Difference between revisions of "Part:BBa K1796014"
(→‎Parameter of Protein)
 
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==Parameter of Protein==
 
==Parameter of Protein==
−
<p> Number of amino acids: 385 </p>
+
<p> Number of amino acids: 378 </p>
 
<p> </p>
 
<p> </p>
−
<p> Molecular weight: 42184.1 </p>
+
<p> Molecular weight: 41400.2 </p>
 
<p> </p>
 
<p> </p>
−
<p> Theoretical pI: 5.54 </p>
+
<p> Theoretical pI: 5.62 </p>
 
<p> </p>
 
<p> </p>
−
<p> Amino acid composition:  </p>
+
<p> Amino acid composition:聽 </p>
 
<p> </p>
 
<p> </p>
−
<p> Ala (A)  43     11.2% </p>
+
<p> Ala (A)  42     11.1% </p>
 
<p> </p>
 
<p> </p>
−
<p> Arg (R)  26       6.8% </p>
+
<p> Arg (R)  25       6.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Asn (N)  9      2.3% </p>
+
<p> Asn (N)  9      2.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Asp (D)  20      5.2% </p>
+
<p> Asp (D)  20      5.3% </p>
 
<p> </p>
 
<p> </p>
 
<p> Cys (C)  5      1.3% </p>
 
<p> Cys (C)  5      1.3% </p>
 
<p> </p>
 
<p> </p>
−
<p> Gln (Q)  15       3.9% </p>
+
<p> Gln (Q)  14       3.7% </p>
 
<p> </p>
 
<p> </p>
−
<p> Glu (E)  31       8.1% </p>
+
<p> Glu (E)  29       7.7% </p>
 
<p> </p>
 
<p> </p>
−
<p> Gly (G)  30       7.8% </p>
+
<p> Gly (G)  29       7.7% </p>
 
<p> </p>
 
<p> </p>
 
<p> His (H)  11      2.9% </p>
 
<p> His (H)  11      2.9% </p>
 
<p> </p>
 
<p> </p>
−
<p> Ile (I)  23       6.0% </p>
+
<p> Ile (I)  22       5.8% </p>
 
<p> </p>
 
<p> </p>
−
<p> Leu (L)  41      10.6% </p>
+
<p> Leu (L)  41      10.8% </p>
 
<p> </p>
 
<p> </p>
−
<p> Lys (K)  14      3.6% </p>
+
<p> Lys (K)  14      3.7% </p>
 
<p> </p>
 
<p> </p>
 
<p> Met (M)  10      2.6% </p>
 
<p> Met (M)  10      2.6% </p>
Line 56: Line 56:
 
<p> Phe (F)  8      2.1% </p>
 
<p> Phe (F)  8      2.1% </p>
 
<p> </p>
 
<p> </p>
−
<p> Pro (P)  14      3.6% </p>
+
<p> Pro (P)  14      3.7% </p>
 
<p> </p>
 
<p> </p>
−
<p> Ser (S)  25      6.5% </p>
+
<p> Ser (S)  25      6.6% </p>
 
<p> </p>
 
<p> </p>
−
<p> Thr (T)  19      4.9% </p>
+
<p> Thr (T)  19      5.0% </p>
 
<p> </p>
 
<p> </p>
 
<p> Trp (W)  5      1.3% </p>
 
<p> Trp (W)  5      1.3% </p>
 
<p> </p>
 
<p> </p>
−
<p> Tyr (Y)  9      2.3% </p>
+
<p> Tyr (Y)  9      2.4% </p>
 
<p> </p>
 
<p> </p>
−
<p> Val (V)  27      7.0% </p>
+
<p> Val (V)  27      7.1% </p>
 
<p> </p>
 
<p> </p>
 
<p> Pyl (O)  0      0.0% </p>
 
<p> Pyl (O)  0      0.0% </p>
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<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): 51 </p>
+
<p> Total number of negatively charged residues (Asp + Glu): 49 </p>
−
<p> Total number of positively charged residues (Arg + Lys): 40 </p>
+
<p> Total number of positively charged residues (Arg + Lys): 39 </p>
 
<p> </p>
 
<p> </p>
−
<p> Atomic composition:Carbon      C              1854 </p>
+
<p> Atomic composition:Carbon      C              1822 </p>
−
<p> Hydrogen    H        2976 </p>
+
<p> Hydrogen    H        2923 </p>
−
<p> Nitrogen    N          528 </p>
+
<p> Nitrogen    N          517 </p>
−
<p> Oxygen      O          565 </p>
+
<p> Oxygen      O          553 </p>
 
