Difference between revisions of "Part:BBa K1080001:Design"
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Note 8 PstI sites CTGCAG (785, 1031, 1385, 1652, 2681, 2825, 3458, 3569) No EcoRI or XbaI sites. 1 SpeI (ACTAGT) (4226) site 23 bp after stop codon. | Note 8 PstI sites CTGCAG (785, 1031, 1385, 1652, 2681, 2825, 3458, 3569) No EcoRI or XbaI sites. 1 SpeI (ACTAGT) (4226) site 23 bp after stop codon. | ||
| + | <b>Amino Acid Sequence</b> | ||
| − | <FONT FACE="courier"> | + | <FONT FACE="courier">GPAKQQVSLD LRDDGAGMFT STSPEMRRVV PDDVKGRVKV KVVYVVLEAQ YQSAISAAVK NINAKNSKVC FEVVGYLLEE LRDQKNLDML KEDVASANIF<br> IGSLIFIEEL AEKIVEAVSP LREKLDACLI FPSMPAVMKL NKLGTFSMAQ LGQSKSVFSE FIKSARKNND NFEEGLLKLV RTLPKVLKYL PSDKAQDAKN<br> FVNSLQYWLG GNSDNLENLL LNTVSNYVPA LKGVDFSVAE PTAYPDVGIW HPLASGMYED LKEYLNWYDT RKDMVFAKDA PVIGLVLQRS HLVTGDEGHY<br> SGVVAELESR GAKVIPVFAG GLDFSAPVKK FFYDPLGSGR TFVDTVVSLT GFALVGGPAR QDAPKAIEAL KNLNVPYLVS LPLVFQTTEE WLDSELGVHP<br> VQVALQVALP ELDGAMEPIV FAGRDSNTGK SHSLPDRIAS LCARAVNWAN LRKKRNAEKK LAVTVFSFPP DKGNVGTAAY LNVFGSIYRV LKNLQREGYD<br> VGALPPSEED LIQSVLTQKE AKFNSTDLHI AYKMKVDEYQ LCPYAEALE ENWGKPPGTL NTNGQELLVY GRQYGNVFIG VQPTFGYEGD PMRLLFSKSA<br> SPHHGFAAYY TFLEKIFKAD AVLHFGTHGS LEFMPGKQVG MSGVCYPDSL IGTIPNLYYY AANNPSEATI AKRRSYANTI SYLTPPAENA GLYKGLKELK<br> ELISSYQGMR ESGRAEQICA TIIETAKLCN LDRDVTLPDA DAKDLTMDMR DSVVGQVYRK LMEIESRLLP CGLHVVGCPP TAEEAVATLV NIAELDRPDN<br> NPPIKGMPGI LARAIGRDIE SIYSGNNKGV LADVDQLQRI TEASRTCVRE FVKDRTGLNG RIGTNWITNL LKFTGFYVDP WVRGLQNGEF ASANREELIT<br> LFNYLEFCLT QVVKDNELGA LVEALNGQYV EPGPGGDPIR NPNVLPTGKN IHALDPQSIP TQAALKSARL VVDRLLDRER DNNGGKYPET IALVLWGTDN<br> IKTYGESLAQ VMMMVGVKPV ADALGRVNKL EVIPLEELGR PRVDVVVNCS GVFRDLFVNQ MLLLDRAIKL AAEQDEPDEM NFVRKHAKQQ AAELGLQSLR<br> DAATRVFSNS SGSYSSNVNL AVENSSWSDE SQLQEMYLKR KSYAFNSDRP GAGGEMQRDV FETAMKTVDV TFQNLDSSEI SLTDVSHYFD SDPTKLVASL<br> RNDGRTPNAY IADTTTANAQ VRTLGETVRL DARTKLLNPK WYEGMLASGY EGVREIQKRM TNTMGWSATS GMVDNWVYDE ANSTFIEDAA MAERLMNTNP<br> NSFRKLVATF LEANGRGYWD AKPEQLERLR QLYMDVEDKI EGVE |
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| + | References and documentation are available. | ||
Please note the modified algorithm for extinction coefficient. | Please note the modified algorithm for extinction coefficient. | ||
| + | -------------------------------------------------------------------------------- | ||
| + | Number of amino acids: 1344 | ||
| − | + | Molecular weight: 148676.1 | |
| − | + | Theoretical pI: 5.33 | |
| − | + | Amino acid composition: Ala (A) 113 8.4% | |
| + | Arg (R) 68 5.1% | ||
| + | Asn (N) 77 5.7% | ||
| + | Asp (D) 81 6.0% | ||
| + | Cys (C) 12 0.9% | ||
| + | Gln (Q) 46 3.4% | ||
| + | Glu (E) 91 6.8% | ||
| + | Gly (G) 97 7.2% | ||
| + | His (H) 14 1.0% | ||
| + | Ile (I) 51 3.8% | ||
| + | Leu (L) 141 10.5% | ||
| + | Lys (K) 78 5.8% | ||
| + | Met (M) 33 2.5% | ||
| + | Phe (F) 49 3.6% | ||
| + | Pro (P) 67 5.0% | ||
| + | Ser (S) 84 6.2% | ||
| + | Thr (T) 65 4.8% | ||
| + | Trp (W) 14 1.0% | ||
| + | Tyr (Y) 49 3.6% | ||
| + | Val (V) 114 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): | + | Total number of negatively charged residues (Asp + Glu): 172 |
