Difference between revisions of "Part:BBa K1080004:Design"

(→‎Design Notes)
(→‎Design Notes)
 
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<b> Amino Acid Sequence </b>
 
<b> Amino Acid Sequence </b>
  
−
<FONT FACE="courier">VGAVVGLGAL LVATDHQKRR SEQMKSFDGD EKEAVKDYFN TAGFERWRKI YGETDEVNKV QLDIRTGHAQ TVDKVLRWVD EEGSVQGITV ADCGCGTGSL<br> AIQLALRGAA VSASDISAAM ASEAEQRYQQ AVAAGQGKAP KVAPKFEALD LESVKGKYDT VTCLDVMIHY PQDKVDAMIT HLAGLSDRRL IISFAPKTLS<br> YSILKRIGEL FPGPSKATRA YLHREEDVEA ALKRAGFKVT KREMTATSFY FSRLLEAIRE </FONT>
+
<FONT FACE="courier">MASEIAQTAD VGSLTFAVGG VGAVVGLGAL LVATDHQKRR SEQMKSFDGD EKEAVKDYFN<br> TAGFERWRKI YGETDEVNKV QLDIRTGHAQ TVDKVLRWVD EEGSVQGITV ADCGCGTGSL<br> AIQLALRGAA VSASDISAAM ASEAEQRYQQ AVAAGQGKAP KVAPKFEALD LESVKGKYDT<br> VTCLDVMIHY PQDKVDAMIT HLAGLSDRRL IISFAPKTLS YSILKRIGEL FPGPSKATRA<br> YLHREEDVEA ALKRAGFKVT KREMTATSFY FSRLLEAIRE </FONT>
 
   
 
   
−
References and documentation are available.
+
References and documentation are available.  
−
 
+
 
Please note the modified algorithm for extinction coefficient.
 
Please note the modified algorithm for extinction coefficient.
  
 
--------------------------------------------------------------------------------
 
--------------------------------------------------------------------------------
−
Number of amino acids: 260
+
Number of amino acids: 280
  
−
Molecular weight: 28533.5
+
Molecular weight: 30440.6
  
−
Theoretical pI: 7.12
+
Theoretical pI: 6.25
  
−
Amino acid composition: Ala (A)  32 12.3%
+
Amino acid composition: Ala (A)  36 12.9%
−
Arg (R)  17   6.5%
+
Arg (R)  17   6.1%
−
Asn (N)  2   0.8%
+
Asn (N)  2   0.7%
−
Asp (D)  17   6.5%
+
Asp (D)  18   6.4%
−
Cys (C)  3   1.2%
+
Cys (C)  3   1.1%
−
Gln (Q)  11   4.2%
+
Gln (Q)  12   4.3%
−
Glu (E)  19   7.3%
+
Glu (E)  20   7.1%
−
Gly (G)  20   7.7%
+
Gly (G)  23   8.2%
−
His (H)  5   1.9%
+
His (H)  5   1.8%
−
Ile (I)  12   4.6%
+
Ile (I)  13   4.6%
−
Leu (L)  21   8.1%
+
Leu (L)  22   7.9%
−
Lys (K)  19   7.3%
+
Lys (K)  19   6.8%
−
Met (M)  5   1.9%
+
Met (M)  6   2.1%
−
Phe (F)   9   3.5%
+
Phe (F) 10   3.6%
−
Pro (P)  6   2.3%
+
Pro (P)  6   2.1%
−
Ser (S)  16   6.2%
+
Ser (S)  18   6.4%
−
Thr (T)  15   5.8%
+
Thr (T)  17   6.1%
−
Trp (W)  2   0.8%
+
Trp (W)  2   0.7%
−
Tyr (Y)  8   3.1%
+
Tyr (Y)  8   2.9%
−
Val (V)  21   8.1%
+
Val (V)  23   8.2%
 
Pyl (O)  0   0.0%
 
Pyl (O)  0   0.0%
 
Sec (U)  0   0.0%
 
Sec (U)  0   0.0%
Line 60: Line 59:
  
  
−
Total number of negatively charged residues (Asp + Glu): 36
+
Total number of negatively charged residues (Asp + Glu): 38
 
Total number of positively charged residues (Arg + Lys): 36
 
Total number of positively charged residues (Arg + Lys): 36
  
 
Atomic composition:
 
Atomic composition:
  