<p> Sulfur      S          15 </p>
 
<p> Sulfur      S          15 </p>
 
<p> </p>
 
<p> </p>
−
<p> Formula: C1854H2976N528O565S15Total number of atoms: 5938 </p>
+
<p> Formula: C1822H2923N517O553S15Total number of atoms: 5830 </p>
 
<p> </p>
 
<p> </p>
 
<p> Extinction coefficients:Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water. </p>
 
<p> Extinction coefficients:Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water. </p>
 
<p> </p>
 
<p> </p>
 
<p> Ext. coefficient    41160 </p>
 
<p> Ext. coefficient    41160 </p>
−
<p> Abs 0.1% (=1 g/l)  0.976, assuming all pairs of Cys residues form cystines </p>
+
<p> Abs 0.1% (=1 g/l)  0.994, assuming all pairs of Cys residues form cystines </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> </p>
 
<p> Ext. coefficient    40910 </p>
 
<p> Ext. coefficient    40910 </p>
−
<p> Abs 0.1% (=1 g/l)  0.970, assuming all Cys residues are reduced </p>
+
<p> Abs 0.1% (=1 g/l)  0.988, assuming all Cys residues are reduced </p>
 
<p> </p>
 
<p> </p>
−
<p> Estimated half-life:The N-terminal of the sequence considered is A (Ala). </p>
+
<p> Estimated half-life:The N-terminal of the sequence considered is M (Met). </p>
 
<p> </p>
 
<p> </p>
−
<p> The estimated half-life is: 4.4 hours (mammalian reticulocytes, in vitro). </p>
+
<p> The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro). </p>
 
<p>                             >20 hours (yeast, in vivo). </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 43.72 </p>
+
<p> Instability index:The instability index (II) is computed to be 44.57 </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: 96.34 </p>
+
<p> Aliphatic index: 96.83 </p>
 +
<p> </p>
 +
<p> Grand average of hydropathicity (GRAVY): -0.106 </p>
 +
<p> </p>
 +
<p> </p>
 
<p> </p>
 
<p> </p>
−
<p> Grand average of hydropathicity (GRAVY): -0.128 </p>
 

Latest revision as of 01:54, 19 September 2015

nifV promoted from Paenibacillus sp. WLY78

homocitrate synthase，provides the organic moiety in all three nitrogenase cofactors.

First, we promoted it ourselves（done by Nan Wang and Nannan Xie).Then we sent the sequences to synthesis, but unfortunately, striction enzyme cut site was involved after they promoted it again. But we were not informed of the error in promotion.After several times failed expriments, we found the problem.We tackled them over the matter, mistakes were corrected, but the correct genes can't arrive on time,it can only arrive after the deadline. Sequence submit is promoted by the synthesis company, containing a PstI in the gene.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 1106
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 1106
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1110
    Illegal BamHI site found at 933
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 1106
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 1106
  • 1000
    COMPATIBLE WITH RFC[1000]


Parameter of Protein

Number of amino acids: 378

Molecular weight: 41400.2

Theoretical pI: 5.62

Amino acid composition:聽

Ala (A) 42 11.1%

Arg (R) 25 6.6%

Asn (N) 9 2.4%

Asp (D) 20 5.3%

Cys (C) 5 1.3%

Gln (Q) 14 3.7%

Glu (E) 29 7.7%

Gly (G) 29 7.7%

His (H) 11 2.9%

Ile (I) 22 5.8%

Leu (L) 41 10.8%

Lys (K) 14 3.7%

Met (M) 10 2.6%

Phe (F) 8 2.1%

Pro (P) 14 3.7%

Ser (S) 25 6.6%

Thr (T) 19 5.0%

Trp (W) 5 1.3%

Tyr (Y) 9 2.4%

Val (V) 27 7.1%

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): 49

Total number of positively charged residues (Arg + Lys): 39

Atomic composition:Carbon C 1822

Hydrogen H 2923

Nitrogen N 517

Oxygen O 553

Sulfur S 15

Formula: C1822H2923N517O553S15Total number of atoms: 5830

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

Ext. coefficient 41160

Abs 0.1% (=1 g/l) 0.994, assuming all pairs of Cys residues form cystines

Ext. coefficient 40910

Abs 0.1% (=1 g/l) 0.988, 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 44.57

This classifies the protein as unstable.

Aliphatic index: 96.83

Grand average of hydropathicity (GRAVY): -0.106