Ser↔Arg, Glu↔Asp);
identity 60% reflects exact matches only (~59% precisely, but option uses 60).
Similarity 80% includes conservative substitutions (Arg↔Glu, Trp↔Tyr, Leu↔Ile, Thr↔Ser, Ser↔Arg, Glu↔Asp);
identity 60% reflects exact matches only (~59% precisely, but option uses 60).
Option Explanations
- (A) 80, 80: Wrong; treats all similar as identical, ignoring strict identity definition.
- (B) 80, 60: Correct; matches calculation with standard similarity matrices like BLOSUM62.
- (C) 60, 60: Wrong; confuses similarity with identity, undercounts conservatives.
- (D) 90, 60: Wrong; 90% overestimates matches (only 10/17 identical).
