1.
David Liu, a student in the department of Lfe Sciences,
got the following mRNA sequence from a rat liver cDNA library.
GCGTCGACGGGCTTGGCATC
GGGCCTCCGCAGCCGCCCAC
CGCCAGAAGCTTCCAGCCTC
ACCACTATGGATCCCCGCAA
AGTGAGCGAGCTTCGGGCCT
TCGTGAAGATGTGTAGGCAG
GACCCGAGCGTCCTGCACAC
CGAGGAAATGCGTTTCCTGA
GGGAGTGGGTGGAGAGCATG
GGGGGTAAAGTACCACCTGC
TACTCATAAAGCGAAGTCAG
AAGAAAACACTAAGGAAGAA
AAAAGAGACAAGACGACAGA
GGACAACATAAAGACAGAGG
AGCCATCGAGTGAGGAGAGC
GATCTAGAAATTGACAATGA
AGGTGTAATTGAAGCAGACA
CTGATGCTCCTCAGGAAATG
GGAGATGAAAATGCAGAGAT
AACTGAGGCGATGATGGATG
AAGCAAATGAAAAGAAGGGG
GCTGCCATCGACGCTCTAAA
TGATGGTGAGCTCCAGAAAG
CCATTGACTTGTTCACAGAC
GCCATCAAGCTAAACCCTCG
CTTGGCCATTCTGTATGCCA
AGAGAGCCAGTGTTTTCGTC
AAATTACAGAAGCCAAATGC
TGCCATCCGAGACTGTGACA
GAGCTATTGAAATAAACCCT
GATTCAGCTCAGCCATACAA
ATGGAGAGGGAAAGCGCACA
GACTCCTGGGTCACTGGGAA
GAAGCAGCTCGCGATCTTGC
CCTGGCCTGTAAATTGGACT
ATGATGAGGACGCCAGTGCA
ATGCTGAGAGAAGTCCAGCC
TCGGGCTCAAAAAATTGCTG
AACATCGGAGAAAGTATGAG
CGAAAACGTGAAGAGCGAGA
GATAAAAGAACGAATAGAAA
GGGTGAAGAAGGCTCGAGAA
GAGCATGAAAAAGCCCAAAG
GGAAGAAGAAGCCAGAAGAC
AATCTGGATCTCAGTTTGGC
TCTTTTCCAGGTGGTTTTCC
TGGGGGAATGCCTGGTAATT
TTCCTGGAGGAATGCCTGGA
ATGGGAGGGGCCATGCCAGG
AATGGCAGGAATGCCTGGAC
TCAACGAAATCCTCAGTGAC
CCAGAGGTTCTTGCAGCCAT
GCAGGATCCAGAAGTCATGG
TGGCTTTCCAGGATGTGGCC
CAGAACCCATCAAATATGTC
AAAATATCAGAACAACCCAA
AGGTTATGAATCTCATCAGT
AAATTGTCAGCCAAGTTTGG
AGGTCACTCATAATGTCAAA
GCCCTTGCTGAATGAAGAAC
AGCTTAGCTCACTTACTGGA
TGTTGCAATAATACAAACCA
GTGTACCTCTGACCTCACCA
GAGAGCTGGGGCGCTTCGAA
GATAATCCCTACCCTCTGCA
TCATATGCGGCTGAGGCATA
TTACAGTGGTTTGCCATTAG
AGTGTTCATTCAGATAATGT
TTTCCTATTAGGAATTACAA
ACTTAAAACATTTTTCAACC
TTAAACATATTTTTTAAAAA
TTTAGGGGATGTCAATTCCT
ACATTTTTCGTTACTAATCT
TTTTGGGTTTTTCCTTTTGA
ATTACTGGGCAAGGAAGGTG
AATGTGGATGATTTACTGCT
TTCATGAATGAAATAAAGAT
TTGTTAGTGGGAAGCAAATA
AAACACATTTAAGTTGATTG
AGTCGGACATACGGTTACTG
CAACATCTTGAATTGTCTTT
AATGTTTTACTTCACAATGA
TCTATTTCAGTAAATCTTTT
GGGACCACCAAAAAAAAAAA
AAAAAAAAAAAAAA
Unfortunately, he doesn't know how to use the sequence analysis tools
availabled in the internet since he did not take Bioinformatics before.
