Difference between revisions of "Part:BBa K1080002:Design"
(→‎Design Notes)
 
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<b>Amino acid sequence:</b>
 
<b>Amino acid sequence:</b>
  
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<FONT FACE="courier"> MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG<br> KSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI<br> DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID<br> AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR<br> AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP<br> PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR<br> AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV<br> QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV<br>  VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT<br> ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY </FONT>
+
<FONT FACE="courier"> MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG<br> TAKSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI<br> DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID<br> AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR<br> AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP<br> PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR<br> AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV<br> QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV<br>  VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT<br> ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY </FONT>
 
    
 
    
 
References and documentation are available.  
 
References and documentation are available.  

Latest revision as of 02:28, 26 September 2013

ChlD


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NotI site found at 1334
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 2039
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 614
    Illegal NgoMIV site found at 1433
    Illegal NgoMIV site found at 1975
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

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


ChlD Clone: DNA sequence from translation start site:


Amino acid sequence:

MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG
TAKSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI
DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID
AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR
AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP
PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR
AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV
QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV
VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT
ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY

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

Number of amino acids: 707

Molecular weight: 76420.1

Theoretical pI: 5.23

Amino acid composition: Ala (A) 88 12.4% Arg (R) 47 6.6% Asn (N) 14 2.0% Asp (D) 51 7.2% Cys (C) 7 1.0% Gln (Q) 31 4.4% Glu (E) 55 7.8% Gly (G) 51 7.2% His (H) 6 0.8% Ile (I) 40 5.7% Leu (L) 60 8.5% Lys (K) 43 6.1% Met (M) 20 2.8% Phe (F) 12 1.7% Pro (P) 50 7.1% Ser (S) 42 5.9% Thr (T) 24 3.4% Trp (W) 1 0.1% Tyr (Y) 16 2.3% Val (V) 49 6.9% 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): 106 Total number of positively charged residues (Arg + Lys): 90

Atomic composition:

Carbon C 3333 Hydrogen H 5435 Nitrogen N 949 Oxygen O 1047 Sulfur S 27

Formula: C3333H5435N949O1047S27 Total number of atoms: 10791

Extinction coefficients:

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

Ext. coefficient 29715 Abs 0.1% (=1 g/l) 0.389, assuming all pairs of Cys residues form cystines


Ext. coefficient 29340 Abs 0.1% (=1 g/l) 0.384, 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 45.56 This classifies the protein as unstable.


Aliphatic index: 87.71

Grand average of hydropathicity (GRAVY): -0.337