Coding
"M"

Part:BBa_K1080004:Design

Designed by: Macquarie University   Group: iGEM13_Macquarie_Australia   (2013-09-22)
Revision as of 02:48, 25 September 2013 by DMC (Talk | contribs) (→‎Design Notes)


ChlM


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 230
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

ChlM 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: PstI, XbaI, SpeI or EcoRI

VGAVVGLGAL LVATDHQKRR SEQMKSFDGD EKEAVKDYFN TAGFERWRKI YGETDEVNKV QLDIRTGHAQ TVDKVLRWVD EEGSVQGITV ADCGCGTGSL
AIQLALRGAA VSASDISAAM ASEAEQRYQQ AVAAGQGKAP KVAPKFEALD LESVKGKYDT VTCLDVMIHY PQDKVDAMIT HLAGLSDRRL IISFAPKTLS
YSILKRIGEL FPGPSKATRA YLHREEDVEA ALKRAGFKVT KREMTATSFY FSRLLEAIRE References and documentation are available.

Please note the modified algorithm for extinction coefficient.

Number of amino acids: 260

Molecular weight: 28533.5

Theoretical pI: 7.12

Amino acid composition: Ala (A) 32 12.3% Arg (R) 17 6.5% Asn (N) 2 0.8% Asp (D) 17 6.5% Cys (C) 3 1.2% Gln (Q) 11 4.2% Glu (E) 19 7.3% Gly (G) 20 7.7% His (H) 5 1.9% Ile (I) 12 4.6% Leu (L) 21 8.1% Lys (K) 19 7.3% Met (M) 5 1.9% Phe (F) 9 3.5% Pro (P) 6 2.3% Ser (S) 16 6.2% Thr (T) 15 5.8% Trp (W) 2 0.8% Tyr (Y) 8 3.1% Val (V) 21 8.1% 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): 36 Total number of positively charged residues (Arg + Lys): 36

Atomic composition:

Carbon C 1258 Hydrogen H 2019 Nitrogen N 355 Oxygen O 385 Sulfur S 8

Formula: C1258H2019N355O385S8 Total number of atoms: 4025

Extinction coefficients:

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

Ext. coefficient 23045 Abs 0.1% (=1 g/l) 0.808, assuming all pairs of Cys residues form cystines


Ext. coefficient 22920 Abs 0.1% (=1 g/l) 0.803, assuming all Cys residues are reduced

Estimated half-life:

The N-terminal of the sequence considered is V (Val).

The estimated half-life is: 

                            100 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 34.87 This classifies the protein as stable.


Aliphatic index: 85.23

Grand average of hydropathicity (GRAVY): -0.267

Source

Chlamydomonas reinhardtii

References