Homework 6Homework 6
Q1:Find its corresponding polypeptide sequence (DNA -> Protein translation).
Ans:
I R P P Y L A L Q C P P L S P A L P R R V
P P R P C P A G M Q R S P P G Y G A Q D D P P S R R D C A W A P G I G
A A A E A R G L P V T N V S P T S P A S P S S L P R S P P R S P E S G R Y G F G R G E R Q
T A D E L R I R R P M N
A F M V W A K D E R K R L A Q Q N P D L H N A V L S K M L G K A W K E L N T A E K R P F V
E E A E R L R V Q
H L R D H P N Y K Y R P R R K K Q E R K V R R L E P G L L L P G L V Q P S A P P E A F A A
A S G S A R S F R E L
P T L G A E F D G L G L P T P E R S P L D G L E P G E A S F F P P P L A P E D C A L R A F
R A P Y A P E L A R D P
S F C Y G A P L G E A L R T A P P A A P L A G L Y Y G T L X X P G P X X N P L S P P P E S
P S L E G T E Q L E P T
A D L W A D V D L T E F D Q Y L N C S R T R P D A T T L P Y H V X L A K L G P R A M S C P
E E S S L I S A L S D
A S S A V Y Y S A C I S G Stop T L S L P S T A S A C G Q V A E L P A P F
L S H M Y V R V C N S L Stop S W W P K
D A I S V A S S F T H L L L G X X C A L G L P Stop D R Q A L D V Q A T S
A R I G G E E A K A F L P F M F Stop N
E A V L F T L P G Y T Y I I Y N T I Y L I F N Stop T F F F K
Q2: Identify this protein. Is it a new protein? If not, what's the name of this protein?
Ans:
It is "(L35032) hmg-box transcription factor [Mus musculus] " gi|1663532 [1663532]
Q3: Report the total number of negatively charged residues and positively charged residues.
Ans:
Ala (A) 45 11.9%
Arg (R) 34 9.0%
Asn (N) 8 2.1%
Asp (D) 17 4.5%
Cys (C) 6 1.6%
Gln (Q) 10 2.7%
Glu (E) 28 7.4%
Gly (G) 27 7.2%
His (H) 4 1.1%
Ile (I) 4 1.1%
Leu (L) 40 10.6%
Lys (K) 11 2.9%
Met (M) 5 1.3%
Phe (F) 11 2.9%
Pro (P) 52 13.8%
Ser (S) 31 8.2%
Thr (T) 15 4.0%
Trp (W) 4 1.1%
Tyr (Y) 12 3.2%
Val (V) 11 2.9%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 2 0.5%
Total number of negatively charged residues (Asp + Glu): 45
Total number of positively charged residues (Arg + Lys): 45
Q4: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%.
Ans:
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Q5: Please help him to use Prosite scanning tool to find out possible functions or pattern of this protein.
Ans:
[1] PDOC00001 PS00001 ASN_GLYCOSYLATION
N-glycosylation site
325-328 NCSR
[2] PDOC00005 PS00005 PKC_PHOSPHO_SITE
Protein kinase C phosphorylation site
Number of matches: 4
1 16-18 SRR
2 61-63 SGR
3 187-189 SAR
4 190-192 SFR
[3] PDOC00006 PS00006 CK2_PHOSPHO_SITE
Casein kinase II phosphorylation site
Number of matches: 7
1 16-19 SRRD
2 73-76 TADE
3 190-193 SFRE
4 212-215 SPLD
5 318-321 TEFD
6 329-332 TRPD
7 351-354 SCPE
[4] PDOC00007 PS00007 TYR_PHOSPHO_SITE
Tyrosine kinase phosphorylation site
57-64 RSPESGRY
[5] PDOC00008 PS00008 MYRISTYL
N-myristoylation site
Number of matches: 6
1 25-30 GIGAAA
2 34-39 GLPVTN
3 186-191 GSARSF
4 216-221 GLEPGE
5 256-261 GAPLGE
6 274-279 GLYYGT
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Q6: Color the protein by the hydrophobicity of the amino acids.
Ans:
10 20 30 40 50 60 70 80 90
| | | | | | | | |
M Q R S P P G Y G A Q D D P P S R R D C
A W A
P G I G A A
A E A R G L
P V T N V S P T S P A S P S S L P R S P P R S P E S G R Y
G F G R G E R Q T A D E L R I R R P M N A
F M V W
A K D E R K R L A Q Q N P D L H N A V L S K
M L G K A
W K E L N T A E K R P F V E E A E R L R V
Q H L R D H P N Y K Y R P R R K K Q E R K V R R L E P G L
L L P G L
V Q P S A P P E A F A A A S G S A R S F R E L P T L G A
E F D G L G L P T P E R S P L D G L E P G E A
S F F P P P L A P E D C A L R A F
R A P Y A P E L A R D P S F C Y G A P L G E A
L R T A P P A A P L A G L Y Y G T L
G T P G P X P N P L S P P P E S P S L
E G T E Q L E P T A D L W A D V D L T E F D Q Y L N C S R T R P D A T T L P Y H V X L
A K L G P R A M S C P E E S S L I S A L S D A S S A
V Y Y S A C I S G
Total number of ALIVMW:109