Difference between revisions of "Part:BBa K1796007"

(→‎Parametre of Protein)
(→‎Parametre of Protein)
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−
==Parametre of Protein==
+
==Parameter of Protein==
 
<p> Number of amino acids: 499 </p>
 
<p> Number of amino acids: 499 </p>
 
<p> </p>
 
<p> </p>
Line 24: Line 24:
 
<p> Theoretical pI: 6.64 </p>
 
<p> Theoretical pI: 6.64 </p>
 
<p> </p>
 
<p> </p>
−
<p> Amino acid composition:  </p>
+
<p> Amino acid composition:聽 </p>
 
<p> </p>
 
<p> </p>
−
<p> Ala (A)  46   9.2% </p>
+
<p> Ala (A)  46       9.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Arg (R)  35   7.0% </p>
+
<p> Arg (R)  35       7.0% </p>
 
<p> </p>
 
<p> </p>
−
<p> Asn (N)  17   3.4% </p>
+
<p> Asn (N)  17       3.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Asp (D)  23   4.6% </p>
+
<p> Asp (D)  23       4.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Cys (C)  16   3.2% </p>
+
<p> Cys (C)  16       3.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Gln (Q)  19   3.8% </p>
+
<p> Gln (Q)  19       3.8% </p>
 
<p> </p>
 
<p> </p>
−
<p> Glu (E)  40   8.0% </p>
+
<p> Glu (E)  40       8.0% </p>
 
<p> </p>
 
<p> </p>
−
<p> Gly (G)  42   8.4% </p>
+
<p> Gly (G)  42       8.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> His (H)  17   3.4% </p>
+
<p> His (H)  17       3.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Ile (I)  30   6.0%         </p>
+
<p> Ile (I)  30       6.0% </p>
 
<p> </p>
 
<p> </p>
−
<p> Leu (L)  27       9.2% </p>
+
<p> Leu (L)  41       8.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Lys (K)  14       4.8% </p>
+
<p> Lys (K)  25       5.0% </p>
 
<p> </p>
 
<p> </p>
−
<p> Met (M)  11      3.7% </p>
+
<p> Met (M)  11      2.2% </p>
 
<p> </p>
 
<p> </p>
−
<p> Phe (F)   9       3.1% </p>
+
<p> Phe (F) 13       2.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Pro (P)   8       2.7% </p>
+
<p> Pro (P) 25       5.0% </p>
 
<p> </p>
 
<p> </p>
−
<p> Ser (S)   9       3.1% </p>
+
<p> Ser (S) 27       5.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Thr (T)  17      5.8% </p>
+
<p> Thr (T)  17      3.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Trp (W)  0       0.0% </p>
+
<p> Trp (W)  2       0.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Tyr (Y)   8       2.7% </p>
+
<p> Tyr (Y) 13       2.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Val (V)  17       5.8% </p>
+
<p> Val (V)  40       8.0% </p>
 
<p> </p>
 
<p> </p>
 
<p> Pyl (O)  0      0.0% </p>
 
<p> Pyl (O)  0      0.0% </p>
Line 76: Line 76:
 
<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): 43 </p>
+
<p> Total number of negatively charged residues (Asp + Glu): 63 </p>
−
<p> Total number of positively charged residues (Arg + Lys): 27 </p>
+
<p> Total number of positively charged residues (Arg + Lys): 60 </p>
 
<p> </p>
 
<p> </p>
−
<p> Atomic composition:Carbon      C              1400 </p>
+
<p> Atomic composition:Carbon      C              2398 </p>
−
<p> Hydrogen    H        2248 </p>
+
<p> Hydrogen    H        3849 </p>
−
<p> Nitrogen    N          386 </p>
+
<p> Nitrogen    N          701 </p>
−
<p> Oxygen      O          444 </p>
+
<p> Oxygen      O          719 </p>
−
<p> Sulfur      S          17 </p>
+
<p> Sulfur      S          27 </p>
 
<p> </p>
 
<p> </p>
−
<p> Formula: C1400H2248N386O444S17Total number of atoms: 4495 </p>
+
<p> Formula: C2398H3849N701O719S27Total number of atoms: 7694 </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    31370 </p>
 +
<p> Abs 0.1% (=1 g/l)  0.572, assuming all pairs of Cys residues form cystines </p>
 
<p> </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>
 
 
<p> </p>
 
<p> </p>
 +
<p> Ext. coefficient    30370 </p>
 +
<p> Abs 0.1% (=1 g/l)  0.553, assuming all Cys residues are reduced </p>
 
<p> </p>
 
<p> </p>
−
<p> Ext. coefficient    11920 </p>
+
<p> Estimated half-life:The N-terminal of the sequence considered is M (Met). </p>
−
<p> Abs 0.1% (=1 g/l)   0.371, assuming all Cys residues are reduced </p>
+
 
<p> </p>
 
<p> </p>
−
<p> Estimated half-life:The N-terminal of the sequence considered is H (His). </p>
+
<p> The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro). </p>
−
<p> </p>
+
<p>                             >20 hours (yeast, in vivo). </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>                             >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 38.27 </p>
+
<p> Instability index:The instability index (II) is computed to be 43.03 </p>
−
<p> This classifies the protein as stable. </p>
+
<p> This classifies the protein as unstable. </p>
 +
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 +
<p> Aliphatic index: 87.96 </p>
 
<p> </p>
 
<p> </p>
−
<p> Aliphatic index: 90.61 </p>
+
<p> Grand average of hydropathicity (GRAVY): -0.253 </p>
 +
<p> Aliphatic index: 92.50 </p>
 
<p> </p>
 
<p> </p>
−
<p> Grand average of hydropathicity (GRAVY): -0.185 </p>
+
<p> Grand average of hydropathicity (GRAVY): -0.161 </p>

Revision as of 01:28, 19 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


Parameter of Protein

Number of amino acids: 499

Molecular weight: 54869.8

Theoretical pI: 6.64

Amino acid composition:聽

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) 41 8.2%

Lys (K) 25 5.0%

Met (M) 11 2.2%

Phe (F) 13 2.6%

Pro (P) 25 5.0%

Ser (S) 27 5.4%

Thr (T) 17 3.4%

Trp (W) 2 0.4%

Tyr (Y) 13 2.6%

Val (V) 40 8.0%

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): 63

Total number of positively charged residues (Arg + Lys): 60

Atomic composition:Carbon C 2398

Hydrogen H 3849

Nitrogen N 701

Oxygen O 719

Sulfur S 27

Formula: C2398H3849N701O719S27Total number of atoms: 7694

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

Ext. coefficient 31370

Abs 0.1% (=1 g/l) 0.572, assuming all pairs of Cys residues form cystines

Ext. coefficient 30370

Abs 0.1% (=1 g/l) 0.553, 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 43.03

This classifies the protein as unstable.

Aliphatic index: 87.96

Grand average of hydropathicity (GRAVY): -0.253

Aliphatic index: 92.50

Grand average of hydropathicity (GRAVY): -0.161