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Computational Molecular Biology 2014, Vol. 4, No. 13, 1-6
http://cmb.biopublisher.ca
2
the best model using mu; tiple templates.
1 Material and Methods
1.1 Sequence retrieval
The amino acid sequence of photosytemII D2 protein
was retrieved from uniprot in fasta format. The detail
information is given in Table 1.
1.2 Physico-chemical characterization of photosytemII
D2 protein
The physico-chemical properties of the protein were
studied by using protparam tool. From this analysis
the theoretical PI, molecular weight, aliphatic index,
extinction coefficient, number of amino acids, total
number of positively and negatively charged residues,
atomic position, chemical formula, instability index
and GRAVY (Grand average of hydropathicity) of the
protein. The detail information is given in Table 2 and
Table 3.
Table 1 Information about PHOTOSYSTEMII D2 protein
UniprotID
Gene
Function
Catalytic activity
Subcellular location
Amino acid length
P06005
psbD
ATP formation
2 H
2
O + 2 plastoquinone + 4
light = O
2
+ 2 plastoquinol
Transmembrane
41-61
125-141
153-166
208-228
279-295
353
Table 2
Physico-chemical properties of
PHOTOSYSTEMII D2 protein
Molecular
weight
Theoretical pI Total number of negatively
charged residues
Total number of positively
charged residues
Total number
of atoms
Aliphatic
index
Grand average of
hydropathicity
(GRAVY)
39507.4 5.46
28
20
5514
88.78
0.358
Table 3
Amino acid composition result
Amino acids
symbols
Number of residues
In percentage
Ala
A
39
11.0%
Arg
R
15
4.2%
Asn
N
15
4.2%
Asp
D
12
3.4%
Cys
C
4
1.1%
Gln
Q
11
3.1%
Glu
E
16
4.5%
Gly
G
31
8.8%
His
H
8
2.3%
Ile
I
13
3.7%
Leu
L
41
11.6%
Lys
K
5
1.4%
Met
M
9
2.5%
Phe
F
39
11.0%
Pro
P
14
4.0%
Ser
S
18
5.1%
Thr
T
20
5.7%
Trp
W
13
3.7%
Tyr
Y
8
2.3%
Val
V
22
6.0%
Pyl
O
0
0.0%
Sec
U
0
0.0%