Difference between revisions of "Part:BBa K1080008:Design"

(→‎Design Notes)
 
Line 1: Line 1:
−
 
 
__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K1080008 short</partinfo>
 
<partinfo>BBa_K1080008 short</partinfo>
Line 5: Line 4:
 
<partinfo>BBa_K1080008 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K1080008 SequenceAndFeatures</partinfo>
  
 +
<b> Amino acid sequence</b>
 +
 +
<FONT FACE="courier">MVIGGGPSGA CAAETLAKGG VETFLLERKL DNCKPCGGAI PLCMVEEFDL PMEIIDRRVT<br> KMKMISPSNR EVDVGKTLSE TEWIGMCRRE VFDDYLRNRA QKLGANIVNG LFMRSEQQSA<br>  EGPFTIHYNS YEDGSKMGKP ATLEVDMIIG ADGANSRIAK EIDAGEYDYA IAFQERIRIP<br> DDKMKYYENL AEMYVGDDVS PDFYGWVFPK YDHVAVGTGT VVNKTAIKQY QQATRDRSKV<br> KTEGGKIIRV EAHPIPEHPR PRRCKGRVAL VGDAAGYVTK CSGEGIYFAA KSGRMAAEAI<br>    VEGSANGTKM CGEDAIRVYL DKWDRKYWTT YKVLDILQKV FYRSNPAREA FVELCEDSYV<br> QKMTFDSYLY KTVVPGNPLD DVKLLVRTVS SILRSNALRS VNSKSVNVSF GSKANEERVM<br> AA </FONT> 
 +
 +
References and documentation are available.
 +
Please note the modified algorithm for extinction coefficient.
 +
 +
--------------------------------------------------------------------------------
 +
Number of amino acids: 422
 +
 +
Molecular weight: 47011.7
 +
 +
Theoretical pI: 7.48
 +
 +
Amino acid composition: Ala (A)  36   8.5%
 +
Arg (R)  28   6.6%
 +
Asn (N)  16   3.8%
 +
Asp (D)  27   6.4%
 +
Cys (C)  9   2.1%
 +
Gln (Q)  9   2.1%
 +
Glu (E)  31   7.3%
 +
Gly (G)  35   8.3%
 +
His (H)  4   0.9%
 +
Ile (I)  24   5.7%
 +
Leu (L)  23   5.5%
 +
Lys (K)  31   7.3%
 +
Met (M)  15   3.6%
 +
Phe (F)  13   3.1%
 +
Pro (P)  17   4.0%
 +
Ser (S)  25   5.9%
 +
Thr (T)  19   4.5%
 +
Trp (W)  4   0.9%
 +
Tyr (Y)  20   4.7%
 +
Val (V)  36   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): 58
 +
Total number of positively charged residues (Arg + Lys): 59
 +
 +
Atomic composition:
 +
 +
Carbon      C       2069
 +
Hydrogen    H       3278
 +
Nitrogen    N       574
 +
Oxygen      O       628
 +
Sulfur      S         24
 +
 +
Formula: C2069H3278N574O628S24
 +
Total number of atoms: 6573
 +
 +
Extinction coefficients:
 +
 +
Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
 +
 +
Ext. coefficient    52300
 +
Abs 0.1% (=1 g/l)  1.112, assuming all pairs of Cys residues form cystines
 +
 +
 +
Ext. coefficient    51800
 +
Abs 0.1% (=1 g/l)  1.102, 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 42.25
 +
This classifies the protein as unstable.
 +
 +
 +
 +
Aliphatic index: 76.71
 +
 +
Grand average of hydropathicity (GRAVY): -0.368
  
 
===Design Notes===
 
===Design Notes===

Latest revision as of 01:48, 26 September 2013

ChlP


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 64

Amino acid sequence

MVIGGGPSGA CAAETLAKGG VETFLLERKL DNCKPCGGAI PLCMVEEFDL PMEIIDRRVT
KMKMISPSNR EVDVGKTLSE TEWIGMCRRE VFDDYLRNRA QKLGANIVNG LFMRSEQQSA
EGPFTIHYNS YEDGSKMGKP ATLEVDMIIG ADGANSRIAK EIDAGEYDYA IAFQERIRIP
DDKMKYYENL AEMYVGDDVS PDFYGWVFPK YDHVAVGTGT VVNKTAIKQY QQATRDRSKV
KTEGGKIIRV EAHPIPEHPR PRRCKGRVAL VGDAAGYVTK CSGEGIYFAA KSGRMAAEAI
VEGSANGTKM CGEDAIRVYL DKWDRKYWTT YKVLDILQKV FYRSNPAREA FVELCEDSYV
QKMTFDSYLY KTVVPGNPLD DVKLLVRTVS SILRSNALRS VNSKSVNVSF GSKANEERVM
AA

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

Number of amino acids: 422

Molecular weight: 47011.7

Theoretical pI: 7.48

Amino acid composition: Ala (A) 36 8.5% Arg (R) 28 6.6% Asn (N) 16 3.8% Asp (D) 27 6.4% Cys (C) 9 2.1% Gln (Q) 9 2.1% Glu (E) 31 7.3% Gly (G) 35 8.3% His (H) 4 0.9% Ile (I) 24 5.7% Leu (L) 23 5.5% Lys (K) 31 7.3% Met (M) 15 3.6% Phe (F) 13 3.1% Pro (P) 17 4.0% Ser (S) 25 5.9% Thr (T) 19 4.5% Trp (W) 4 0.9% Tyr (Y) 20 4.7% Val (V) 36 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): 58 Total number of positively charged residues (Arg + Lys): 59

Atomic composition:

Carbon C 2069 Hydrogen H 3278 Nitrogen N 574 Oxygen O 628 Sulfur S 24

Formula: C2069H3278N574O628S24 Total number of atoms: 6573

Extinction coefficients:

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

Ext. coefficient 52300 Abs 0.1% (=1 g/l) 1.112, assuming all pairs of Cys residues form cystines


Ext. coefficient 51800 Abs 0.1% (=1 g/l) 1.102, 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 42.25 This classifies the protein as unstable.


Aliphatic index: 76.71

Grand average of hydropathicity (GRAVY): -0.368

Design Notes

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

Source

Chlamydomonas reinhardtii

References