sVIETNAM NATIONAL UNIVERSITY – HO CHI MINH

CITY INTERNATIONAL UNIVERSITY

BIOINFORMATICS - ASSIGNMENT 3

Lecture: Prof. Nguyen Minh Thanh

Class: Thursday Morning

Date of submission: Wed 22/3/2023

Full name: Nguyen Ngoc Van - BTBTIU19143 (25%)

Le Thi Thanh Tinh - BTBTIU21260 (25%)

Nguyen Thi Tien - BTBTIU21259 (25%)

Do Bao Tran - BTBTIU21167 (25%)

Question 1: In the NCBI database, retrieve the protein sequences for mouse
hypoxanthine phosphoribosyl transferase (HPRT) (NP_038584) and the same enzyme
from E. coli (CAD7366119) in FASTA format.

- Mouse hypoxanthine phosphoribosyl transferase (HPRT) (NP_038584) in

FASTA format
> hypoxanthine-guanine phosphoribosyltransferase [Mus musculus]
MPTRSPSVVISDDEPGYDLDLFCIPNHYAEDLEKVFIPHGLIMDRTERLARDVM
KEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSYCN
DQSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVKQYSPKMVKV
ASLLVKRTSRSVGYRPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGK
AKYKA

- The same enzyme from E. coli (CAD7366119) in FASTA format.

>NP_038584.2 hypoxanthine-guanine phosphoribosyltransferase [Mus musculus]
MPTRSPSVVISDDEPGYDLDLFCIPNHYAEDLEKVFIPHGLIMDRTERLARDVM
KEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSYCN
DQSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVKQYSPKMVKV
ASLLVKRTSRSVGYRPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGK
AKYKA

a. Perform a local alignment of the two sequences using Water in EMBL-EBI

EMBOSS
(https://www.ebi.ac.uk/Tools/psa/). Report identity, similarity & gaps (ratio &
percent)
 Ratio Percent (%)

Identity 60/175 34.3

Similarity 95/175 54.3

Gaps 13/175 7.4

b. Perform a global alignment of the two sequences using Needle in EMBL-EBI

EMBOSS (https://www.ebi.ac.uk/Tools/psa/). Report identity, similarity & gaps
(ratio & percent) then compare the results with those from the local alignment
(length, identity, similarity, gap, score).
 Ratio Percent (%)

Identity 63/227 27.8

Similarity 101/227 44.5

Gaps 54/227 23.8

Compare global alignment and local alignment

Global alignment Local alignment

Length 227 175

Identity ((ratio (percent)) 63/227 (27.8%) 60/175 (34.4%)

Similarity ((ratio (percent)) 101/227 (44.5%) 95/175 (54.3%)

Gap ((ratio (percent)) 54/227 (23.8%) 13/175(7.4%)

Score 250.5 256.5

c. Change the default gap open and extend from “10/0.5” to “5/0.1” and run the
local alignment. Report identity, similarity & gaps (ratio & percent), then
compare the results with previous local alignment (gap opening & gap extension
based on the alignment output of each set-up).
Gap opening: 10 → 5
Gap extension: 0.5 → 0.11
Identity ((ratio (percent)): 73/206 (35.4%)
Similarity ((ratio (percent)): 107/206 (51.9%)
Gaps ((ratio (percent)): 45/206 (21.8%)

● Compare with the previous local alignment

10/0.5 (previous) 5/0.1 (adjusted parameter)

Gaps 13/175 (7.4%) 45/206 (21.8%)

Default parameter

Adjusted parameters

- Gaps: There are more gap openings in the result of adjusted parameters than
the result of default parameters. In general, the results of adjusted parameters
have larger gap extensions than the default parameters.
Question 2: In the NCBI database, retrieve the protein sequences for human
(NP_000509),
Pan troglodytes (XP_508242), Canis familiaris (NP_001257813), Mus musculus
(NP_058652), Gallus gallus (NP_990820). Perform multiple sequence alignment for
these sequences (https://www.ebi.ac.uk/Tools/msa/clustalo/) and investigate the first
60 residues of the alignment. Answer the following questions:

a. What is the identity (%)?

% identity = (identical matches/total length) x 100 = (34/60) x 100 = 56.67%

b. What is the similarity (%)?

% similarity = ((identical matches + strongly similar properties)/total length) x 100
= ((34+8)/60) x 100 = 70%

c. What is the gaps (%)?

% gaps = (0/60) x 100 = 0%

d. Which species have 100% identity when comparing the first 60 residues?

NP_000509.1 hemoglobin subunit beta [Homo sapiens]

XP_508242.1 hemoglobin subunit beta [Pan troglodytes]
When comparing the first 60 residues, the sequence of hemoglobin subunit beta from
Homo sapiens is 100% identical with Pan troglodytes.