Difference between revisions of "Part:BBa K1080000:Design"
(→Design Notes) |
(→Design Notes) |
||
(One intermediate revision by the same user not shown) | |||
Line 16: | Line 16: | ||
"ProtParam" at http://au.expasy.org/tools | "ProtParam" at http://au.expasy.org/tools | ||
− | No Biobrick restriction sites (EcoRI, XbaI, SpeI or PstI) | + | No Biobrick restriction sites (EcoRI, XbaI, SpeI or PstI). |
<b>Amino Acid Sequence</b> | <b>Amino Acid Sequence</b> | ||
− | <FONT FACE="courier">RPIFPFTAIV GQDEMKLALI LNVIDPKIGG VMIMGDRGTG KSTTIRALAD LLPEMQVVAN DPFNSDPTDP ELMSEEVRNR | + | <FONT FACE="courier"> MAATEVKAAE GRTEKELGQA RPIFPFTAIV GQDEMKLALI LNVIDPKIGG VMIMGDRGTG KSTTIRALAD LLPEMQVVAN DPFNSDPTDP ELMSEEVRNR<br> VKAGEQLPVS SKKIPMVDLP LGATEDRVCG TIDIEKALTE GVKAFEPGLL AKANRGILYV DEVNLLDDHL VDVLLDSAAS GWNTVEREGI SISHPARFIL<br> VGSGNPEEGE LRPQLLDRFG MHAQIGTVKD PRLRVQIVSQ RSTFDENPAA FRKDYEAGQM ALTQRIVDAR KLLKQGEVNY DFRVKISQIC SDLNVDGIRG<br> DIVTNRAAKA LAAFEGRTEV TPEDIYRVIP LCLRHRLRKD PLAEIDDGDR VREIFKQVFG ME </FONT> |
References and documentation are available. | References and documentation are available. | ||
Line 26: | Line 26: | ||
-------------------------------------------------------------------------------- | -------------------------------------------------------------------------------- | ||
− | Number of amino acids: | + | Number of amino acids: 362 |
− | Molecular weight: | + | Molecular weight: 39952.7 |
− | Theoretical pI: 5. | + | Theoretical pI: 5.11 |
− | Amino acid composition: Ala (A) | + | Amino acid composition: Ala (A) 31 8.6% |
− | Arg (R) | + | Arg (R) 28 7.7% |
− | Asn (N) 12 3. | + | Asn (N) 12 3.3% |
− | Asp (D) 29 8. | + | Asp (D) 29 8.0% |
− | Cys (C) 3 0. | + | Cys (C) 3 0.8% |
− | Gln (Q) | + | Gln (Q) 13 3.6% |
− | Glu (E) | + | Glu (E) 29 8.0% |
− | Gly (G) | + | Gly (G) 28 7.7% |
− | His (H) 4 1. | + | His (H) 4 1.1% |
− | Ile (I) 25 | + | Ile (I) 25 6.9% |
− | Leu (L) | + | Leu (L) 34 9.4% |
− | Lys (K) | + | Lys (K) 19 5.2% |
− | Met (M) | + | Met (M) 10 2.8% |
− | Phe (F) 12 3. | + | Phe (F) 12 3.3% |
− | Pro (P) 19 5. | + | Pro (P) 19 5.2% |
− | Ser (S) 14 | + | Ser (S) 14 3.9% |
− | Thr (T) | + | Thr (T) 17 4.7% |
Trp (W) 1 0.3% | Trp (W) 1 0.3% | ||
− | Tyr (Y) 4 1. | + | Tyr (Y) 4 1.1% |
− | Val (V) | + | Val (V) 30 8.3% |
Pyl (O) 0 0.0% | Pyl (O) 0 0.0% | ||
Sec (U) 0 0.0% | Sec (U) 0 0.0% | ||
Line 60: | Line 60: | ||
− | Total number of negatively charged residues (Asp + Glu): | + | Total number of negatively charged residues (Asp + Glu): 58 |
− | Total number of positively charged residues (Arg + Lys): | + | Total number of positively charged residues (Arg + Lys): 47 |
Atomic composition: | Atomic composition: | ||
− | Carbon C | + | Carbon C 1752 |
− | Hydrogen H | + | Hydrogen H 2857 |
− | Nitrogen N | + | Nitrogen N 499 |
− | Oxygen O | + | Oxygen O 539 |
− | Sulfur S | + | Sulfur S 13 |
− | Formula: | + | Formula: C1752H2857N499O539S13 |
− | Total number of atoms: | + | Total number of atoms: 5660 |
Extinction coefficients: | Extinction coefficients: | ||
Line 79: | Line 79: | ||