−
Carbon      C       1258
+
Carbon      C       1340
−
Hydrogen    H       2019
+
Hydrogen    H       2150
−
Nitrogen    N       355
+
Nitrogen    N       376
−
Oxygen      O       385
+
Oxygen      O       414
−
Sulfur      S         8
+
Sulfur      S         9
  
−
Formula: C1258H2019N355O385S8
+
Formula: C1340H2150N376O414S9
−
Total number of atoms: 4025
+
Total number of atoms: 4289
  
 
Extinction coefficients:
 
Extinction coefficients:
Line 79: Line 78:
  
 
Ext. coefficient    23045
 
Ext. coefficient    23045
−
Abs 0.1% (=1 g/l)  0.808, assuming all pairs of Cys residues form cystines
+
Abs 0.1% (=1 g/l)  0.757, assuming all pairs of Cys residues form cystines
  
  
 
Ext. coefficient    22920
 
Ext. coefficient    22920
−
Abs 0.1% (=1 g/l)  0.803, assuming all Cys residues are reduced
+
Abs 0.1% (=1 g/l)  0.753, assuming all Cys residues are reduced
  
 
Estimated half-life:
 
Estimated half-life:
  
−
The N-terminal of the sequence considered is V (Val).
+
The N-terminal of the sequence considered is M (Met).
  
 
The estimated half-life is:  
 
The estimated half-life is:  
−
                             100 hours (mammalian reticulocytes, in vitro).
+
                             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).
Line 97: Line 96:
 
Instability index:
 
Instability index:
  
−
The instability index (II) is computed to be 34.87
+
The instability index (II) is computed to be 34.88
 
This classifies the protein as stable.
 
This classifies the protein as stable.
  
  
  
−
Aliphatic index: 85.23
+
Aliphatic index: 85.43
 +
 
 +
Grand average of hydropathicity (GRAVY): -0.198
 +
 +
 
  
−
Grand average of hydropathicity (GRAVY): -0.267
+
SIB Swiss Institute of Bioinformatics | Disclaimer
  
 
===Source===
 
===Source===

Latest revision as of 10:27, 25 September 2013


ChlM


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 230
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

ChlM 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 restriction sites: PstI, XbaI, SpeI or EcoRI

Amino Acid Sequence

MASEIAQTAD VGSLTFAVGG VGAVVGLGAL LVATDHQKRR SEQMKSFDGD EKEAVKDYFN
TAGFERWRKI YGETDEVNKV QLDIRTGHAQ TVDKVLRWVD EEGSVQGITV ADCGCGTGSL
AIQLALRGAA VSASDISAAM ASEAEQRYQQ AVAAGQGKAP KVAPKFEALD LESVKGKYDT
VTCLDVMIHY PQDKVDAMIT HLAGLSDRRL IISFAPKTLS YSILKRIGEL FPGPSKATRA
YLHREEDVEA ALKRAGFKVT KREMTATSFY FSRLLEAIRE

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

Number of amino acids: 280

Molecular weight: 30440.6

Theoretical pI: 6.25

Amino acid composition: Ala (A) 36 12.9% Arg (R) 17 6.1% Asn (N) 2 0.7% Asp (D) 18 6.4% Cys (C) 3 1.1% Gln (Q) 12 4.3% Glu (E) 20 7.1% Gly (G) 23 8.2% His (H) 5 1.8% Ile (I) 13 4.6% Leu (L) 22 7.9% Lys (K) 19 6.8% Met (M) 6 2.1% Phe (F) 10 3.6% Pro (P) 6 2.1% Ser (S) 18 6.4% Thr (T) 17 6.1% Trp (W) 2 0.7% Tyr (Y) 8 2.9% Val (V) 23 8.2% 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): 38 Total number of positively charged residues (Arg + Lys): 36

Atomic composition:

Carbon C 1340 Hydrogen H 2150 Nitrogen N 376 Oxygen O 414 Sulfur S 9

Formula: C1340H2150N376O414S9 Total number of atoms: 4289

Extinction coefficients:

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

Ext. coefficient 23045 Abs 0.1% (=1 g/l) 0.757, assuming all pairs of Cys residues form cystines


Ext. coefficient 22920 Abs 0.1% (=1 g/l) 0.753, 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 34.88 This classifies the protein as stable.


Aliphatic index: 85.43

Grand average of hydropathicity (GRAVY): -0.198


SIB Swiss Institute of Bioinformatics | Disclaimer

Source

Chlamydomonas reinhardtii

References