Difference between revisions of "Part:BBa K1080005:Design"
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CTH1 Clone: DNA sequence from translation start site: | CTH1 Clone: DNA sequence from translation start site: | ||
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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 | ||
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"ProtParam" at http://au.expasy.org/tools | "ProtParam" at http://au.expasy.org/tools | ||
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− | + | <b>Amino acid sequence</b> | |
+ | <b><FONT FACE="courier">MVAATAAPQE VEGFKVMRDG IKVASDETLL TPRFYTTDFD EMERLFSLEL NKNMDMEEFE<br> AMLNEFKLDY NQRHFVRNET FKEAAEKIQG PTRKIFIEFL ERSCTAEFSG FLLYKELGRR<br> LKATNPVVAE IFTLMSRDEA RHAGFLNKAM SDFNLALDLG FLTKNRKYTF FKPKFIFYAT<br> YLSEKIGYWR YISIYRHLQR NPDNQLYPLF EYFENWCQDE NRHGDFFTAV LKARPEMVND<br> WAAKLWSRFF CLSVYITMYL NDHQRDAFYS SLGLNTTQFN QHVIIETNKS TERIFPAVPD<br> VENPEFFRRM DLLVKYNAQL VNIGSMNLPS PIKAIMKAPI LERMVAEVFQ VFIMTPKESG<br> SYDLDANKTA LVY </FONT> | ||
− | + | References and documentation are available. | |
− | + | Please note the modified algorithm for extinction coefficient. | |
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+ | -------------------------------------------------------------------------------- | ||
+ | Number of amino acids: 373 | ||
− | + | Molecular weight: 43873.3 | |
− | + | Theoretical pI: 5.98 | |
− | + | Amino acid composition: Ala (A) 28 7.5% | |
+ | Arg (R) 23 6.2% | ||
+ | Asn (N) 23 6.2% | ||
+ | Asp (D) 19 5.1% | ||
+ | Cys (C) 3 0.8% | ||
+ | Gln (Q) 11 2.9% | ||
+ | Glu (E) 31 8.3% | ||
+ | Gly (G) 12 3.2% | ||
+ | His (H) 6 1.6% | ||
+ | Ile (I) 18 4.8% | ||
+ | Leu (L) 35 9.4% | ||
+ | Lys (K) 23 6.2% | ||
+ | Met (M) 15 4.0% | ||
+ | Phe (F) 33 8.8% | ||
+ | Pro (P) 15 4.0% | ||
+ | Ser (S) 17 4.6% | ||
+ | Thr (T) 21 5.6% | ||
+ | Trp (W) 4 1.1% | ||
+ | Tyr (Y) 17 4.6% | ||
+ | Val (V) 19 5.1% | ||
+ | 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): | + | Total number of negatively charged residues (Asp + Glu): 50 |
− | Total number of positively charged residues (Arg + Lys): | + | Total number of positively charged residues (Arg + Lys): 46 |
Atomic composition: | Atomic composition: | ||
− | Carbon C | + | Carbon C 1999 |
− | Hydrogen H | + | Hydrogen H 3041 |
− | Nitrogen N | + | Nitrogen N 515 |
− | Oxygen O | + | Oxygen O 563 |
− | Sulfur S | + | Sulfur S 18 |
− | Formula: | + | Formula: C1999H3041N515O563S18 |
− | Total number of atoms: | + | Total number of atoms: 6136 |
Extinction coefficients: | Extinction coefficients: | ||
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Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | ||
− | Ext. coefficient | + | Ext. coefficient 47455 |
− | Abs 0.1% (=1 g/l) | + | Abs 0.1% (=1 g/l) 1.082, assuming all pairs of Cys residues form cystines |
− | Ext. coefficient | + | Ext. coefficient 47330 |
− | Abs 0.1% (=1 g/l) | + | Abs 0.1% (=1 g/l) 1.079, assuming all Cys residues are reduced |
Estimated half-life: | Estimated half-life: | ||
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Instability index: | Instability index: | ||
− | The instability index (II) is computed to be | + | The instability index (II) is computed to be 36.26 |
This classifies the protein as stable. | This classifies the protein as stable. | ||
− | Aliphatic index: | + | Aliphatic index: 77.69 |
− | Grand average of hydropathicity (GRAVY): -0. | + | Grand average of hydropathicity (GRAVY): -0.313 |
===Source=== | ===Source=== |
Revision as of 10:33, 25 September 2013
CTH1
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 305
Illegal BglII site found at 413 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI.rc site found at 103
Illegal BsaI.rc site found at 259
Illegal BsaI.rc site found at 880
Design Notes
Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence
CTH1 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
Amino acid sequence
MVAATAAPQE VEGFKVMRDG IKVASDETLL TPRFYTTDFD EMERLFSLEL NKNMDMEEFE
AMLNEFKLDY NQRHFVRNET FKEAAEKIQG PTRKIFIEFL ERSCTAEFSG FLLYKELGRR
LKATNPVVAE IFTLMSRDEA RHAGFLNKAM SDFNLALDLG FLTKNRKYTF FKPKFIFYAT
YLSEKIGYWR YISIYRHLQR NPDNQLYPLF EYFENWCQDE NRHGDFFTAV LKARPEMVND
WAAKLWSRFF CLSVYITMYL NDHQRDAFYS SLGLNTTQFN QHVIIETNKS TERIFPAVPD
VENPEFFRRM DLLVKYNAQL VNIGSMNLPS PIKAIMKAPI LERMVAEVFQ VFIMTPKESG
SYDLDANKTA LVY
References and documentation are available. Please note the modified algorithm for extinction coefficient.
Number of amino acids: 373
Molecular weight: 43873.3
Theoretical pI: 5.98
Amino acid composition: Ala (A) 28 7.5% Arg (R) 23 6.2% Asn (N) 23 6.2% Asp (D) 19 5.1% Cys (C) 3 0.8% Gln (Q) 11 2.9% Glu (E) 31 8.3% Gly (G) 12 3.2% His (H) 6 1.6% Ile (I) 18 4.8% Leu (L) 35 9.4% Lys (K) 23 6.2% Met (M) 15 4.0% Phe (F) 33 8.8% Pro (P) 15 4.0% Ser (S) 17 4.6% Thr (T) 21 5.6% Trp (W) 4 1.1% Tyr (Y) 17 4.6% Val (V) 19 5.1% 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): 50
Total number of positively charged residues (Arg + Lys): 46
Atomic composition:
Carbon C 1999 Hydrogen H 3041 Nitrogen N 515 Oxygen O 563 Sulfur S 18
Formula: C1999H3041N515O563S18 Total number of atoms: 6136
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 47455 Abs 0.1% (=1 g/l) 1.082, assuming all pairs of Cys residues form cystines
Ext. coefficient 47330
Abs 0.1% (=1 g/l) 1.079, 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 36.26 This classifies the protein as stable.
Aliphatic index: 77.69
Grand average of hydropathicity (GRAVY): -0.313
Source
Chlamydomonas reinhardtii
===References===