Difference between revisions of "Part:BBa K1080009:Design"
(One intermediate revision by the same user not shown) | |||
Line 1: | Line 1: | ||
− | |||
__NOTOC__ | __NOTOC__ | ||
<partinfo>BBa_K1080009 short</partinfo> | <partinfo>BBa_K1080009 short</partinfo> | ||
Line 7: | Line 6: | ||
===Design Notes=== | ===Design Notes=== | ||
− | + | Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence | |
+ | |||
+ | <b> Amino acid sequence</b><FONT FACE="courier"> | ||
+ | |||
+ | MNQQATEEKS DTNSAARQML GMKGAALETD IWKIRVQLTK PVTWIPLIWG VACGAAASGH YQWNNPTQIA QLLTCMMMSG PFLTGYTQTI NDWYDREIDA INEPYRPIPS GRISERDVIV QIWVLLLGGI GLAYTLDQWA GHTTPVMLQL TIFGSFISYI YSAPPLKLKQ SGWAGNYALG SSYIALPWWA GQALFGTLTL DVMALTIAYS LAGLGIAIVN DFKSIEGDRQ MGLQSLPVAF GVDTAKWICV STIDVTQLGV AAYLAWGLHE ELYGAVLLAL ILPQIYFQYK YFLPDPIAND VKYQASAQPF LVFGLLTAGL ACGHHVNAVA AAASAAGAL </FONT> | ||
+ | |||
+ | References and documentation are available. | ||
+ | Please note the modified algorithm for extinction coefficient. | ||
+ | |||
+ | -------------------------------------------------------------------------------- | ||
+ | Number of amino acids: 339 | ||
+ | |||
+ | Molecular weight: 36830.6 | ||
+ | |||
+ | Theoretical pI: 5.30 | ||
+ | |||
+ | Amino acid composition: Ala (A) 43 12.7% | ||
+ | Arg (R) 7 2.1% | ||
+ | Asn (N) 10 2.9% | ||
+ | Asp (D) 14 4.1% | ||
+ | Cys (C) 4 1.2% | ||
+ | Gln (Q) 20 5.9% | ||
+ | Glu (E) 9 2.7% | ||
+ | Gly (G) 30 8.8% | ||
+ | His (H) 5 1.5% | ||
+ | Ile (I) 26 7.7% | ||
+ | Leu (L) 40 11.8% | ||
+ | Lys (K) 10 2.9% | ||
+ | Met (M) 9 2.7% | ||
+ | Phe (F) 10 2.9% | ||
+ | Pro (P) 16 4.7% | ||
+ | Ser (S) 18 5.3% | ||
+ | Thr (T) 21 6.2% | ||
+ | Trp (W) 12 3.5% | ||
+ | Tyr (Y) 16 4.7% | ||
+ | Val (V) 19 5.6% | ||
+ | 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): 23 | ||
+ | Total number of positively charged residues (Arg + Lys): 17 | ||
+ | |||
+ | Atomic composition: | ||
+ | |||
+ | Carbon C 1694 | ||
+ | Hydrogen H 2600 | ||
+ | Nitrogen N 422 | ||
+ | Oxygen O 471 | ||
+ | Sulfur S 13 | ||
+ | |||
+ | Formula: C1694H2600N422O471S13 | ||
+ | Total number of atoms: 5200 | ||
+ | |||
+ | Extinction coefficients: | ||
+ | |||
+ | Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | ||
+ | |||
+ | Ext. coefficient 90090 | ||
+ | Abs 0.1% (=1 g/l) 2.446, assuming all pairs of Cys residues form cystines | ||
+ | |||
+ | |||
+ | Ext. coefficient 89840 | ||
+ | Abs 0.1% (=1 g/l) 2.439, 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 26.91 | ||
+ | This classifies the protein as stable. | ||
+ | |||
+ | |||
+ | |||
+ | Aliphatic index: 104.87 | ||
+ | Grand average of hydropathicity (GRAVY): 0.327 | ||
+ | |||
Latest revision as of 01:52, 26 September 2013
ChlG
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 386
Illegal BglII site found at 875
Illegal BamHI site found at 155 - 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
Amino acid sequence
MNQQATEEKS DTNSAARQML GMKGAALETD IWKIRVQLTK PVTWIPLIWG VACGAAASGH YQWNNPTQIA QLLTCMMMSG PFLTGYTQTI NDWYDREIDA INEPYRPIPS GRISERDVIV QIWVLLLGGI GLAYTLDQWA GHTTPVMLQL TIFGSFISYI YSAPPLKLKQ SGWAGNYALG SSYIALPWWA GQALFGTLTL DVMALTIAYS LAGLGIAIVN DFKSIEGDRQ MGLQSLPVAF GVDTAKWICV STIDVTQLGV AAYLAWGLHE ELYGAVLLAL ILPQIYFQYK YFLPDPIAND VKYQASAQPF LVFGLLTAGL ACGHHVNAVA AAASAAGAL
References and documentation are available. Please note the modified algorithm for extinction coefficient.
Number of amino acids: 339
Molecular weight: 36830.6
Theoretical pI: 5.30
Amino acid composition: Ala (A) 43 12.7% Arg (R) 7 2.1% Asn (N) 10 2.9% Asp (D) 14 4.1% Cys (C) 4 1.2% Gln (Q) 20 5.9% Glu (E) 9 2.7% Gly (G) 30 8.8% His (H) 5 1.5% Ile (I) 26 7.7% Leu (L) 40 11.8% Lys (K) 10 2.9% Met (M) 9 2.7% Phe (F) 10 2.9% Pro (P) 16 4.7% Ser (S) 18 5.3% Thr (T) 21 6.2% Trp (W) 12 3.5% Tyr (Y) 16 4.7% Val (V) 19 5.6% 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): 23
Total number of positively charged residues (Arg + Lys): 17
Atomic composition:
Carbon C 1694 Hydrogen H 2600 Nitrogen N 422 Oxygen O 471 Sulfur S 13
Formula: C1694H2600N422O471S13 Total number of atoms: 5200
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 90090 Abs 0.1% (=1 g/l) 2.446, assuming all pairs of Cys residues form cystines
Ext. coefficient 89840
Abs 0.1% (=1 g/l) 2.439, 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 26.91 This classifies the protein as stable.
Aliphatic index: 104.87
Grand average of hydropathicity (GRAVY): 0.327
Source
Chlamydomonas reinhardtii