HOMEWORK#7

Sequence analysis / model building

• due on 12/31/1997

• David Liu, a student in the department of Lfe Sciences, got the following mRNA sequence from a rat liver cDNA library.

GCGTCGACGGGCTTGGCATCGGGCCTCCGCAGC CGCCCACCGCCAGAAGCTTCCAGCCT

CACCACTATGGATCCCCGCAAAGTGAGCGA GCTTCGGGCCTTCGTGAAGATGTGTAGG

CAGGACCCGAGCGTCCTGCACACCGAGGAA ATGCGTTTCCTGAGGGAGTGGGTGGAGA

GCATGGGGGGTAAAGTACCACCTGCTACTCA TAAAGCGAAGTCAGAAGAAAACACTAA

GGAAGAAAAAAGAGACAAGACGACAGAGG ACAACATAAAGACAGAGGAGCCATCGAG

TGAGGAGAGCGATCTAGAAATTGACAATGAA GGTGTAATTGAAGCAGACACTGATGCT

CCTCAGGAAATGGGAGATGAAAATGCAGAG ATAACTGAGGCGATGATGGATGAAGCAA

ATGAAAAGAAGGGGGCTGCCATCGACGCTCT AAATGATGGTGAGCTCCAGAAAGCCAT

TGACTTGTTCACAGACGCCATCAAGCTAAACC CTCGCTTGGCCATTCTGTATGCCAAGA

GAGCCAGTGTTTTCGTCAAATTACAGAAGCCA AATGCTGCCATCCGAGACTGTGACAGA

GCTATTGAAATAAACCCTGATTCAGCTCAGCC ATACAAATGGAGAGGGAAAGCGCACA

GACTCCTGGGTCACTGGGAAGAAGCAGCTCG CGATCTTGCCCTGGCCTGTAAATTGGAC

TATGATGAGGACGCCAGTGCAATGCTGAGAG AAGTCCAGCCTCGGGCTCAAAAAATTGC

TGAACATCGGAGAAAGTATGAGCGAAAACGT GAAGAGCGAGAGATAAAAGAACGAAT

AGAAAGGGTGAAGAAGGCTCGAGAAGAGCA TGAAAAAGCCCAAAGGGAAGAAGAAGC

CAGAAGACAATCTGGATCTCAGTTTGGCTCTT TTCCAGGTGGTTTTCCTGGGGGAATGC

CTGGTAATTTTCCTGGAGGAATGCCTGGAATG GGAGGGGCCATGCCAGGAATGGCAGG

AATGCCTGGACTCAACGAAATCCTCAGTGAC CCAGAGGTTCTTGCAGCCATGCAGGATC

CAGAAGTCATGGTGGCTTTCCAGGATGTGGC CCAGAACCCATCAAATATGTCAAAATAT

CAGAACAACCCAAAGGTTATGAATCTCATCA GTAAATTGTCAGCCAAGTTTGGAGGTCA

CTCATAATGTCAAAGCCCTTGCTGAATGAAG AACAGCTTAGCTCACTTACTGGATGTTG

CAATAATACAAACCAGTGTACCTCTGACCTC ACCAGAGAGCTGGGGCGCTTCGAAGATA

ATCCCTACCCTCTGCATCATATGCGGCTGAGG CATATTACAGTGGTTTGCCATTAGAGT

GTTCATTCAGATAATGTTTTCCTATTAGGAATT ACAAACTTAAAACATTTTTCAACCTTA

AACATATTTTTTAAAAATTTAGGGGATGTCAA TTCCTACATTTTTCGTTACTAATCTTTT

TGGGTTTTTCCTTTTGAATTACTGGGCAAGGA AGGTGAATGTGGATGATTTACTGCTTT

CATGAATGAAATAAAGATTTGTTAGTGGGAA GCAAATAAAACACATTTAAGTTGATTG

AGTCGGACATACGGTTACTGCAACATCTTGA ATTGTCTTTAATGTTTTACTTCACAATG

ATCTATTTCAGTAAATCTTTTGGGACCACCAA AAAAAAAAAAAAAAAAAAAAAAA

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

  MDPRKVSELRAFVKMCRQDPSVLHTEEMRFLREWVESMGGKVPPATHKA KSEENTKEEKRDKTTEDNIKTEEPSSEESDLEIDNEGVIEADTDAPQEMGDENAE ITEAMMDEANEKKGAAIDALNDGELQKAIDLFTDAIKLNPRLAILYAKRASVFV KLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEEAARDLALACKL DYDEDASAMLREVQPRAQKIAEHRRKYERKREEREIKERIERVKKAREEHEKA QREEEARRQSGSQFGSFPGGFPGGMPGNFPGGMPGMGGAMPGMAGMPGLNEI LSDPEVLAAMQDPEVMVAFQDVAQNPSNMSKYQNNPKVMNLISKLSAKFGGHS

• (2) Identify this protein. Is it a new protein? What kind of rat is this protein belong to? (China, Noway, German.....)
  It is not a new protein but has been previously identified. It belongs to Norway rats.

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

  Total number of negatively charged residues (Asp + Glu): 69
  Total number of positively charged residues (Arg + Lys): 56

• (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%.

  Click here to see the diagram.

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

  Here is the result of searching.

• (6) Color the protein by the hydrophobicity of the amino acids.

  Here is the colored protein.