BT203IU Bioinformatics

Assignment 4

Protein localization & Prediction of protein structure

Due date: 20:00, 2 Dec. 2019

(Submission via email is acceptable)

Question 1: Performing Phobius for the following protein identifier, whether they have trans-
membrane segments if so specify how many are present and their position (the starting and ending
amino acids). Whether they have a signal peptide if so what are the starting and ending amino acids
of N-region, H-region and C-region. Prepare the results as a table.

a. Q6IWH7
b. P0C9J4
c. P14009
d. Q43495
e. P50927

Question 2: Performing ProtParam for the accession number P29139. Report the following
parameters:

a. Number of amino acids

b. Molecular weight
c. Theoretical pI
d. Total number of negatively charged residues (Asp + Glu)
e. Total number of positively charged residues (Arg + Lys)
f. Extinction coefficient
g. In vivo half-life
h. The instability index (II)
i. Is this protein acidic or basic and stable or unstable?

Question 3: Performing Comparative modelling for P01326 (https://swissmodel.expasy.org/)

a. What can you say about the structural similarity of top-four templates? What ligands are present
in each of them?
b. Build model with a template 1efe.1.A. Report sequence identity. What can you conclude about
the quality of this modelling?
c. Build model with a template 1zei.1.A. Report sequence identity & types of ligands in this
template. What can you conclude about the quality of this modelling?
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