Difference between revisions of "Part:BBa K1080003:Design"

(→‎Design Notes)
(→‎Design Notes)
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GUN4 Clone: DNA sequence from translation start site:
 
GUN4 Clone: DNA sequence from translation start site:
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Regions in BOLD are the sequence of the leader region in the pET100 plasmid.
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Translated the DNA sequence into a protein sequence
 
Translated the DNA sequence into a protein sequence
 
using "Translate" at http://au.expasy.org/tools
 
using "Translate" at http://au.expasy.org/tools
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No Biobrick sites: EcoRI, PstI, SpeI or XbaI
 
No Biobrick sites: EcoRI, PstI, SpeI or XbaI
  
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<b>ATG CGG GGT TCT CAT CAT CAT CAT CAT CAT GGT ATG GCT AGC ATG ACT GGT GGA
 
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CAG CAA ATG GGT CGG GAT CTG TAC GAC GAT GAC GAT AAG GAT CAT CCC TTC ACC</b>
 
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−
 
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<FONT FACE="courier">ATGGCGATGCGCGTCACCGTCGCTGCGGGCAAGCTGGACTCTGTCTCCCTGTTCGGTGGA
 
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GACACCGCCAGCCTGATGGGCGGTTCACAGACTGTGGAGAAGAAGAAGTCCGGCAAGGAG
 
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GCTGTGATGGAGGTGCAGCTCAGCTCCACGGCGGGCATCGACTACACCGTCCTGCGCGAC
 
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CACCTCGCCAACGGCGAGTTCCGCGAGGCCGAGGACGAGACTCGCGCTCTGCTGATCAAG
 
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CTTGCTGGCCCGGAGGCGGTCAAGCGCAACTGGGTTTACTTCACCGAGGTGAAGAACATT
 
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TCCGTCACCGATTTCCAGACCCTGGACAACCTGTGGAAGGCGTCCAGCAACAACAAGTTC
 
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GGCTACAGCGTTCAGAAGGAGATCTGGGTGCAGAACCAGAAGCGCTGGCCCAAGTTCTTC
 
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AAGCAGATTGACTGGACCCAGGGCGAGAACAACAACTACCGGAAGTGGCCCATGGAGTTC
 
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ATCTACAGCATGGACGCCCCCCGCGGCCACCTGCCCCTCACCAACGCGCTCCGAGGGACG
 
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CAGCTGTTCCAGGCGATCATGGAGCACCCAGCGTTCGAGAAGTCCAGCACGGCAAAGACG
 
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CTTGATCAGAAGGCGGCGGAGGCCGCCGGGCGGACACAGTCGCTGTTCTAAGCTCTCAGC
 
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AGCTCAGCGGCTGATCCTGCCAGGTGTTGTAT</FONT>
 
  
  

Revision as of 01:43, 25 September 2013


GUN4


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NotI site found at 719
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 404
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence.

GUN4 Clone: DNA sequence from translation start site:

Translated the DNA sequence into a protein sequence using "Translate" at http://au.expasy.org/tools Then used the translated protein sequence to analyse the protein using "ProtParam" at http://au.expasy.org/tools

No Biobrick sites: EcoRI, PstI, SpeI or XbaI


Amino acid sequence

MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDHPFTMAMR VTVAAGKLDS VSLFGGDTAS

LMGGSQTVEK KKSGKEAVME VQLSSTAGID YTVLRDHLAN GEFREAEDET RALLIKLAGP

EAVKRNWVYF TEVKNISVTD FQTLDNLWKA SSNNKFGYSV QKEIWVQNQK RWPKFFKQID

WTQGENNNYR KWPMEFIYSM DAPRGHLPLT NALRGTQLFQ AIMEHPAFEK SSTAKTLDQK

AAEAAGRTQS LF

Number of amino acids: 252

Molecular weight: 28476.0

Theoretical pI: 7.18

Amino acid composition:

Ala (A) 22 8.7% Arg (R) 12 4.8% Asn (N) 11 4.4% Asp (D) 16 6.3% Cys (C) 0 0.0% Gln (Q) 14 5.6% Glu (E) 15 6.0% Gly (G) 19 7.5% His (H) 10 4.0% Ile (I) 7 2.8% Leu (L) 18 7.1% Lys (K) 19 7.5% Met (M) 11 4.4% Phe (F) 12 4.8% Pro (P) 7 2.8% Ser (S) 17 6.7% Thr (T) 17 6.7% Trp (W) 6 2.4% Tyr (Y) 6 2.4% Val (V) 13 5.2%

Asx (B) 0 0.0% Glx (Z) 0 0.0% Xaa (X) 0 0.0%

Total number of negatively charged residues (Asp + Glu): 31 Total number of positively charged residues (Arg + Lys): 31

Atomic composition:

Carbon C 1255 Hydrogen H 1940 Nitrogen N 358 Oxygen O 380 Sulfur S 11

Formula: C1255H1940N358O380S11 Total number of atoms: 3944

Extinction coefficients:

Extinction coefficients are in units of M-1 cm-1, at 280 nm.

Ext. coefficient 41940 Abs 0.1% (=1 g/l) 1.473, assuming ALL Cys residues appear as half cystines


Estimated half-life:

The N-terminal of the sequence considered is M (Met).

The estimated half-life is: 

                            30 hours (mammalian reticulocytes, in vitro).
                           >20 hours (yeast, in vivo).
                           >10 hours (Escherichia coli, in vivo).


Instability index:

The instability index (II) is computed to be 22.16 This classifies the protein as stable.


Aliphatic index: 62.38

Grand average of hydropathicity (GRAVY): -0.655

Source

Chlamydomonas reinhardtii

References