Difference between revisions of "Part:BBa K1080004:Design"

 
(→‎Design Notes)
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===Design Notes===
 
===Design Notes===
−
sdrgdtr
 
  
 +
ChlM Clone: DNA sequence from translation start site:
 +
Regions in BOLD are the sequence of the leader region in the pET100 plasmid.
 +
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 sites: PstI, XbaI, SpeI or EcoRI
 +
 +
<b>ATG CGG GGT TCT CAT CAT CAT CAT CAT CAT GGT ATG GCT AGC ATG ACT GGT GGA
 +
 +
CAG CAA ATG GGT CGG GAT CTG TAC GAC GAT GAC GAT AAG GAT CAT CCC TTC ACC</b>
 +
 +
 +
<FONT FACE="courier">ATGGCTTCTGAGATTGCTCAAACTGCCGATGTTGGCTCGCTGACCTTCGCGGTTGGCGGA
 +
 +
GTGGGCGCTGTTGTGGGCCTGGGCGCCCTGCTTGTCGCTACTGACCCTCAGAAGCGCCGC
 +
 +
TCGGAGCAGATGAAGTCATTCGACGGCGATGAGAAGGAGGCGGTGAAGGACTACTTCAAC
 +
 +
ACTGCCGGCTTCGAGCGCTGGCGCAAGATCTACGGCGAGACGGACGAGGTGAACAAGGTG
 +
 +
CAGCTGGACATCCGCACTGGCCACGCGCAGACGGTGGACAAGGTGCTGCGCTGGGTGGAC
 +
 +
GAGGAGGGCAGCGTGCAGGGCATCACCGTGGCGGACTGCGGCTGCGGGACAGGCAGCCTG
 +
 +
GCCATCCCGCTGGCGCTGCGCGGCGCCGCCGTCAGCGCCTCCGACATCTCCGCCGCCATG
 +
 +
GCGTCTGAGGCGGAGCAGCGCTACCAGCAGGCGGTGGCGGCCGGGCAGGGCAAGGCGCCC
 +
 +
AAGGTGGCGCCCAAGTTCGAGGCGCTGGACCTGGAGTCCGTCAAGGGCAAGTACGACACG
 +
 +
GTCACTTGCCTGGACGTGATGATTCACTACCCCCAGGACAAGGTGGACGCCATGATCACG
 +
 +
CACCTGGCGGGTCTGTCCGACCGCCGCCTCATCATCTCGTTCGCACCCAAGACGCTGTCG
 +
 +
TACAGCATCCTCAAGCGCATTGGCGAGCTGTTCCCCGGCCCCAGCAAGGCCACCCGCGCC
 +
 +
TACCTGCACCGTGAGGAGGACGTGGAGGCTGCCCTCAAGCGCGCCGGCTTCAAGGTCACC
 +
 +
AAGCGTGAGATGACCGCCACCAGCTTCTACTTCTCGCGCCTGCTGGAGGCCATCCGCGAG
 +
 +
TAATCTCGCAAACGTTCTCGTGTAAATAGCGTAGCAGTGCAGGACTGGTGTAAGGACTGA
 +
 +
TGGACTCGGACCGGCGCTGCGGCCGGGTATGAGGGCATGGGCGTGGGCGCTGCTAGGGTG
 +
 +
CTACGGTGCAGCGCGGTTTTGACGGGCTATAGACATTTATGTGACTGAGTGACGGGCGGA
 +
 +
TAGCCAAAACGATTGTGTGAACG</FONT>
 +
 +
<b>Amino acid sequence</b>
 +
 +
<FONT FACE="courier">MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDHPFTMASE IAQTADVGSL TFAVGGVGAV
