Difference between revisions of "Part:BBa K1796007"
(→‎Parametre of Protein)
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==Parametre of Protein==
 
==Parametre of Protein==
−
Number of amino acids: 499
+
<p> Number of amino acids: 499 </p>
−
 
+
<p> </p>
−
Molecular weight: 54869.8
+
<p> Molecular weight: 54869.8 </p>
−
 
+
<p> </p>
−
Theoretical pI: 6.64
+
<p> Theoretical pI: 6.64 </p>
−
 
+
<p> </p>
−
Amino acid composition:  
+
<p> Amino acid composition:  </p>
−
Ala (A)  46   9.2%
+
<p> </p>
−
Arg (R)  35   7.0%
+
<p> Ala (A)  46   9.2% </p>
−
Asn (N)  17   3.4%
+
<p> </p>
−
Asp (D)  23   4.6%
+
<p> Arg (R)  35   7.0% </p>
−
Cys (C)  16   3.2%
+
<p> </p>
−
Gln (Q)  19   3.8%
+
<p> Asn (N)  17   3.4% </p>
−
Glu (E)  40   8.0%
+
<p> </p>
−
Gly (G)  42   8.4%
+
<p> Asp (D)  23   4.6% </p>
−
His (H)  17   3.4%
+
<p> </p>
−
Ile (I)  30   6.0%
+
<p> Cys (C)  16   3.2% </p>
−
Leu (L)  41   8.2%
+
<p> </p>
−
Lys (K)  25   5.0%
+
<p> Gln (Q)  19   3.8% </p>
−
Met (M)  11   2.2%
+
<p> </p>
−
Phe (F) 13   2.6%
+
<p> Glu (E)  40   8.0% </p>
−
Pro (P) 25   5.0%
+
<p> </p>
−
Ser (S) 27   5.4%
+
<p> Gly (G)  42   8.4% </p>
−
Thr (T)  17   3.4%
+
<p> </p>
−
Trp (W)   2   0.4%
+
<p> His (H)  17   3.4% </p>
−
Tyr (Y) 13   2.6%
+
<p> </p>
−
Val (V)  40   8.0%
+
<p> Ile (I)  30   6.0%         </p>
−
Pyl (O)  0   0.0%
+
<p> </p>
−
Sec (U)  0   0.0%
+
<p> Leu (L)  27      9.2% </p>
−
 
+
<p> </p>
−
  (B)  0   0.0%
+
<p> Lys (K)  14      4.8% </p>
−
  (Z)  0   0.0%
+
<p> </p>
−
  (X)  0   0.0%
+
<p> Met (M)  11       3.7% </p>
−
 
+
<p> </p>
−
 
+
<p> Phe (F)  9      3.1% </p>
−
Total number of negatively charged residues (Asp + Glu): 63
+
<p> </p>
−
Total number of positively charged residues (Arg + Lys): 60
+
<p> Pro (P)  8      2.7% </p>
−
 
+
<p> </p>
−
Atomic composition:
+
<p> Ser (S)  9      3.1% </p>
−
 
+
<p> </p>
−
Carbon      C       2398
+
<p> Thr (T)  17       5.8% </p>
−
Hydrogen    H       3849
+
<p> </p>
−
Nitrogen    N       701
+
<p> Trp (W)  0      0.0% </p>
−
Oxygen      O       719
+
<p> </p>
−
Sulfur      S         27
+
<p> Tyr (Y)  8      2.7% </p>
−
 
+
<p> </p>
−
Formula: C2398H3849N701O719S27
+
<p> Val (V)  17      5.8% </p>
−
Total number of atoms: 7694
+
<p> </p>
−
 
+
<p> Pyl (O)  0       0.0% </p>
−
Extinction coefficients:
+
<p> </p>
−
 
+
<p> Sec (U)  0       0.0% </p>
−
Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
+
<p> </p>
−
 
+
<p> (B)  0         0.0% </p>
−
Ext. coefficient    31370
+
<p> </p>
−
Abs 0.1% (=1 g/l)  0.572, assuming all pairs of Cys residues form cystines
+
<p> (Z)  0         0.0% </p>
−
 
+
<p> </p>
−
 
+
<p> (X)  0         0.0% </p>
−
Ext. coefficient    30370
+
<p> </p>
−
Abs 0.1% (=1 g/l)  0.553, assuming all Cys residues are reduced
+
<p> Total number of negatively charged residues (Asp + Glu): 43 </p>
−
 
+
<p> Total number of positively charged residues (Arg + Lys): 27 </p>
−
Estimated half-life:
+
<p> </p>
−
 