Could you help him to do the following analysis?
- Find its corresponding polypeptide sequence
(DNA ->: Protein translation).
- Identify this protein. Is it a new protein? What kind of rat is this
protein belong to? (China, Noway, German......)
- Report the total number ofnegatively charged residues and
positively charged residues.
- Draw the hydrophobicity map for this protein using Eisenberg
hydrophobicity scale with window size 7. The relative weight of
edges compared to the window center should set to 40%.
- Please help him to use protein scanning tool to find out possible
functions or pattern of this protein.
- Color the protein by the hydrophobicity of the amino acids.
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A S T G L A S G L R S R P P P E A S S L T T Met D P R K V S E L R A F V
K Met C R Q D P S V L H T E E Met R F L R E W V E S Met G G K V P P A T H K
A K S E E N T K E E K R D K T T E D N I K T E E P S S E E S D L E I D N E G
V I E A D T D A P Q E Met G D E N A E I T E A Met Met D E A N E K K G A A I
D A L N D G E L Q K A I D L F T D A I K L N P R L A I L Y A K R A S V F V K
L Q K P N A A I R D C D R A I E I N P D S A Q P Y K W R G K A H R L L G H W
E E A A R D L A L A C K L D Y D E D A S A Met L R E V Q P R A Q K I A E H R
R K Y E R K R E E R E I K E R I E R V K K A R E E H E K A Q R E E E A R R Q
S G S Q F G S F P G G F P G G Met P G N F P G G Met P G Met G G A Met P G Met
A G Met P G L N E I L S D P E V L A A Met Q D P E V Met V A F Q D V A Q N P
S N Met S K Y Q N N P K V Met N L I S K L S A K F G G H S
Stop C Q S P C Stop
Met K N S L A H L L D V A I I Q T S V P L T S P E S W G A S K I I P T L C I
I C G Stop G I L Q W F A I R V F I Q I Met F S Y Stop E L Q T Stop N I F Q P
Stop T Y F L K I Stop G Met S I P T F F V T N L F G F F L L N Y W A R K V N
V D D L L L S Stop Met K Stop R F V S G K Q I K H I Stop V D Stop V G H T V
T A T S Stop I V F N V L L H N D L F Q Stop I F W D H Q K K K K K K K
- It is 100% identical to the protein: sp|P50503|HIP_RAT (HIP) HSC70-INTERACTING PROTEIN.
So it's not a new protein and belongs to Rattus norvegicus ,a Norway rat.
- Total number of negatively charged residues (Asp + Glu): 69
Total number of positively charged residues (Arg + Lys): 56
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- Therer are 5 patterns:
[1] PDOC00001 PS00001 ASN_GLYCOSYLATION
N-glycosylation site
343-346 NMSK
[2] PDOC00004 PS00004 CAMP_PHOSPHO_SITE
cAMP- and cGMP-dependent protein kinase phosphorylation site
Number of matches: 3
1 4-7 RKVS
2 152-155 KRAS
3 270-273 RRQS
[3] PDOC00005 PS00005 PKC_PHOSPHO_SITE
Protein kinase C phosphorylation site
Number of matches: 2
1 46-48 THK
2 361-363 SAK
[4] PDOC00006 PS00006 CK2_PHOSPHO_SITE
Casein kinase II phosphorylation site
Number of matches: 5
1 55-58 TKEE
2 63-66 TTED
3 74-77 SSEE
4 78-81 SDLE
5 317-320 SDPE
[5] PDOC00008 PS00008 MYRISTYL
N-myristoylation site
Number of matches: 10
1 86-91 GVIEAD
2 274-279 GSQFGS
3 278-283 GSFPGG
4 282-287 GGFPGG
5 286-291 GGMPGN
6 287-292 GMPGNF
7 290-295 GNFPGG
8 294-299 GGMPGM
9 298-303 GMGGAM
10 301-306 GAMPGM
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Green=DENQRHSTK; Yellow=CM;
Blue=AGILPV; Red=FYW
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