 +
 +
VGLGALLVAT DPQKRRSEQM KSFDGDEKEA VKDYFNTAGF ERWRKIYGET DEVNKVQLDI
 +
 +
RTGHAQTVDK VLRWVDEEGS VQGITVADCG CGTGSLAIPL ALRGAAVSAS DISAAMASEA
 +
 +
EQRYQQAVAA GQGKAPKVAP KFEALDLESV KGKYDTVTCL DVMIHYPQDK VDAMITHLAG
 +
 +
LSDRRLIISF APKTLSYSIL KRIGELFPGP SKATRAYLHR EEDVEAALKR AGFKVTKREM
 +
 +
TATSFYFSRL LEAIRE</FONT>
 +
 +
Number of amino acids: 316
 +
 +
Molecular weight: 34495.0
 +
 +
Theoretical pI: 6.14
 +
 +
Amino acid composition:
 +
 +
Ala (A)  37 11.7%
 +
Arg (R)  19   6.0%
 +
Asn (N)  2   0.6%
 +
Asp (D)  24   7.6%
 +
Cys (C)  3   0.9%
 +
Gln (Q)  13   4.1%
 +
Glu (E)  20   6.3%
 +
Gly (G)  28   8.9%
 +
His (H)  11   3.5%
 +
Ile (I)  13   4.1%
 +
Leu (L)  23   7.3%
 +
Lys (K)  20   6.3%
 +
Met (M)  10   3.2%
 +
Phe (F)  11   3.5%
 +
Pro (P)  9   2.8%
 +
Ser (S)  20   6.3%
 +
Thr (T)  19   6.0%
 +
Trp (W)  2   0.6%
 +
Tyr (Y)  9   2.8%
 +
Val (V)  23   7.3%
 +
 +
Asx (B)  0   0.0%
 +
Glx (Z)  0   0.0%
 +
Xaa (X)  0   0.0%
 +
 +
Total number of negatively charged residues (Asp + Glu): 44
 +
Total number of positively charged residues (Arg + Lys): 39
 +
 +
Atomic composition:
 +
 +
Carbon      C       1509
 +
Hydrogen    H       2396
 +
Nitrogen    N       432
 +
Oxygen      O       468
 +
Sulfur      S         13
 +
 +
Formula: C1509H2396N432O468S13
 +
Total number of atoms: 4818
 +
 +
Extinction coefficients:
 +
 +
Extinction coefficients are in units of  M-1 cm-1, at 280 nm.
 +
 +
Ext. coefficient    24535
 +
Abs 0.1% (=1 g/l)  0.711, assuming ALL Cys residues appear as half cystines
 +
 +
 +
 +
Ext. coefficient    24410
 +
Abs 0.1% (=1 g/l)  0.708, assuming NO Cys residues appear as half cystines
 +
 +
 +
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 33.76
 +
This classifies the protein as stable.
 +
 +
 +
 +
Aliphatic index: 77.25
 +
 +
Grand average of hydropathicity (GRAVY): -0.339
  
