Coding
"D"

Part:BBa_K1080002:Design

Designed by: Macquarie University   Group: iGEM13_Macquarie_Australia   (2013-09-22)
Revision as of 06:32, 24 September 2013 by DMC (Talk | contribs) (→‎Design Notes)

ChlD


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NotI site found at 1334
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 2039
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 614
    Illegal NgoMIV site found at 1433
    Illegal NgoMIV site found at 1975
  • 1000
    COMPATIBLE 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:

MGRDLYDDDD KDHPFTLRAM KVSEEDSKGF DADVSTRLAR

SYPLAAVVGQ DNIKQALLLG AVDTGLGGIA IAGRRGTAKS IMARGLHALL PPIEVVEGSI

CNADPEDPRS WEAGLAEKYA GGPVKTKMRS APFVQIPLGV TEDRLVGTVD IEASMKEGKT

VFQPGLLAEA HRGILYVDEI NLLDDGIANL LLSILSDGVN VVEREGISIS HPCRPLLIAT

YNPEEGPLRE HLLDRIAIGL SADVPSTSDE RVKAIDAAIR FQDKPQDTID DTAELTDALR

TSVILAREYL KDVTIAPEQV TYIVEEARRG GVQGHRAELY AVKCAKACAA LEGRERVNKD

DLRQAVQLVI LPRATILDQP PPEQEQPPPP PPPPPPPPPQ DQMEDEDQEE KEDEKEEEEK

ENEDQDEPEI PQEFMFESEG VIMDPSILMF AQQQQRAQGR SGRAKTLIFS DDRGRYIKPM

LPKGDKVKRL AVDATLRAAA PYQKIRRQQA ISEGKVQRKV YVDKPDMRSK KLARKAGALV

IFVVDASGSM ALNRMSAAKG ACMRLLAESY TSRDQVCLIP FYGDKAEVLL PPSKSIAMAR

RRLDSLPCGG GSPLAHGLST AVRVGMQASQ AGEVGRVMMV LITDGRANVS LAKSNEDPEA

LKPDAPKPTA DSLKDEVRDM AKKAASAGIN VLVIDTENKF VSTGFAEEIS KAAQGKYYYL

PNASDAAIAA AASGAMAAAK GGY


References and documentation are available.

Please note the modified algorithm for extinction coefficient.


Number of amino acids: 743

Molecular weight: 80527.5

Theoretical pI: 5.37

Amino acid composition: Ala (A) 89 12.0% Arg (R) 49 6.6% Asn (N) 14 1.9% Asp (D) 57 7.7% Cys (C) 7 0.9% Gln (Q) 33 4.4% Glu (E) 55 7.4% Gly (G) 56 7.5% His (H) 13 1.7% Ile (I) 40 5.4% Leu (L) 62 8.3% Lys (K) 44 5.9% Met (M) 23 3.1% Phe (F) 13 1.7% Pro (P) 51 6.9% Ser (S) 44 5.9% Thr (T) 26 3.5% Trp (W) 1 0.1% Tyr (Y) 17 2.3% Val (V) 49 6.6% 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): 112 Total number of positively charged residues (Arg + Lys): 93

Atomic composition:

Carbon C 3504 Hydrogen H 5684 Nitrogen N 1008 Oxygen O 1102 Sulfur S 30

Formula: C3504H5684N1008O1102S30 Total number of atoms: 11328

Extinction coefficients:

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

Ext. coefficient 31205 Abs 0.1% (=1 g/l) 0.388, assuming all pairs of Cys residues form cystines


Ext. coefficient 30830 Abs 0.1% (=1 g/l) 0.383, 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 44.71 This classifies the protein as unstable.


Aliphatic index: 84.64

Grand average of hydropathicity (GRAVY): -0.392

Source

Chlamydomonas reinhardtii

References