+
<p> Atomic composition:Carbon      C             1400 </p>
−
The N-terminal of the sequence considered is M (Met).
+
<p> Hydrogen    H         2248 </p>
−
 
+
<p> Nitrogen    N         386 </p>
−
The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
+
<p> Oxygen      O         444 </p>
−
                            >20 hours (yeast, in vivo).
+
<p> Sulfur      S           17 </p>
−
                             >10 hours (Escherichia coli, in vivo).
+
<p> </p>
−
 
+
<p> Formula: C1400H2248N386O444S17Total number of atoms: 4495 </p>
−
 
+
<p> </p>
−
Instability index:
+
<p> Extinction coefficients:This protein does not contain any Trp residues. Experience shows that </p>
−
 
+
<p> this could result in more than 10% error in the computed extinction coefficient. </p>
−
The instability index (II) is computed to be 43.03
+
<p> </p>
−
This classifies the protein as unstable.
+
<p> Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water. </p>
−
 
+
<p> </p>
−
 
+
<p> Ext. coefficient    12295 </p>
−
 
+
<p> Abs 0.1% (=1 g/l)  0.383, assuming all pairs of Cys residues form cystines </p>
−
Aliphatic index: 87.96
+
<p> </p>
−
 
+
<p> </p>
−
Grand average of hydropathicity (GRAVY): -0.253
+
<p> Ext. coefficient    11920 </p>
 +
<p> Abs 0.1% (=1 g/l)  0.371, assuming all Cys residues are reduced </p>
 +
<p> </p>
 +
<p> Estimated half-life:The N-terminal of the sequence considered is H (His). </p>
 +
<p> </p>
 +
<p> The estimated half-life is: 3.5 hours (mammalian reticulocytes, in vitro). </p>
 +
<p>                             10 min (yeast, in vivo). </p>
 +
<p>                             >10 hours (Escherichia coli, in vivo). </p>
 +
<p> </p>
 +
<p> </p>
 +
<p> Instability index:The instability index (II) is computed to be 38.27 </p>
 +
<p> This classifies the protein as stable. </p>
 +
<p> </p>
 +
<p> </p>
 +
<p> </p>
 +
<p> Aliphatic index: 90.61 </p>
 +
<p> </p>
 +
<p> Grand average of hydropathicity (GRAVY): -0.185 </p>

Revision as of 22:09, 18 September 2015

nifB from Paenibacillus sp. WLY78

essential for biosynthesis of the active-site nitrogenase cofactor and encodes a radical A-adenosylmethionine(SAM)-dependent enzyme that inserts the central carbon atom into the eight-Fe core of nifB cofactor(nifB-co).

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 1156
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 1156
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 1156
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 1156
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 1156
    Illegal AgeI site found at 129
    Illegal AgeI site found at 1089
    Illegal AgeI site found at 1444
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 1261


Parametre of Protein

Number of amino acids: 499

Molecular weight: 54869.8

Theoretical pI: 6.64

Amino acid composition: 

Ala (A) 46 9.2%

Arg (R) 35 7.0%

Asn (N) 17 3.4%

Asp (D) 23 4.6%

Cys (C) 16 3.2%

Gln (Q) 19 3.8%

Glu (E) 40 8.0%

Gly (G) 42 8.4%

His (H) 17 3.4%

Ile (I) 30 6.0%

Leu (L) 27 9.2%

Lys (K) 14 4.8%

Met (M) 11 3.7%

Phe (F) 9 3.1%

Pro (P) 8 2.7%

Ser (S) 9 3.1%

Thr (T) 17 5.8%

Trp (W) 0 0.0%

Tyr (Y) 8 2.7%

Val (V) 17 5.8%

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): 43

Total number of positively charged residues (Arg + Lys): 27

Atomic composition:Carbon C 1400

Hydrogen H 2248

Nitrogen N 386

Oxygen O 444

Sulfur S 17

Formula: C1400H2248N386O444S17Total number of atoms: 4495

Extinction coefficients:This protein does not contain any Trp residues. Experience shows that

this could result in more than 10% error in the computed extinction coefficient.

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

Ext. coefficient 12295

Abs 0.1% (=1 g/l) 0.383, assuming all pairs of Cys residues form cystines

Ext. coefficient 11920

Abs 0.1% (=1 g/l) 0.371, assuming all Cys residues are reduced

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

The estimated half-life is: 3.5 hours (mammalian reticulocytes, in vitro).

10 min (yeast, in vivo).

>10 hours (Escherichia coli, in vivo).

Instability index:The instability index (II) is computed to be 38.27

This classifies the protein as stable.

Aliphatic index: 90.61

Grand average of hydropathicity (GRAVY): -0.185