hk4

HOMEWORK #4 due on 5/19

Kevin Lyu, a graduate student in our department, got a cDNA that encode a protein from rice. Here is the sequence:
CGGCACGAGCAGCAACTTAACTTGATCTTCGTGTGACCGATCGATGGCTCGCGCGGGACATAATAAGTAT
GTGGCGCGCGTGATGGTGGTGGCGCTGCTGTTGGCCGCGCGGGCACCCGTGACATGCGGGCAGGTGGTGA
GCACTTGGGCGCCGTGCATCATGTACGCCGACGGGGAGGGTGTCGCCCCCACCGGCGGCTGCTGCGACGG
GGTCAGGACCCTCAACTCCGCCGCCGCCACCACCGCCGACCGCCAGACCACCTGCGCCTGCCTCAAGCAG
CAGACCAAGGCCATGGGCCGGCTGAGGCCCGACCACGTCGCCGGCATCCCCTCCAAGTGCGGGGTCAACA
TCCCCTACGCTATCAGCCCTTCCACCGACTGCTCCAGGGTGCACTGAGTGGATCAACGTCAAGTGATGCC
ACAATAATAATGGAGAGATGGATCCATCGATCTGCGGCTCTCATTTTGCGGTTGCTATCTGCAATATTCG
TCGTCGTCGGAGAGATCGAGCTAGAAATGCATGTTACTCCTCCGTTCTGTTACTATCTGCTTACCTGTTG
CTTCGTGCGGTTTGATAGTGTCGTTATAGCTAGTGTAAGAGTGTGAGGGTTGATTTTGATCTGTCTCCTT
TACGGGACGAGGGGCACGGCGAATCATGCATGAATCTTAGAGGACCTGCTTGCATTGTACCTTACTCAGT
GCATGCTTCAATATATATCCATCAAATGAAGATCTTTTAATGAAAAAAAAAAAAAAAAAAAAAAAA

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?

(1) Find its corresponding polypeptide sequence (DNA -> Protein translation).

