HOMEWORK#8
Sequence analysis / model building
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David Liu, a student in the department
of Lfe Sciences, got a clone from E coli. Here is the DNA sequence:
TGGATGCCATGTTCCGGAGGTAATATGAAGAAATCAATATTATTTATTTTTCTTT
CTGTATTGTCTTTTTCACCTTTCGCTCAGGATGCTAAACCAGTAGAGTCTTCAAA
AGAAAAAATCACACTAGAATCAAAAAAATGTAACATTGCAAAAAAAAGTAATA
AAAGTGGTCCTGAAAGCATGAATAGTAGCAATTACTGCTGTGAATTGTGTTGTA
ATCCTGCTTGTACCGGGTGCTATTAATAATATAAAGGGAACTAAACAGTTCCCT
TTATATTTGTTCTGATTCTGATGATGTCTGTAACGTATGTCCTGTTGCTTTGTTG
AATAAATCGA
Unfortunately, he doesn't know how
to use the sequence analysis tools availabled in the internet since he
did not take Bioinformatics course before. Could you help him to do the
following analysis?
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(1) Find its corresponding polypeptide
sequence (DNA -> Protein translation).
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Poly peptide sequence of the
given DNA sequence
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MPCSGGNMKK SILFIFLSVL SFSPFAQDAK PVESSKEKIT LESKKCNIAK
KSNKSGPESM NSSNYCCELC CNPACTGCY
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(2) Identify this protein. Is it a
new protein?
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HEAT-STABLE ENTEROTOXIN A4 PRECURSOR
(STA4) FROM E.Coli
No, It is not a new protein.
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(3) Report the total number of negatively
charged residues and positively charged residues.
Total
number of negatively charged residues (Asp + Glu): 6
Total number of positively charged residues (Arg + Lys): 10
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(4) Color
the protein by its charge.
Colour Key:
K
D E
MPCSGGNMKK
SILFIFLSVL SFSPFAQDAK
PVESSKEKIT
LESKKCNIAK
KSNKSGPESM
NSSNYCCELC CNPACTGCY
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(5) Draw the hydrophobicity map for
this protein using Eisenberg hydrophobicity scale with window size 7. The
relative weight of the window edges compared to the window center should
set to 40%.
SEQUENCE:
MPCSGGNMKK SILFIFLSVL SFSPFAQDAK
PVESSKEKIT LESKKCNIAK KSNKSGPESM NSSNYCCELC CNPACTGCY
SEQUENCE LENGTH: 79
Using the scale Hphob. / Eisenberg
et al., the individual values for the 20 amino acids are:
Ala: 0.620 Arg: -2.530
Asn: -0.780 Asp: -0.900 Cys: 0.290 Gln:-0.850
Glu: -0.740 Gly: 0.480 His: -0.400 Ile: 1.380
Leu: 1.060 Lys: -1.500 Met: 0.640 Phe:
1.190 Pro: 0.120 Ser: -0.180 Thr: -0.050
Trp: 0.810 Tyr: 0.260 Val: 1.080 Asx: -0.840
Glx:-0.795 Xaa: -0.000
Weights for window positions
1,..,7, using linear weight variation model:
1
2 3 4
5 6 7
0.40 0.60
0.80 1.00 0.80 0.60 0.40
edge
center
edge
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(6) Please help him to use Prosite
scanning tool to find out possible functions or pattern of this protein.
BOTH HEAT-STABLE AND HEAT-LABILE ENTEROTOXINS
ARE
PRODUCED BY PATHOGENIC STRAINS OF E.COLI AND EFFECT
THE
DIGESTIVE TRACT OF MAMMALS.
Prosite is
so slow I tried for more than 24 hrs getting nothing
System
error occured
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(7) Calculate its pI
and molecular weight.
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Molecular
weight = 8555.9