Difference between revisions of "Part:BBa K1080010:Design"
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===Design Notes=== | ===Design Notes=== | ||
| − | Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence | + | Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence. |
| + | |||
| + | <b>Amino acid sequence</b> | ||
| + | |||
| + | <FONT FACE="courier">MAPAAASADK ATAAEYYALV CNAEWFFMDP QNESVAEQLR EKVRFFKEQN KERDFFIVPN PKWLDAKFPE QAKQVKRPCV ALVSTDKMWI TFMKLRLDRV LKIDLKSMPA SEVLAAGEAL PDFKPDGKWT APYARYTPGW WNVFLPNH </F> | ||
| + | |||
| + | |||
| + | References and documentation are available. | ||
| + | Please note the modified algorithm for extinction coefficient. | ||
| + | |||
| + | -------------------------------------------------------------------------------- | ||
| + | Number of amino acids: 148 | ||
| + | |||
| + | Molecular weight: 17073.7 | ||
| + | |||
| + | Theoretical pI: 8.50 | ||
| + | |||
| + | Amino acid composition: Ala (A) 20 13.5% | ||
| + | Arg (R) 7 4.7% | ||
| + | Asn (N) 6 4.1% | ||
| + | Asp (D) 9 6.1% | ||
| + | Cys (C) 2 1.4% | ||
| + | Gln (Q) 5 3.4% | ||
| + | Glu (E) 10 6.8% | ||
| + | Gly (G) 3 2.0% | ||
| + | His (H) 1 0.7% | ||
| + | Ile (I) 3 2.0% | ||
| + | Leu (L) 11 7.4% | ||
| + | Lys (K) 14 9.5% | ||
| + | Met (M) 5 3.4% | ||
| + | Phe (F) 10 6.8% | ||
| + | Pro (P) 12 8.1% | ||
| + | Ser (S) 5 3.4% | ||
| + | Thr (T) 5 3.4% | ||
| + | Trp (W) 6 4.1% | ||
| + | Tyr (Y) 4 2.7% | ||
| + | Val (V) 10 6.8% | ||
| + | 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): 19 | ||
| + | Total number of positively charged residues (Arg + Lys): 21 | ||
| + | |||
| + | Atomic composition: | ||
| + | |||
| + | Carbon C 785 | ||
| + | Hydrogen H 1190 | ||
| + | Nitrogen N 202 | ||
| + | Oxygen O 212 | ||
| + | Sulfur S 7 | ||
| + | |||
| + | Formula: C785H1190N202O212S7 | ||
| + | Total number of atoms: 2396 | ||
| + | |||
| + | Extinction coefficients: | ||
| + | |||
| + | Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | ||
| + | |||
| + | Ext. coefficient 39085 | ||
| + | Abs 0.1% (=1 g/l) 2.289, assuming all pairs of Cys residues form cystines | ||
| + | |||
| + | |||
| + | Ext. coefficient 38960 | ||
| + | Abs 0.1% (=1 g/l) 2.282, 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 35.64 | ||
| + | This classifies the protein as stable. | ||
| + | |||
| + | |||
| + | |||
| + | Aliphatic index: 70.00 | ||
| + | |||
| + | Grand average of hydropathicity (GRAVY): -0.385 | ||
| + | |||
===Source=== | ===Source=== | ||
Revision as of 01:56, 26 September 2013
YCF54
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 108
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 270
Design Notes
Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence.
Amino acid sequence
MAPAAASADK ATAAEYYALV CNAEWFFMDP QNESVAEQLR EKVRFFKEQN KERDFFIVPN PKWLDAKFPE QAKQVKRPCV ALVSTDKMWI TFMKLRLDRV LKIDLKSMPA SEVLAAGEAL PDFKPDGKWT APYARYTPGW WNVFLPNH </F>
References and documentation are available.
Please note the modified algorithm for extinction coefficient.
Number of amino acids: 148
Molecular weight: 17073.7
Theoretical pI: 8.50
Amino acid composition: Ala (A) 20 13.5% Arg (R) 7 4.7% Asn (N) 6 4.1% Asp (D) 9 6.1% Cys (C) 2 1.4% Gln (Q) 5 3.4% Glu (E) 10 6.8% Gly (G) 3 2.0% His (H) 1 0.7% Ile (I) 3 2.0% Leu (L) 11 7.4% Lys (K) 14 9.5% Met (M) 5 3.4% Phe (F) 10 6.8% Pro (P) 12 8.1% Ser (S) 5 3.4% Thr (T) 5 3.4% Trp (W) 6 4.1% Tyr (Y) 4 2.7% Val (V) 10 6.8% 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): 19
Total number of positively charged residues (Arg + Lys): 21
Atomic composition:
Carbon C 785 Hydrogen H 1190 Nitrogen N 202 Oxygen O 212 Sulfur S 7
Formula: C785H1190N202O212S7 Total number of atoms: 2396
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 39085 Abs 0.1% (=1 g/l) 2.289, assuming all pairs of Cys residues form cystines
Ext. coefficient 38960
Abs 0.1% (=1 g/l) 2.282, 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 35.64 This classifies the protein as stable.
Aliphatic index: 70.00
Grand average of hydropathicity (GRAVY): -0.385
Source
Chlamydomonas reinhardtii
===References===