Difference between revisions of "Part:BBa K1080005:Design"

(→‎Design Notes)
(→‎Design Notes)
 
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<b>Amino acid sequence</b>
 
<b>Amino acid sequence</b>
  
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<b><FONT FACE="courier">MVAATAAPQE VEGFKVMRDG IKVASDETLL TPRFYTTDFD EMERLFSLEL NKNMDMEEFE<br> AMLNEFKLDY NQRHFVRNET FKEAAEKIQG PTRKIFIEFL ERSCTAEFSG FLLYKELGRR<br> LKATNPVVAE IFTLMSRDEA RHAGFLNKAM SDFNLALDLG FLTKNRKYTF FKPKFIFYAT<br> YLSEKIGYWR YISIYRHLQR NPDNQLYPLF EYFENWCQDE NRHGDFFTAV LKARPEMVND<br> WAAKLWSRFF CLSVYITMYL NDHQRDAFYS SLGLNTTQFN QHVIIETNKS TERIFPAVPD<br> VENPEFFRRM DLLVKYNAQL VNIGSMNLPS PIKAIMKAPI LERMVAEVFQ VFIMTPKESG<br> SYDLDANKTA LVY  </FONT>
+
<FONT FACE="courier">MVAATAAPQE VEGFKVMRDG IKVASDETLL TPRFYTTDFD EMERLFSLEL NKNMDMEEFE<br> AMLNEFKLDY NQRHFVRNET FKEAAEKIQG PTRKIFIEFL ERSCTAEFSG FLLYKELGRR<br> LKATNPVVAE IFTLMSRDEA RHAGFLNKAM SDFNLALDLG FLTKNRKYTF FKPKFIFYAT<br> YLSEKIGYWR YISIYRHLQR NPDNQLYPLF EYFENWCQDE NRHGDFFTAV LKARPEMVND<br> WAAKLWSRFF CLSVYITMYL NDHQRDAFYS SLGLNTTQFN QHVIIETNKS TERIFPAVPD<br> VENPEFFRRM DLLVKYNAQL VNIGSMNLPS PIKAIMKAPI LERMVAEVFQ VFIMTPKESG<br> SYDLDANKTA LVY  </FONT>
  
 
References and documentation are available.  
 
References and documentation are available.  

Latest revision as of 10:34, 25 September 2013


CTH1


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 305
    Illegal BglII site found at 413
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 103
    Illegal BsaI.rc site found at 259
    Illegal BsaI.rc site found at 880


Design Notes

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


CTH1 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


Amino acid sequence

MVAATAAPQE VEGFKVMRDG IKVASDETLL TPRFYTTDFD EMERLFSLEL NKNMDMEEFE
AMLNEFKLDY NQRHFVRNET FKEAAEKIQG PTRKIFIEFL ERSCTAEFSG FLLYKELGRR
LKATNPVVAE IFTLMSRDEA RHAGFLNKAM SDFNLALDLG FLTKNRKYTF FKPKFIFYAT
YLSEKIGYWR YISIYRHLQR NPDNQLYPLF EYFENWCQDE NRHGDFFTAV LKARPEMVND
WAAKLWSRFF CLSVYITMYL NDHQRDAFYS SLGLNTTQFN QHVIIETNKS TERIFPAVPD
VENPEFFRRM DLLVKYNAQL VNIGSMNLPS PIKAIMKAPI LERMVAEVFQ VFIMTPKESG
SYDLDANKTA LVY

References and documentation are available. Please note the modified algorithm for extinction coefficient.

Number of amino acids: 373

Molecular weight: 43873.3

Theoretical pI: 5.98

Amino acid composition: Ala (A) 28 7.5% Arg (R) 23 6.2% Asn (N) 23 6.2% Asp (D) 19 5.1% Cys (C) 3 0.8% Gln (Q) 11 2.9% Glu (E) 31 8.3% Gly (G) 12 3.2% His (H) 6 1.6% Ile (I) 18 4.8% Leu (L) 35 9.4% Lys (K) 23 6.2% Met (M) 15 4.0% Phe (F) 33 8.8% Pro (P) 15 4.0% Ser (S) 17 4.6% Thr (T) 21 5.6% Trp (W) 4 1.1% Tyr (Y) 17 4.6% Val (V) 19 5.1% 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): 50 Total number of positively charged residues (Arg + Lys): 46

Atomic composition:

Carbon C 1999 Hydrogen H 3041 Nitrogen N 515 Oxygen O 563 Sulfur S 18

Formula: C1999H3041N515O563S18 Total number of atoms: 6136

Extinction coefficients:

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

Ext. coefficient 47455 Abs 0.1% (=1 g/l) 1.082, assuming all pairs of Cys residues form cystines


Ext. coefficient 47330 Abs 0.1% (=1 g/l) 1.079, assuming all Cys residues are reduced

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 36.26 This classifies the protein as stable.


Aliphatic index: 77.69

Grand average of hydropathicity (GRAVY): -0.313

Source

Chlamydomonas reinhardtii

References