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

(→‎Design Notes)
(→‎Design Notes)
 
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ChlM Clone: DNA sequence from translation start site:
 
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
 
Translated the DNA sequence into a protein sequence
 
using "Translate" at http://au.expasy.org/tools
 
using "Translate" at http://au.expasy.org/tools
Line 15: Line 15:
 
"ProtParam" at http://au.expasy.org/tools
 
"ProtParam" at http://au.expasy.org/tools
  
−
No Biobrick sites: PstI, XbaI, SpeI or EcoRI
+
No Biobrick restriction 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
+
<b> Amino Acid Sequence </b>
  
−
CAG CAA ATG GGT CGG GAT CTG TAC GAC GAT GAC GAT AAG GAT CAT CCC TTC ACC</b>
+
<FONT FACE="courier">MASEIAQTAD VGSLTFAVGG VGAVVGLGAL LVATDHQKRR SEQMKSFDGD EKEAVKDYFN<br> TAGFERWRKI YGETDEVNKV QLDIRTGHAQ TVDKVLRWVD EEGSVQGITV ADCGCGTGSL<br> AIQLALRGAA VSASDISAAM ASEAEQRYQQ AVAAGQGKAP KVAPKFEALD LESVKGKYDT<br> VTCLDVMIHY PQDKVDAMIT HLAGLSDRRL IISFAPKTLS YSILKRIGEL FPGPSKATRA<br> YLHREEDVEA ALKRAGFKVT KREMTATSFY FSRLLEAIRE </FONT>
 +
 +
References and documentation are available.
 +
Please note the modified algorithm for extinction coefficient.
  
 +
--------------------------------------------------------------------------------
 +
Number of amino acids: 280
  
−
<FONT FACE="courier">ATGGCTTCTGAGATTGCTCAAACTGCCGATGTTGGCTCGCTGACCTTCGCGGTTGGCGGA
+
Molecular weight: 30440.6
  
−
GTGGGCGCTGTTGTGGGCCTGGGCGCCCTGCTTGTCGCTACTGACCCTCAGAAGCGCCGC
+
Theoretical pI: 6.25
  
−
TCGGAGCAGATGAAGTCATTCGACGGCGATGAGAAGGAGGCGGTGAAGGACTACTTCAAC
+
Amino acid composition: Ala (A)  36 12.9%
 +
Arg (R)  17   6.1%
 +
Asn (N)  2   0.7%
 +
Asp (D)  18   6.4%
 +
Cys (C)  3   1.1%
 +
Gln (Q)  12   4.3%
 +
Glu (E)  20   7.1%
 +
Gly (G)  23   8.2%
 +
His (H)  5   1.8%
 +
Ile (I)  13   4.6%
 +
Leu (L)  22   7.9%
 +
Lys (K)  19   6.8%
 +
Met (M)  6   2.1%
 +
Phe (F)  10   3.6%
 +
Pro (P)  6   2.1%
 +
Ser (S)  18   6.4%
 +
Thr (T)  17   6.1%
 +
Trp (W)  2   0.7%
 +
Tyr (Y)  8   2.9%
 +
Val (V)  23   8.2%
 +
Pyl (O)  0   0.0%
 +
Sec (U)  0   0.0%
  
−
ACTGCCGGCTTCGAGCGCTGGCGCAAGATCTACGGCGAGACGGACGAGGTGAACAAGGTG
+
(B)  0   0.0%
 +
(Z)  0   0.0%
 +
(X)  0   0.0%
  
−
CAGCTGGACATCCGCACTGGCCACGCGCAGACGGTGGACAAGGTGCTGCGCTGGGTGGAC
 
  
−
GAGGAGGGCAGCGTGCAGGGCATCACCGTGGCGGACTGCGGCTGCGGGACAGGCAGCCTG
+
Total number of negatively charged residues (Asp + Glu): 38
−
 
+
Total number of positively charged residues (Arg + Lys): 36
−
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:
 
Atomic composition:
  
−
Carbon      C       1509
+
Carbon      C       1340
−
Hydrogen    H       2396
+
Hydrogen    H       2150
−
Nitrogen    N       432
+
Nitrogen    N       376
−
Oxygen      O       468
+
Oxygen      O       414
−
Sulfur      S         13
+
Sulfur      S         9
  
−
Formula: C1509H2396N432O468S13
+
Formula: C1340H2150N376O414S9
−
Total number of atoms: 4818
+
Total number of atoms: 4289
  
 
Extinction coefficients:
 
Extinction coefficients:
  
−
Extinction coefficients are in units of  M-1 cm-1, at 280 nm.
+
Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
  
−
Ext. coefficient    24535
+
Ext. coefficient    23045
−
Abs 0.1% (=1 g/l)  0.711, assuming ALL Cys residues appear as half cystines
+
Abs 0.1% (=1 g/l)  0.757, assuming all pairs of Cys residues form cystines
  
  
−
 
+
Ext. coefficient    22920
−
Ext. coefficient    24410
+
Abs 0.1% (=1 g/l)  0.753, assuming all Cys residues are reduced
−
Abs 0.1% (=1 g/l)  0.708, assuming NO Cys residues appear as half cystines
+
−
 
+
  
 
Estimated half-life:
 
Estimated half-life:
Line 144: Line 96:
 
Instability index:
 
Instability index:
  
−
The instability index (II) is computed to be 33.76
+
The instability index (II) is computed to be 34.88
 
This classifies the protein as stable.
 
This classifies the protein as stable.
  
  
  
−
Aliphatic index: 77.25
+
Aliphatic index: 85.43
 +
 
 +
Grand average of hydropathicity (GRAVY): -0.198
 +
 +
 
  
−
Grand average of hydropathicity (GRAVY): -0.339
+
SIB Swiss Institute of Bioinformatics | Disclaimer
  
 
===Source===
 
===Source===

Latest revision as of 10:27, 25 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:

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

Amino Acid Sequence

MASEIAQTAD VGSLTFAVGG 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: 280

Molecular weight: 30440.6

Theoretical pI: 6.25

Amino acid composition: Ala (A) 36 12.9% Arg (R) 17 6.1% Asn (N) 2 0.7% Asp (D) 18 6.4% Cys (C) 3 1.1% Gln (Q) 12 4.3% Glu (E) 20 7.1% Gly (G) 23 8.2% His (H) 5 1.8% Ile (I) 13 4.6% Leu (L) 22 7.9% Lys (K) 19 6.8% Met (M) 6 2.1% Phe (F) 10 3.6% Pro (P) 6 2.1% Ser (S) 18 6.4% Thr (T) 17 6.1% Trp (W) 2 0.7% Tyr (Y) 8 2.9% Val (V) 23 8.2% 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): 38 Total number of positively charged residues (Arg + Lys): 36

Atomic composition:

Carbon C 1340 Hydrogen H 2150 Nitrogen N 376 Oxygen O 414 Sulfur S 9

Formula: C1340H2150N376O414S9 Total number of atoms: 4289

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) 0.757, assuming all pairs of Cys residues form cystines


Ext. coefficient 22920 Abs 0.1% (=1 g/l) 0.753, 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 34.88 This classifies the protein as stable.


Aliphatic index: 85.43

Grand average of hydropathicity (GRAVY): -0.198


SIB Swiss Institute of Bioinformatics | Disclaimer

Source

Chlamydomonas reinhardtii

References