Difference between revisions of "Part:BBa K1080003:Design"
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<b>Amino acid sequence</b> | <b>Amino acid sequence</b> | ||
| − | <FONT FACE="courier"> | + | <FONT FACE="courier">MAMRVTVAAG KLDSVSLFGG DTASLMGGSQ TVEKKKSGKE AVMEVQLSST AGIDYTVLRD<br> HLANGEFREA EDETRALLIK LAGPEAVKRN WVYFTEVKNI SVTDFQTLDN LWKASSNNKF<br> GYSVQKEIWV QNQKRWPKFF KQIDWTQGEN NNYRKWPMEF IYSMDAPRGH LPLTNALRGT<br> QLFQAIMEHP AFEKSSTAKT LDQKAAEAAG RTQSLF |
| + | References and documentation are available. | ||
| + | Please note the modified algorithm for extinction coefficient. | ||
| − | + | -------------------------------------------------------------------------------- | |
| + | Number of amino acids: 216 | ||
| − | + | Molecular weight: 24350.6 | |
| − | + | Theoretical pI: 8.98 | |
| − | + | Amino acid composition: Ala (A) 21 9.7% | |
| − | + | Arg (R) 10 4.6% | |
| − | + | Asn (N) 11 5.1% | |
| − | + | Asp (D) 10 4.6% | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | Amino acid composition: | + | |
| − | + | ||
| − | Ala (A) 21 9. | + | |
| − | Arg (R) | + | |
| − | Asn (N) 11 | + | |
| − | Asp (D) | + | |
Cys (C) 0 0.0% | Cys (C) 0 0.0% | ||
| − | Gln (Q) 12 5. | + | Gln (Q) 12 5.6% |
| − | Glu (E) 15 6. | + | Glu (E) 15 6.9% |
| − | Gly (G) | + | Gly (G) 14 6.5% |
| − | His (H) | + | His (H) 3 1.4% |
| − | Ile (I) 7 3. | + | Ile (I) 7 3.2% |
| − | Leu (L) | + | Leu (L) 17 7.9% |
| − | Lys (K) | + | Lys (K) 18 8.3% |
| − | Met (M) | + | Met (M) 7 3.2% |
| − | Phe (F) | + | Phe (F) 11 5.1% |
| − | Pro (P) | + | Pro (P) 6 2.8% |
| − | Ser (S) 15 6. | + | Ser (S) 15 6.9% |
| − | Thr (T) | + | Thr (T) 15 6.9% |
| − | Trp (W) 6 2. | + | Trp (W) 6 2.8% |
| − | Tyr (Y) | + | Tyr (Y) 5 2.3% |
| − | Val (V) 13 | + | Val (V) 13 6.0% |
Pyl (O) 0 0.0% | Pyl (O) 0 0.0% | ||
Sec (U) 0 0.0% | Sec (U) 0 0.0% | ||
| Line 71: | Line 61: | ||
| − | Total number of negatively charged residues (Asp + Glu): | + | Total number of negatively charged residues (Asp + Glu): 25 |
| − | Total number of positively charged residues (Arg + Lys): | + | Total number of positively charged residues (Arg + Lys): 28 |
Atomic composition: | Atomic composition: | ||
| − | Carbon C | + | Carbon C 1085 |
| − | Hydrogen H | + | Hydrogen H 1693 |
| − | Nitrogen N | + | Nitrogen N 299 |
| − | Oxygen O | + | Oxygen O 325 |
| − | Sulfur S | + | Sulfur S 7 |
| − | Formula: | + | Formula: C1085H1693N299O325S7 |
| − | Total number of atoms: | + | Total number of atoms: 3409 |
Extinction coefficients: | Extinction coefficients: | ||
| Line 89: | Line 79: | ||
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | ||
| − | Ext. coefficient | + | Ext. coefficient 40450 |
| − | Abs 0.1% (=1 g/l) 1. | + | Abs 0.1% (=1 g/l) 1.661 |
Estimated half-life: | Estimated half-life: | ||
| Line 104: | Line 94: | ||
Instability index: | Instability index: | ||
| − | The instability index (II) is computed to be 22. | + | The instability index (II) is computed to be 22.44 |
This classifies the protein as stable. | This classifies the protein as stable. | ||
| − | Aliphatic index: | + | Aliphatic index: 70.51 |
| − | Grand average of hydropathicity (GRAVY): -0. | + | Grand average of hydropathicity (GRAVY): -0.508 |
===Source=== | ===Source=== | ||
Revision as of 10:22, 25 September 2013
GUN4
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NotI site found at 719
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 404
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Design Notes
Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence.
GUN4 Clone: DNA sequence from translation start site:
Translated the DNA sequence into a protein sequence using "Translate" at http://au.expasy.org/tools Then used the translated protein sequence to analyse the protein using "ProtParam" at http://au.expasy.org/tools
No Biobrick sites: EcoRI, PstI, SpeI or XbaI
Amino acid sequence
MAMRVTVAAG KLDSVSLFGG DTASLMGGSQ TVEKKKSGKE AVMEVQLSST AGIDYTVLRD
HLANGEFREA EDETRALLIK LAGPEAVKRN WVYFTEVKNI SVTDFQTLDN LWKASSNNKF
GYSVQKEIWV QNQKRWPKFF KQIDWTQGEN NNYRKWPMEF IYSMDAPRGH LPLTNALRGT
QLFQAIMEHP AFEKSSTAKT LDQKAAEAAG RTQSLF
References and documentation are available.
Please note the modified algorithm for extinction coefficient.
Number of amino acids: 216
Molecular weight: 24350.6
Theoretical pI: 8.98
Amino acid composition: Ala (A) 21 9.7% Arg (R) 10 4.6% Asn (N) 11 5.1% Asp (D) 10 4.6% Cys (C) 0 0.0% Gln (Q) 12 5.6% Glu (E) 15 6.9% Gly (G) 14 6.5% His (H) 3 1.4% Ile (I) 7 3.2% Leu (L) 17 7.9% Lys (K) 18 8.3% Met (M) 7 3.2% Phe (F) 11 5.1% Pro (P) 6 2.8% Ser (S) 15 6.9% Thr (T) 15 6.9% Trp (W) 6 2.8% Tyr (Y) 5 2.3% Val (V) 13 6.0% 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): 25
Total number of positively charged residues (Arg + Lys): 28
Atomic composition:
Carbon C 1085 Hydrogen H 1693 Nitrogen N 299 Oxygen O 325 Sulfur S 7
Formula: C1085H1693N299O325S7 Total number of atoms: 3409
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 40450 Abs 0.1% (=1 g/l) 1.661
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 22.44 This classifies the protein as stable.
Aliphatic index: 70.51
Grand average of hydropathicity (GRAVY): -0.508
Source
Chlamydomonas reinhardtii
===References===