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

(→‎Design Notes)
(→‎Design Notes)
Line 96: Line 96:
 
The N-terminal of the sequence considered is M (Met).
 
The N-terminal of the sequence considered is M (Met).
  
−
The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
+
The estimated half-life is:  
 +
                            30 hours (mammalian reticulocytes, in vitro).
 
                             >20 hours (yeast, in vivo).
 
                             >20 hours (yeast, in vivo).
 
                             >10 hours (Escherichia coli, in vivo).
 
                             >10 hours (Escherichia coli, in vivo).

Revision as of 02:16, 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

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: 232

Molecular weight: 26272.6

Theoretical pI: 6.45

Amino acid composition:

Ala (A) 21 9.1% Arg (R) 11 4.7% Asn (N) 11 4.7% Asp (D) 16 6.9% Cys (C) 0 0.0% Gln (Q) 12 5.2% Glu (E) 15 6.5% Gly (G) 15 6.5% His (H) 4 1.7% Ile (I) 7 3.0% Leu (L) 18 7.8% Lys (K) 19 8.2% Met (M) 8 3.4% Phe (F) 12 5.2% Pro (P) 7 3.0% Ser (S) 15 6.5% Thr (T) 16 6.9% Trp (W) 6 2.6% Tyr (Y) 6 2.6% Val (V) 13 5.6% Pyl (O) 0 0.0% Sec (U) 0 0.0% 

(B)   0	  0.0%
(Z)   0	  0.0%
(X)   0	  0.0%


Total number of negatively charged residues (Asp + Glu): 31 Total number of positively charged residues (Arg + Lys): 30

Atomic composition:

Carbon C 1167 Hydrogen H 1809 Nitrogen N 321 Oxygen O 355 Sulfur S 8

Formula: C1167H1809N321O355S8 Total number of atoms: 3660

Extinction coefficients:

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

Ext. coefficient 41940 Abs 0.1% (=1 g/l) 1.596

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 22.94 This classifies the protein as stable.


Aliphatic index: 67.33

Grand average of hydropathicity (GRAVY): -0.594

Source

Chlamydomonas reinhardtii

References