Continute from last homework
Help David to analyze the the gene product in ExPasy.
1. Using DNA -> Protein translator to translate gene.
From the ExPasy analysis I found the frame 2 is the translated protein sequence most likely to be correct.
The frame 2 sequence is as follows:
K K I K K M N K P Q T I Y E K L G G E N A M K A A V P L F Y K K V L A D E R V K H F F K N T D M D H Q T K Q Stop T D F L T M L L G G P N H Y K G K N M T E A H K G M N L Q N L H F D A I I E N L A A T L K E L G V T D A V I N E A A K V I E H T R K D M L G K Stop D S C C C C L Y S T I I N Y Y L T H H Q I N S N S T Q L N L S D F N K N Y L L Stop _ E Y L L C I V M Y R L L K M M I K T N P M V P D P R I
But the real sequence should be from the sixth amino acid (M) to the 127th amino acid (K),as follows:
MNKPQTIYEKLGGENAMKAAVPLFYKKVLADERVKHFFKNTDMDHQTKQQTDFLTMLLGGPN HYKGKNMTEAHKGMNLQNLHFDAIIENLAATLKELGVTDAVINEAAKVIEHTRKDMLGK
Where the first "stop" in the sequence is not a stop codon but translated as Q .
2. Calaulate pI, molecular weight, amino acid composition of the protein.
PI=8.78
MW=13683.82
Amino acid composition:
|
Ala(A)
|
11
|
9.1%
|
|
Arg(R)
|
2
|
1.7%
|
|
Asn(n)
|
9
|
7.4%
|
|
Asp(D)
|
7
|
5.8%
|
|
Cys(C)
|
0
|
0%
|
|
Gln(Q)
|
5
|
4.1%
|
|
Glu(E)
|
8
|
6.6%
|
|
Gly(G)
|
8
|
6.6%
|
|
His(H)
|
6
|
5.0%
|
|
Ile(I)
|
5
|
4.1%
|
|
Leu(L)
|
12
|
9.9%
|
|
Lys(K)
|
15
|
12.4%
|
|
Met(M)
|
7
|
5.8%
|
|
Phe(F)
|
5
|
4.1%
|
|
Pro(p)
|
3
|
2.5%
|
|
Ser(S)
|
0
|
0%
|
|
Thr(T)
|
9
|
7.4%
|
|
Trp(W)
|
0
|
0%
|
|
Tyr(Y)
|
3
|
2.5%
|
|
Val(V)
|
6
|
5.0%
|
|
Asx(B)
|
0
|
0%
|
|
Glx(Z)
|
0
|
0%
|
|
Xaa(X)
|
0
|
0%
|
3. Predict a-helice of the protein.
4. Compute the hydrophobic profile of the protein (show the window and weight you used).
The Kyte & Doolitttle hydrophobic analysis----
The window size I used was 9.
And the Relative weight of the window edges compared to the window center is 80%.
And the weight variation model I used was exponential.
This profile scale was normalized from 0 to 1