Difference between revisions of "Part:BBa K1796010"
(→‎Parameter of Protein)
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==Parameter of Protein==
 
==Parameter of Protein==
−
<p> Number of amino acids: 1386 </p>
+
<p> Number of amino acids: 452 </p>
 
<p> </p>
 
<p> </p>
−
<p> Molecular weight: 113485.5 </p>
+
<p> Molecular weight: 49505.3 </p>
 
<p> </p>
 
<p> </p>
−
<p> Theoretical pI: 4.98 </p>
+
<p> Theoretical pI: 6.01 </p>
 
<p> </p>
 
<p> </p>
−
<p> Amino acid composition: </p>
+
<p> Amino acid composition:  </p>
 
<p> </p>
 
<p> </p>
−
<p> Ala (A) 349      25.2% </p>
+
<p> Ala (A) 39      8.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Arg (R)   0       0.0% </p>
+
<p> Arg (R) 29       6.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Asn (N)   0       0.0% </p>
+
<p> Asn (N) 11       2.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Asp (D)   0       0.0% </p>
+
<p> Asp (D) 19       4.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Cys (C) 338      24.4% </p>
+
<p> Cys (C)   7      1.5% </p>
 
<p> </p>
 
<p> </p>
−
<p> Gln (Q)   0       0.0% </p>
+
<p> Gln (Q) 16       3.5% </p>
 
<p> </p>
 
<p> </p>
−
<p> Glu (E)   0       0.0% </p>
+
<p> Glu (E) 37       8.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Gly (G) 383     27.6% </p>
+
<p> Gly (G) 45     10.0% </p>
 
<p> </p>
 
<p> </p>
−
<p> His (H)   0       0.0% </p>
+
<p> His (H) 10       2.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Ile (I)   0       0.0% </p>
+
<p> Ile (I) 30       6.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Leu (L)   0       0.0% </p>
+
<p> Leu (L) 38       8.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Lys (K)   0       0.0% </p>
+
<p> Lys (K) 21       4.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Met (M)   0       0.0% </p>
+
<p> Met (M) 10       2.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Phe (F)   0       0.0% </p>
+
<p> Phe (F) 12       2.7% </p>
 
<p> </p>
 
<p> </p>
−
<p> Pro (P)   0       0.0% </p>
+
<p> Pro (P) 21       4.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Ser (S)   0       0.0% </p>
+
<p> Ser (S) 32       7.1% </p>
 
<p> </p>
 
<p> </p>
−
<p> Thr (T) 316      22.8% </p>
+
<p> Thr (T) 24      5.3% </p>
 
<p> </p>
 
<p> </p>
−
<p> Trp (W)  0       0.0% </p>
+
<p> Trp (W)  6       1.3% </p>
 
<p> </p>
 
<p> </p>
−
<p> Tyr (Y)   0       0.0% </p>
+
<p> Tyr (Y) 15       3.3% </p>
 
<p> </p>
 
<p> </p>
−
<p> Val (V)   0       0.0% </p>
+
<p> Val (V) 30       6.6% </p>
 
<p> </p>
 
<p> </p>
 
<p> Pyl (O)  0      0.0% </p>
 
<p> Pyl (O)  0      0.0% </p>
Line 77: Line 77:
 
<p> (X)  0          0.0% </p>
 
<p> (X)  0          0.0% </p>
 
<p> </p>
 
<p> </p>
−
<p> Total number of negatively charged residues (Asp + Glu): 0 </p>
+
<p> Total number of negatively charged residues (Asp + Glu): 56 </p>
−
<p> Total number of positively charged residues (Arg + Lys): 0 </p>
+
<p> Total number of positively charged residues (Arg + Lys): 50 </p>
 
<p> </p>
 
<p> </p>
−
<p> Atomic composition:Carbon      C              4091 </p>
+
<p> Atomic composition:Carbon      C              2187 </p>
−
<p> Hydrogen    H        6798 </p>
+
<p> Hydrogen    H        3471 </p>
−
<p> Nitrogen    N         1386 </p>
+
<p> Nitrogen    N         613 </p>
−
<p> Oxygen      O         1703 </p>
+
<p> Oxygen      O         663 </p>
−
<p> Sulfur      S         338 </p>
+
<p> Sulfur      S           17 </p>
 
<p> </p>
 
<p> </p>
−
<p> Formula: C4091H6798N1386O1703S338Total number of atoms: 14316 </p>
+
<p> Formula: C2187H3471N613O663S17Total number of atoms: 6951 </p>
 
<p> </p>
 
<p> </p>
−
<p> Extinction coefficients:This protein does not contain any Trp residues. Experience shows that </p>
+
<p> Extinction coefficients:Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water. </p>
−
<p> this could result in more than 10% error in the computed extinction coefficient. </p>
+
 