Ext. coefficient 11585 | Ext. coefficient 11585 | ||
− | Abs 0.1% (=1 g/l) 0. | + | Abs 0.1% (=1 g/l) 0.290, assuming all pairs of Cys residues form cystines |
Ext. coefficient 11460 | Ext. coefficient 11460 | ||
− | Abs 0.1% (=1 g/l) 0. | + | Abs 0.1% (=1 g/l) 0.287, assuming all Cys residues are reduced |
Estimated half-life: | Estimated half-life: | ||
− | The N-terminal of the sequence considered is | + | The N-terminal of the sequence considered is M (Met). |
The estimated half-life is: | The estimated half-life is: | ||
− | + | 30 hours (mammalian reticulocytes, in vitro). | |
− | + | >20 hours (yeast, in vivo). | |
− | + | >10 hours (Escherichia coli, in vivo). | |
Instability index: | Instability index: | ||
− | The instability index (II) is computed to be 29. | + | The instability index (II) is computed to be 29.73 |
This classifies the protein as stable. | This classifies the protein as stable. | ||
− | Aliphatic index: | + | Aliphatic index: 96.16 |
− | Grand average of hydropathicity (GRAVY): -0. | + | Grand average of hydropathicity (GRAVY): -0.250 |
===Source=== | ===Source=== |
Latest revision as of 09:12, 25 September 2013
ChlI1
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 231
Illegal BglII site found at 887
Illegal BglII site found at 1082
Illegal BamHI site found at 279 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Design Notes
Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence
ChlI1 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 (EcoRI, XbaI, SpeI or PstI).
Amino Acid Sequence
MAATEVKAAE GRTEKELGQA RPIFPFTAIV GQDEMKLALI LNVIDPKIGG VMIMGDRGTG KSTTIRALAD LLPEMQVVAN DPFNSDPTDP ELMSEEVRNR
VKAGEQLPVS SKKIPMVDLP LGATEDRVCG TIDIEKALTE GVKAFEPGLL AKANRGILYV DEVNLLDDHL VDVLLDSAAS GWNTVEREGI SISHPARFIL
VGSGNPEEGE LRPQLLDRFG MHAQIGTVKD PRLRVQIVSQ RSTFDENPAA FRKDYEAGQM ALTQRIVDAR KLLKQGEVNY DFRVKISQIC SDLNVDGIRG
DIVTNRAAKA LAAFEGRTEV TPEDIYRVIP LCLRHRLRKD PLAEIDDGDR VREIFKQVFG ME
References and documentation are available. Please note the modified algorithm for extinction coefficient.
Number of amino acids: 362
Molecular weight: 39952.7
Theoretical pI: 5.11
Amino acid composition: Ala (A) 31 8.6% Arg (R) 28 7.7% Asn (N) 12 3.3% Asp (D) 29 8.0% Cys (C) 3 0.8% Gln (Q) 13 3.6% Glu (E) 29 8.0% Gly (G) 28 7.7% His (H) 4 1.1% Ile (I) 25 6.9% Leu (L) 34 9.4% Lys (K) 19 5.2% Met (M) 10 2.8% Phe (F) 12 3.3% Pro (P) 19 5.2% Ser (S) 14 3.9% Thr (T) 17 4.7% Trp (W) 1 0.3% Tyr (Y) 4 1.1% Val (V) 30 8.3% 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): 47
Atomic composition:
Carbon C 1752 Hydrogen H 2857 Nitrogen N 499 Oxygen O 539 Sulfur S 13
Formula: C1752H2857N499O539S13 Total number of atoms: 5660
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 11585 Abs 0.1% (=1 g/l) 0.290, assuming all pairs of Cys residues form cystines
Ext. coefficient 11460
Abs 0.1% (=1 g/l) 0.287, 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 29.73 This classifies the protein as stable.
Aliphatic index: 96.16
Grand average of hydropathicity (GRAVY): -0.250
Source
Chlamydomonas reinhardtii