5'3' Frame 1
R H E Q Q L N L I F V Stop P I D G S R G T Stop Stop V C G A R D G G G A A V G R A G T R D Met R A G G E H
L G A V H H V R R R G G C R P H R R L L R R G Q D P Q L R R R H H R R P P D H L R L P Q A A D Q G H G P A
E A R P R R R H P L Q V R G Q H P L R Y Q P F H R L L Q G A L S G S T S S D A T I I Met E R W I H R S A A L I
L R L L S A I F V V V G E I E L E Met H V T P P F C Y Y L L T C C F V R F D S V V I A S V R V Stop G L I L I C
L L Y G T R G T A N H A Stop I L E D L L A L Y L T Q C Met L Q Y I S I K Stop R S F N E K K K K K K K
5'3' Frame 2
G T S S N L T Stop S S C D R S Met A R A G H N K Y V A R V Met V V A L L L A A R A P V T C G Q V V S T W
A P C I Met Y A D G E G V A P T G G C C D G V R T L N S A A A T T A D R Q T T C A C L K Q Q T K A Met G
R L R P D H V A G I P S K C G V N I P Y A I S P S T D C S R V H Stop V D Q R Q V Met P Q Stop Stop W R D G
S I D L R L S F C G C Y L Q Y S S S S E R S S Stop K C Met L L L R S V T I C L P V A S C G L I V S L Stop L V
Stop E C E G Stop F Stop S V S F T G R G A R R I Met H E S Stop R T C L H C T L L S A C F N I Y P S N E D L L
Met K K K K K K K K
5'3' Frame 3
A R A A T Stop L D L R V T D R W L A R D I I S Met W R A Stop W W W R C C W P R G H P Stop H A G R W
Stop A L G R R A S C T P T G R V S P P P A A A A T G S G P S T P P P P P P P T A R P P A P A S S S R P R P W
A G Stop G P T T S P A S P P S A G S T S P T L S A L P P T A P G C T E W I N V K Stop C H N N N G E Met D P
S I C G S H F A V A I C N I R R R R R D R A R N A C Y S S V L L L S A Y L L L R A V Stop Stop C R Y S Stop C
K S V R V D F D L S P L R D E G H G E S C Met N L R G P A C I V P Y S V H A S I Y I H Q Met K I F Stop Stop
K K K K K K K
3'5' Frame 1
F F F F F F F F H Stop K I F I Stop W I Y I E A C T E Stop G T Met Q A G P L R F Met H D S P C P S S R K G D R
S K S T L T L L H Stop L Stop R H Y Q T A R S N R Stop A D S N R T E E Stop H A F L A R S L R R R R I L Q I A
T A K Stop E P Q I D G S I S P L L L W H H L T L I H S V H P G A V G G R A D S V G D V D P A L G G D A G D
V V G P Q P A H G L G L L L E A G A G G L A V G G G G G G G V E G P D P V A A A A G G G D T L P V G V H
D A R R P S A H H L P A C H G C P R G Q Q Q R H H H H A R H I L I Met S R A S H R S V T R R S S Stop V A A
R A
3'5' Frame 2
F F F F F F F F I K R S S F D G Y I L K H A L S K V Q C K Q V L Stop D S C Met I R R A P R P V K E T D Q N Q
P S H S Y T S Y N D T I K P H E A T G K Q I V T E R R S N Met H F Stop L D L S D D D E Y C R Stop Q P Q N E
S R R S Met D P S L H Y Y C G I T Stop R Stop S T Q C T L E Q S V E G L I A Stop G Met L T P H L E G Met P A
T W S G L S R P Met A L V C C L R Q A Q V V W R S A V V A A A E L R V L T P S Q Q P P V G A T P S P S A Y
Met Met H G A Q V L T T C P H V T G A R A A N S S A T T I T R A T Y L L C P A R A I D R S H E D Q V K L L LV P
3'5' Frame 3
F F F F F F F S L K D L H L Met D I Y Stop S Met H Stop V R Y N A S R S S K I H A Stop F A V P L V P Stop R R
Q I K I N P H T L T L A I T T L S N R T K Q Q V S R Stop Stop Q N G G V T C I S S S I S P T T T N I A D S N R K
Met R A A D R W I H L S I I I V A S L D V D P L S A P W S S R W K G Stop Stop R R G C Stop P R T W R G C R
R R G R A S A G P W P W S A A Stop G R R R W S G G R R W W R R R S Stop G S Stop P R R S S R R W G R H PP R R R T Stop C T A P K C S P P A R Met S R V P A R P T A A P P P S R A P H T Y Y V P R E P S I G H T K I K
L S C C S C

But the most possible sequence is:
ARAGHNKYVARVMVVALLLAARAPVTCGQVVSTWAPCIMYADGEGVA
PTGGCCDGVRTLNSAAATTADRQTTCACLKQQTKAMGRLRPDHVAGIP
SKCGVNIPYAISPSTDCSRVH

(2) Identify this protein. Is it a new protein? If not, what's the name of this protein?

Oryza sativa lipid transfer protein

(3) Report the total number of negatively charged residues and positively charged residues.

Negatively charged residues : 6
Positively charged residues : 15

(4) 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%.

(5) Is there any hydrophobic region in this protein? Can you explain the possible role for this region?

May be a Transmembrane dormain or Substrate binding site.

(6) Please help him to use Prosite scanning tool to find out possible functions or pattern of this protein.

N-glycosylation site	5-8 NLTS
N-myristoylation site	1-6 GTSSNL 43-47 GQVVST 59-64 GVAPTG 65-70 GCCDGV 185-190 GLIVSL
Casein kinase II phosphorylation site	8-11 SSCD 79-82 TTAD 160-163 SSSE 231-234 SNED
Protein kinase C phosphorylation site	162-164 SER 165-167 SSK 202-204 TGR
Plant lipid transfer proteins signature	108-129 IPSKCGVNIPYAISPSTDCSRV

(7) Color the protein by the hydrophobicity of the amino acids.

10 20 30 40 50 60 70

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ARAGHNKYVARVMVVALLLAARAPVTCGQVVSTWAPCIMYADGEGVAPTGGCCDGVRTLNSAAATTADRQ

TTCACLKQQTKAMGRLRPDHVAGIPSKCGVNIPYAISPSTDCSRVH

(8)