Practical 8

23 March 2023

Questions 1. Obtain the hydrophobicity profile for the sequences (Q1.fasta) and
identify the -helices and βstrands. Hydrophobicity values: A: 13.85 D: 11.61 C: 15.37
E: 11.38 F: 13.93 G: 13.34 H: 13.82 I: 15.28 K: 11.58 L: 14.13 M: 13.86 N: 13.02 P: 12.35
Q: 12.61 R: 13.10 S: 13.39 T: 12.70 V: 14.56 W: 15.48 Y: 13.88

The hydrophobicity profile for the given 3 sequences are given below.

Sequence 1
[1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1,
0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1,
0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0]
Alpha Strands:
Beta barrel:
Position 4 to 10 [1 0 1 0 1 0]
Position 44 to 50 [0 1 0 1 0 1]
Position 45 to 51 [1 0 1 0 1 0]
Position 46 to 52 [0 1 0 1 0 1]
Position 58 to 64 [0 1 0 1 0 1]

Sequence 2
[0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0,
0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 1, 1,
0, 1, 0, 0, 1, 1, 1]
Alpha Strands:
Position 2 to 5 - [1 1 0 0 1 1 0 0]
Position 4 to 7 - [0 0 1 1 0 0 1 1]
Position 35 to 38 - [1 1 0 0 1 1 0 0]
Position 37 to 40 - [0 0 1 1 0 0 1 1]
Beta barrel:
Position 24 to 30 [1 0 1 0 1 0]
Position 55 to 61 [1 0 1 0 1 0]
Position 56 to 62 [0 1 0 1 0 1]

Sequence 3
[0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0,
1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 1]
Alpha Strands:
Beta barrel:
Position 45 to 51 [1 0 1 0 1 0]

Code is in the folder

2. Calcualte the amphiphatic index for the helices and strands found in Q1. Use stretch lengths of 8
and 6 for -helices and β-strands, respectively.

Amphipathic Index Sequence 1 Sequence 2 Sequence 3

alpha-Helices -none 8.24 -none

4.36
7.77
5.30
 β-strands 1.31 2.49 2.01
3.48 1.16
3.89 1.34
3.37
1.72

3. Plot the hydrophobicity profile for the sequence (Q2.fasta) with window lengths 9 and 19 and
list the transmembrane segments.

Code attached in folder

4. Use ScanProsite tool (https://prosite.expasy.org/scanprosite/ - select option 2), to search for

the patterns a) [SV]-T-[VT]-[DERK](2)-{IL} and b) [FILV]Qxxx{RK}Gxxx[RK]xx[FILVWY] in in
UniProtKB (Include Swiss-Prot, isoforms). List the number of matches for each pattern.
First sequence has 10408 hits on 10000 sequences
Second sequence has 3828 hits on 3765 sequences

5. Write a program to identify the patterns (refer Q4) in the sequence database (Q4.fasta). List the
matches along with the sequence header and location of the matches in the sequence.

6. Identify the beta barrel membrane proteins with the following pattern: [K,R,H,Q,F,E]-x-G-
[I,V,L,F,A,C]-x-[ I,V,L,F,M,Y,W]-x-[ I,V,L,F,W] Use:
http://www.bioinformatics.org/sms2/protein_pattern.html and
http://prosite.expasy.org/scanprosite/ Hint: Modify the patterns according to the input format of
the server.
First removed commas and spaces from the sequence
[KRHQFE].G.[IVLFAC].[IVLFMYW].[IVLFW] showed 11,866 hits on 10000 sequences.

Deadline: 29 th March 2023