<p> </p>
 
<p> </p>
−
<p> Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water. </p>
+
<p> Ext. coefficient    55725 </p>
 +
<p> Abs 0.1% (=1 g/l)  1.126, assuming all pairs of Cys residues form cystines </p>
 
<p> </p>
 
<p> </p>
−
<p> Ext. coefficient    21125 </p>
 
−
<p> Abs 0.1% (=1 g/l)  0.186, assuming all pairs of Cys residues form cystines </p>
 
 
<p> </p>
 
<p> </p>
 +
<p> Ext. coefficient    55350 </p>
 +
<p> Abs 0.1% (=1 g/l)  1.118, assuming all Cys residues are reduced </p>
 
<p> </p>
 
<p> </p>
−
<p> Ext. coefficient        0 </p>
+
<p> Estimated half-life:The N-terminal of the sequence considered is E (Glu). </p>
−
<p> Abs 0.1% (=1 g/l)   0.000, assuming all Cys residues are reduced </p>
+
 
<p> </p>
 
<p> </p>
−
<p> Estimated half-life:The N-terminal of the sequence considered is C (Cys). </p>
+
<p> The estimated half-life is: 1 hours (mammalian reticulocytes, in vitro). </p>
−
<p> </p>
+
<p>                             30 min (yeast, in vivo). </p>
−
<p> The estimated half-life is: 1.2 hours (mammalian reticulocytes, in vitro). </p>
+
−
<p>                             >20 hours (yeast, in vivo). </p>
+
 
<p>                             >10 hours (Escherichia coli, in vivo). </p>
 
<p>                             >10 hours (Escherichia coli, in vivo). </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
−
<p> Instability index:The instability index (II) is computed to be 42.28 </p>
+
<p> Instability index:The instability index (II) is computed to be 40.70 </p>
 
<p> This classifies the protein as unstable. </p>
 
<p> This classifies the protein as unstable. </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
−
<p> Aliphatic index: 25.18 </p>
+
<p> Aliphatic index: 86.55 </p>
 +
<p> </p>
 +
<p> Grand average of hydropathicity (GRAVY): -0.239 </p>
 +
<p> </p>
 +
<p> </p>
 
<p> </p>
 
<p> </p>
−
<p> Grand average of hydropathicity (GRAVY): 0.793 </p>
 

Revision as of 01:40, 19 September 2015

nifE promoted from Paenibacillus sp. WLY78

Function: scaffold


Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 1369
    Illegal PstI site found at 1015
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 1369
    Illegal PstI site found at 1015
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 1369
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 1369
    Illegal PstI site found at 1015
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 1369
    Illegal PstI site found at 1015
    Illegal NgoMIV site found at 360
    Illegal NgoMIV site found at 607
  • 1000
    COMPATIBLE WITH RFC[1000]


Parameter of Protein

Number of amino acids: 452

Molecular weight: 49505.3

Theoretical pI: 6.01

Amino acid composition: 

Ala (A) 39 8.6%

Arg (R) 29 6.4%

Asn (N) 11 2.4%

Asp (D) 19 4.2%

Cys (C) 7 1.5%

Gln (Q) 16 3.5%

Glu (E) 37 8.2%

Gly (G) 45 10.0%

His (H) 10 2.2%

Ile (I) 30 6.6%

Leu (L) 38 8.4%

Lys (K) 21 4.6%

Met (M) 10 2.2%

Phe (F) 12 2.7%

Pro (P) 21 4.6%

Ser (S) 32 7.1%

Thr (T) 24 5.3%

Trp (W) 6 1.3%

Tyr (Y) 15 3.3%

Val (V) 30 6.6%

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): 56

Total number of positively charged residues (Arg + Lys): 50

Atomic composition:Carbon C 2187

Hydrogen H 3471

Nitrogen N 613

Oxygen O 663

Sulfur S 17

Formula: C2187H3471N613O663S17Total number of atoms: 6951

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

Ext. coefficient 55725

Abs 0.1% (=1 g/l) 1.126, assuming all pairs of Cys residues form cystines

Ext. coefficient 55350

Abs 0.1% (=1 g/l) 1.118, assuming all Cys residues are reduced

Estimated half-life:The N-terminal of the sequence considered is E (Glu).

The estimated half-life is: 1 hours (mammalian reticulocytes, in vitro).

30 min (yeast, in vivo).

>10 hours (Escherichia coli, in vivo).

Instability index:The instability index (II) is computed to be 40.70

This classifies the protein as unstable.

Aliphatic index: 86.55

Grand average of hydropathicity (GRAVY): -0.239