 
===Source===
 
===Source===

Revision as of 03:21, 24 September 2013


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: Regions in BOLD are the sequence of the leader region in the pET100 plasmid. 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 sites: PstI, XbaI, SpeI or EcoRI

ATG CGG GGT TCT CAT CAT CAT CAT CAT CAT GGT ATG GCT AGC ATG ACT GGT GGA

CAG CAA ATG GGT CGG GAT CTG TAC GAC GAT GAC GAT AAG GAT CAT CCC TTC ACC


ATGGCTTCTGAGATTGCTCAAACTGCCGATGTTGGCTCGCTGACCTTCGCGGTTGGCGGA

GTGGGCGCTGTTGTGGGCCTGGGCGCCCTGCTTGTCGCTACTGACCCTCAGAAGCGCCGC

TCGGAGCAGATGAAGTCATTCGACGGCGATGAGAAGGAGGCGGTGAAGGACTACTTCAAC

ACTGCCGGCTTCGAGCGCTGGCGCAAGATCTACGGCGAGACGGACGAGGTGAACAAGGTG

CAGCTGGACATCCGCACTGGCCACGCGCAGACGGTGGACAAGGTGCTGCGCTGGGTGGAC

GAGGAGGGCAGCGTGCAGGGCATCACCGTGGCGGACTGCGGCTGCGGGACAGGCAGCCTG

GCCATCCCGCTGGCGCTGCGCGGCGCCGCCGTCAGCGCCTCCGACATCTCCGCCGCCATG

GCGTCTGAGGCGGAGCAGCGCTACCAGCAGGCGGTGGCGGCCGGGCAGGGCAAGGCGCCC

AAGGTGGCGCCCAAGTTCGAGGCGCTGGACCTGGAGTCCGTCAAGGGCAAGTACGACACG

GTCACTTGCCTGGACGTGATGATTCACTACCCCCAGGACAAGGTGGACGCCATGATCACG

CACCTGGCGGGTCTGTCCGACCGCCGCCTCATCATCTCGTTCGCACCCAAGACGCTGTCG

TACAGCATCCTCAAGCGCATTGGCGAGCTGTTCCCCGGCCCCAGCAAGGCCACCCGCGCC

TACCTGCACCGTGAGGAGGACGTGGAGGCTGCCCTCAAGCGCGCCGGCTTCAAGGTCACC

AAGCGTGAGATGACCGCCACCAGCTTCTACTTCTCGCGCCTGCTGGAGGCCATCCGCGAG

TAATCTCGCAAACGTTCTCGTGTAAATAGCGTAGCAGTGCAGGACTGGTGTAAGGACTGA

TGGACTCGGACCGGCGCTGCGGCCGGGTATGAGGGCATGGGCGTGGGCGCTGCTAGGGTG

CTACGGTGCAGCGCGGTTTTGACGGGCTATAGACATTTATGTGACTGAGTGACGGGCGGA

TAGCCAAAACGATTGTGTGAACG

Amino acid sequence

MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDHPFTMASE IAQTADVGSL TFAVGGVGAV

VGLGALLVAT DPQKRRSEQM KSFDGDEKEA VKDYFNTAGF ERWRKIYGET DEVNKVQLDI

RTGHAQTVDK VLRWVDEEGS VQGITVADCG CGTGSLAIPL ALRGAAVSAS DISAAMASEA

EQRYQQAVAA GQGKAPKVAP KFEALDLESV KGKYDTVTCL DVMIHYPQDK VDAMITHLAG

LSDRRLIISF APKTLSYSIL KRIGELFPGP SKATRAYLHR EEDVEAALKR AGFKVTKREM

TATSFYFSRL LEAIRE

Number of amino acids: 316

Molecular weight: 34495.0

Theoretical pI: 6.14

Amino acid composition:

Ala (A) 37 11.7% Arg (R) 19 6.0% Asn (N) 2 0.6% Asp (D) 24 7.6% Cys (C) 3 0.9% Gln (Q) 13 4.1% Glu (E) 20 6.3% Gly (G) 28 8.9% His (H) 11 3.5% Ile (I) 13 4.1% Leu (L) 23 7.3% Lys (K) 20 6.3% Met (M) 10 3.2% Phe (F) 11 3.5% Pro (P) 9 2.8% Ser (S) 20 6.3% Thr (T) 19 6.0% Trp (W) 2 0.6% Tyr (Y) 9 2.8% Val (V) 23 7.3%

Asx (B) 0 0.0% Glx (Z) 0 0.0% Xaa (X) 0 0.0%

Total number of negatively charged residues (Asp + Glu): 44 Total number of positively charged residues (Arg + Lys): 39

Atomic composition:

Carbon C 1509 Hydrogen H 2396 Nitrogen N 432 Oxygen O 468 Sulfur S 13

Formula: C1509H2396N432O468S13 Total number of atoms: 4818

Extinction coefficients:

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

Ext. coefficient 24535 Abs 0.1% (=1 g/l) 0.711, assuming ALL Cys residues appear as half cystines


Ext. coefficient 24410 Abs 0.1% (=1 g/l) 0.708, assuming NO Cys residues appear as half cystines


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 33.76 This classifies the protein as stable.


Aliphatic index: 77.25

Grand average of hydropathicity (GRAVY): -0.339

Source

Chlamydomonas reinhardtii

References