Coding
"Eye 1"

Part:BBa_K1080000:Design

Designed by: Macquarie University   Group: iGEM13_Macquarie_Australia   (2013-09-22)
Revision as of 02:24, 25 September 2013 by DMC (Talk | contribs) (→‎Design Notes)


ChlI1


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 231
    Illegal BglII site found at 887
    Illegal BglII site found at 1082
    Illegal BamHI site found at 279
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence

ChlI1 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 restriction sites (EcoRI, XbaI, SpeI or PstI). Note This won’t work with the highlighted tag in the magnesium chelatase reaction.

Amino Acid Sequence

ProtParam

User-provided sequence:

RPIFPFTAIV GQDEMKLALI LNVIDPKIGG VMIMGDRGTG KSTTIRALAD LLPEMQVVAN DPFNSDPTDP ELMSEEVRNR VKAGEQLPVS SKKIPMVDLP
LGATEDRVCG TIDIEKALTE GVKAFEPGLL AKANRGILYV DEVNLLDDHL VDVLLDSAAS GWNTVEREGI SISHPARFIL VGSGNPEEGE LRPQLLDRFG MHAQIGTVKD PRLRVQIVSQ RSTFDENPAA FRKDYEAGQM ALTQRIVDAR KLLKQGEVNY DFRVKISQIC SDLNVDGIRG DIVTNRAAKA LAAFEGRTEV TPEDIYRVIP LCLRHRLRKD PLAEIDDGDR VREIFKQVFG ME

References and documentation are available. Please note the modified algorithm for extinction coefficient.

Number of amino acids: 342

Molecular weight: 37880.4

Theoretical pI: 5.14

Amino acid composition: Ala (A) 26 7.6% Arg (R) 27 7.9% Asn (N) 12 3.5% Asp (D) 29 8.5% Cys (C) 3 0.9% Gln (Q) 12 3.5% Glu (E) 25 7.3% Gly (G) 26 7.6% His (H) 4 1.2% Ile (I) 25 7.3% Leu (L) 33 9.6% Lys (K) 17 5.0% Met (M) 9 2.6% Phe (F) 12 3.5% Pro (P) 19 5.6% Ser (S) 14 4.1% Thr (T) 15 4.4% Trp (W) 1 0.3% Tyr (Y) 4 1.2% Val (V) 29 8.5% 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): 54 Total number of positively charged residues (Arg + Lys): 44

Atomic composition:

Carbon C 1666 Hydrogen H 2711 Nitrogen N 473 Oxygen O 508 Sulfur S 12

Formula: C1666H2711N473O508S12 Total number of atoms: 5370

Extinction coefficients:

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

Ext. coefficient 11585 Abs 0.1% (=1 g/l) 0.306, assuming all pairs of Cys residues form cystines


Ext. coefficient 11460 Abs 0.1% (=1 g/l) 0.303, assuming all Cys residues are reduced

Estimated half-life:

The N-terminal of the sequence considered is R (Arg).

The estimated half-life is: 

                           1 hours (mammalian reticulocytes, in vitro).
                           2 min (yeast, in vivo).
                           2 min (Escherichia coli, in vivo).


Instability index:

The instability index (II) is computed to be 29.48 This classifies the protein as stable.


Aliphatic index: 98.33

Grand average of hydropathicity (GRAVY): -0.227

Source

Chlamydomonas reinhardtii

References