Difference between revisions of "Part:BBa K1080011:Design"
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<partinfo>BBa_K1080011 short</partinfo> | <partinfo>BBa_K1080011 short</partinfo> | ||
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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. |
| + | |||
| + | |||
| + | ChlI2 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 | ||
| + | |||
| + | <FONT FACE="courier"> | ||
| + | |||
| + | MPSTKAAKKP NFPFVKIQGQ EEMKLALLLN VVDPNIGGVL IMGDRGTAKS VAVRALVDML<br> PDIDVVEGDA FNSSPTDPKF MGPDTLQRFR NGEKLPTVRM RTPLVELPLG ATEDRICGTI<br> DIEKALTQGI KAYEPGLLAK ANRGILYVDE VNLLDDGLVD VVLDSSASGL NTVEREGVSI<br> VHPARFIMIG SGNPQEGELR PQLLDRFGMS VNVATLQDTK QRTQLVLDRL AYEADPDAFV<br> DSCKAEQTAL TDKLEAARQR LRSVKISEEL QILISDICSR LDVDGLRGDI VINRAAKALV<br> AFEGRTEVTT NDVERVISGC LNHRLRKDPL DPIDNGTKVA ILFKRMTDPE IMKREEEAKK<br> </FONT> | ||
| + | |||
| + | Please note the modified algorithm for extinction coefficient. | ||
| + | |||
| + | -------------------------------------------------------------------------------- | ||
| + | Number of amino acids: 393 | ||
| + | |||
| + | Molecular weight: 42954.3 | ||
| + | |||
| + | Theoretical pI: 5.78 | ||
| + | |||
| + | Amino acid composition: Ala (A) 38 9.7% | ||
| + | Arg (R) 30 7.6% | ||
| + | Asn (N) 14 3.6% | ||
| + | Asp (D) 32 8.1% | ||
| + | Cys (C) 4 1.0% | ||
| + | Gln (Q) 12 3.1% | ||
| + | Glu (E) 28 7.1% | ||
| + | Gly (G) 29 7.4% | ||
| + | His (H) 2 0.5% | ||
| + | Ile (I) 22 5.6% | ||
| + | Leu (L) 41 10.4% | ||
| + | Lys (K) 27 6.9% | ||
| + | Met (M) 10 2.5% | ||
| + | Phe (F) 10 2.5% | ||
| + | Pro (P) 22 5.6% | ||
| + | Ser (S) 16 4.1% | ||
| + | Thr (T) 21 5.3% | ||
| + | Trp (W) 1 0.3% | ||
| + | Tyr (Y) 3 0.8% | ||
| + | Val (V) 31 7.9% | ||
| + | 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): 60 | ||
| + | Total number of positively charged residues (Arg + Lys): 57 | ||
| + | |||
| + | Atomic composition: | ||
| + | |||
| + | Carbon C 1875 | ||
| + | Hydrogen H 3103 | ||
| + | Nitrogen N 541 | ||
| + | Oxygen O 580 | ||
| + | Sulfur S 14 | ||
| + | |||
| + | Formula: C1875H3103N541O580S14 | ||
| + | Total number of atoms: 6113 | ||
| + | |||
| + | Extinction coefficients: | ||
| + | |||
| + | Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | ||
| + | |||
| + | Ext. coefficient 10220 | ||
| + | Abs 0.1% (=1 g/l) 0.238, assuming all pairs of Cys residues form cystines | ||
| + | |||
| + | |||
| + | Ext. coefficient 9970 | ||
| + | Abs 0.1% (=1 g/l) 0.232, 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 32.87 | ||
| + | This classifies the protein as stable. | ||
| + | |||
| − | |||
| − | + | Aliphatic index: 95.06 | |
| − | + | Grand average of hydropathicity (GRAVY): -0.296 | |
Latest revision as of 02:03, 26 September 2013
ChlI2
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 523
- 21COMPATIBLE WITH RFC[21]
- 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.
ChlI2 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
MPSTKAAKKP NFPFVKIQGQ EEMKLALLLN VVDPNIGGVL IMGDRGTAKS VAVRALVDML
PDIDVVEGDA FNSSPTDPKF MGPDTLQRFR NGEKLPTVRM RTPLVELPLG ATEDRICGTI
DIEKALTQGI KAYEPGLLAK ANRGILYVDE VNLLDDGLVD VVLDSSASGL NTVEREGVSI
VHPARFIMIG SGNPQEGELR PQLLDRFGMS VNVATLQDTK QRTQLVLDRL AYEADPDAFV
DSCKAEQTAL TDKLEAARQR LRSVKISEEL QILISDICSR LDVDGLRGDI VINRAAKALV
AFEGRTEVTT NDVERVISGC LNHRLRKDPL DPIDNGTKVA ILFKRMTDPE IMKREEEAKK
Please note the modified algorithm for extinction coefficient.
Number of amino acids: 393
Molecular weight: 42954.3
Theoretical pI: 5.78
Amino acid composition: Ala (A) 38 9.7% Arg (R) 30 7.6% Asn (N) 14 3.6% Asp (D) 32 8.1% Cys (C) 4 1.0% Gln (Q) 12 3.1% Glu (E) 28 7.1% Gly (G) 29 7.4% His (H) 2 0.5% Ile (I) 22 5.6% Leu (L) 41 10.4% Lys (K) 27 6.9% Met (M) 10 2.5% Phe (F) 10 2.5% Pro (P) 22 5.6% Ser (S) 16 4.1% Thr (T) 21 5.3% Trp (W) 1 0.3% Tyr (Y) 3 0.8% Val (V) 31 7.9% 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): 60
Total number of positively charged residues (Arg + Lys): 57
Atomic composition:
Carbon C 1875 Hydrogen H 3103 Nitrogen N 541 Oxygen O 580 Sulfur S 14
Formula: C1875H3103N541O580S14 Total number of atoms: 6113
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 10220 Abs 0.1% (=1 g/l) 0.238, assuming all pairs of Cys residues form cystines
Ext. coefficient 9970
Abs 0.1% (=1 g/l) 0.232, 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 32.87 This classifies the protein as stable.
Aliphatic index: 95.06
Grand average of hydropathicity (GRAVY): -0.296