Difference between revisions of "Part:BBa K1080002:Design"
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<partinfo>BBa_K1080002 short</partinfo> | <partinfo>BBa_K1080002 short</partinfo> | ||
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ChlD Clone: DNA sequence from translation start site: | ChlD Clone: DNA sequence from translation start site: | ||
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− | <b> | + | <b>Amino acid sequence:</b> |
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+ | <FONT FACE="courier"> MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG<br> TAKSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI<br> DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID<br> AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR<br> AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP<br> PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR<br> AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV<br> QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV<br> VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT<br> ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY </FONT> | ||
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+ | References and documentation are available. | ||
Please note the modified algorithm for extinction coefficient. | Please note the modified algorithm for extinction coefficient. | ||
+ | -------------------------------------------------------------------------------- | ||
+ | Number of amino acids: 707 | ||
− | + | Molecular weight: 76420.1 | |
− | + | Theoretical pI: 5.23 | |
− | + | Amino acid composition: Ala (A) 88 12.4% | |
+ | Arg (R) 47 6.6% | ||
+ | Asn (N) 14 2.0% | ||
+ | Asp (D) 51 7.2% | ||
+ | Cys (C) 7 1.0% | ||
+ | Gln (Q) 31 4.4% | ||
+ | Glu (E) 55 7.8% | ||
+ | Gly (G) 51 7.2% | ||
+ | His (H) 6 0.8% | ||
+ | Ile (I) 40 5.7% | ||
+ | Leu (L) 60 8.5% | ||
+ | Lys (K) 43 6.1% | ||
+ | Met (M) 20 2.8% | ||
+ | Phe (F) 12 1.7% | ||
+ | Pro (P) 50 7.1% | ||
+ | Ser (S) 42 5.9% | ||
+ | Thr (T) 24 3.4% | ||
+ | Trp (W) 1 0.1% | ||
+ | Tyr (Y) 16 2.3% | ||
+ | Val (V) 49 6.9% | ||
+ | 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): | + | Total number of negatively charged residues (Asp + Glu): 106 |
− | Total number of positively charged residues (Arg + Lys): | + | Total number of positively charged residues (Arg + Lys): 90 |
Atomic composition: | Atomic composition: | ||
− | Carbon C | + | Carbon C 3333 |
− | Hydrogen H | + | Hydrogen H 5435 |
− | Nitrogen N | + | Nitrogen N 949 |
− | Oxygen O | + | Oxygen O 1047 |
− | Sulfur S | + | Sulfur S 27 |
− | Formula: | + | Formula: C3333H5435N949O1047S27 |
− | Total number of atoms: | + | Total number of atoms: 10791 |
Extinction coefficients: | Extinction coefficients: | ||
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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 29715 |
− | Abs 0.1% (=1 g/l) 0. | + | Abs 0.1% (=1 g/l) 0.389, assuming all pairs of Cys residues form cystines |
− | Ext. coefficient | + | Ext. coefficient 29340 |
− | Abs 0.1% (=1 g/l) 0. | + | Abs 0.1% (=1 g/l) 0.384, assuming all Cys residues are reduced |
Estimated half-life: | Estimated half-life: | ||
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The N-terminal of the sequence considered is M (Met). | The N-terminal of the sequence considered is M (Met). | ||
− | The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro). | + | The estimated half-life is: |
+ | 30 hours (mammalian reticulocytes, in vitro). | ||
>20 hours (yeast, in vivo). | >20 hours (yeast, in vivo). | ||
>10 hours (Escherichia coli, in vivo). | >10 hours (Escherichia coli, in vivo). | ||
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Instability index: | Instability index: | ||
− | The instability index (II) is computed to be | + | The instability index (II) is computed to be 45.56 |
This classifies the protein as unstable. | This classifies the protein as unstable. | ||
− | Aliphatic index: | + | Aliphatic index: 87.71 |
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− | + | Grand average of hydropathicity (GRAVY): -0.337 |
Latest revision as of 02:28, 26 September 2013
ChlD
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NotI site found at 1334
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 2039
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 614
Illegal NgoMIV site found at 1433
Illegal NgoMIV site found at 1975 - 1000COMPATIBLE WITH RFC[1000]
Design Notes
Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence
ChlD Clone: DNA sequence from translation start site:
Amino acid sequence:
MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG
TAKSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI
DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID
AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR
AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP
PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR
AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV
QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV
VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT
ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY
References and documentation are available. Please note the modified algorithm for extinction coefficient.
Number of amino acids: 707
Molecular weight: 76420.1
Theoretical pI: 5.23
Amino acid composition: Ala (A) 88 12.4% Arg (R) 47 6.6% Asn (N) 14 2.0% Asp (D) 51 7.2% Cys (C) 7 1.0% Gln (Q) 31 4.4% Glu (E) 55 7.8% Gly (G) 51 7.2% His (H) 6 0.8% Ile (I) 40 5.7% Leu (L) 60 8.5% Lys (K) 43 6.1% Met (M) 20 2.8% Phe (F) 12 1.7% Pro (P) 50 7.1% Ser (S) 42 5.9% Thr (T) 24 3.4% Trp (W) 1 0.1% Tyr (Y) 16 2.3% Val (V) 49 6.9% 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): 106
Total number of positively charged residues (Arg + Lys): 90
Atomic composition:
Carbon C 3333 Hydrogen H 5435 Nitrogen N 949 Oxygen O 1047 Sulfur S 27
Formula: C3333H5435N949O1047S27 Total number of atoms: 10791
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 29715 Abs 0.1% (=1 g/l) 0.389, assuming all pairs of Cys residues form cystines
Ext. coefficient 29340
Abs 0.1% (=1 g/l) 0.384, 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 45.56 This classifies the protein as unstable.
Aliphatic index: 87.71
Grand average of hydropathicity (GRAVY): -0.337