| − | Total number of positively charged residues (Arg + Lys): | + | Total number of positively charged residues (Arg + Lys): 146 |
Atomic composition: | Atomic composition: | ||
| − | Carbon C | + | Carbon C 6616 |
| − | Hydrogen H | + | Hydrogen H 10441 |
| − | Nitrogen N | + | Nitrogen N 1791 |
| − | Oxygen O | + | Oxygen O 2010 |
| − | Sulfur S | + | Sulfur S 45 |
| − | Formula: | + | Formula: C6616H10441N1791O2010S45 |
| − | Total number of atoms: | + | Total number of atoms: 20903 |
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 150760 |
| − | Abs 0.1% (=1 g/l) | + | Abs 0.1% (=1 g/l) 1.014, assuming all pairs of Cys residues form cystines |
| − | Ext. coefficient | + | Ext. coefficient 150010 |
| − | Abs 0.1% (=1 g/l) | + | Abs 0.1% (=1 g/l) 1.009, 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 G (Gly). |
The estimated half-life is: | The estimated half-life is: | ||
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Instability index: | Instability index: | ||
| − | The instability index (II) is computed to be 32. | + | The instability index (II) is computed to be 32.91 |
This classifies the protein as stable. | This classifies the protein as stable. | ||
| − | Aliphatic index: | + | Aliphatic index: 88.72 |
| − | Grand average of hydropathicity (GRAVY): -0. | + | Grand average of hydropathicity (GRAVY): -0.257 |
===Source=== | ===Source=== | ||
Revision as of 02:36, 25 September 2013
ChlH
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 1928
Illegal BglII site found at 2234
Illegal BglII site found at 3620 - 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 486
Illegal NgoMIV site found at 2152
Illegal AgeI site found at 1132
Illegal AgeI site found at 2650
Illegal AgeI site found at 2704
Illegal AgeI site found at 2923 - 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI.rc site found at 2254
Illegal BsaI.rc site found at 3049
Illegal SapI.rc site found at 2979
Design Notes
CR-ChlH sequence with His Tag in pET15b. Sequence from Translation start site.
Note 8 PstI sites CTGCAG (785, 1031, 1385, 1652, 2681, 2825, 3458, 3569) No EcoRI or XbaI sites. 1 SpeI (ACTAGT) (4226) site 23 bp after stop codon.
Amino Acid Sequence
GPAKQQVSLD LRDDGAGMFT STSPEMRRVV PDDVKGRVKV KVVYVVLEAQ YQSAISAAVK NINAKNSKVC FEVVGYLLEE LRDQKNLDML KEDVASANIF
IGSLIFIEEL AEKIVEAVSP LREKLDACLI FPSMPAVMKL NKLGTFSMAQ LGQSKSVFSE FIKSARKNND NFEEGLLKLV RTLPKVLKYL PSDKAQDAKN
FVNSLQYWLG GNSDNLENLL LNTVSNYVPA LKGVDFSVAE PTAYPDVGIW HPLASGMYED LKEYLNWYDT RKDMVFAKDA PVIGLVLQRS HLVTGDEGHY
SGVVAELESR GAKVIPVFAG GLDFSAPVKK FFYDPLGSGR TFVDTVVSLT GFALVGGPAR QDAPKAIEAL KNLNVPYLVS LPLVFQTTEE WLDSELGVHP
VQVALQVALP ELDGAMEPIV FAGRDSNTGK SHSLPDRIAS LCARAVNWAN LRKKRNAEKK LAVTVFSFPP DKGNVGTAAY LNVFGSIYRV LKNLQREGYD
VGALPPSEED LIQSVLTQKE AKFNSTDLHI AYKMKVDEYQ LCPYAEALE ENWGKPPGTL NTNGQELLVY GRQYGNVFIG VQPTFGYEGD PMRLLFSKSA
SPHHGFAAYY TFLEKIFKAD AVLHFGTHGS LEFMPGKQVG MSGVCYPDSL IGTIPNLYYY AANNPSEATI AKRRSYANTI SYLTPPAENA GLYKGLKELK
ELISSYQGMR ESGRAEQICA TIIETAKLCN LDRDVTLPDA DAKDLTMDMR DSVVGQVYRK LMEIESRLLP CGLHVVGCPP TAEEAVATLV NIAELDRPDN
NPPIKGMPGI LARAIGRDIE SIYSGNNKGV LADVDQLQRI TEASRTCVRE FVKDRTGLNG RIGTNWITNL LKFTGFYVDP WVRGLQNGEF ASANREELIT
LFNYLEFCLT QVVKDNELGA LVEALNGQYV EPGPGGDPIR NPNVLPTGKN IHALDPQSIP TQAALKSARL VVDRLLDRER DNNGGKYPET IALVLWGTDN
IKTYGESLAQ VMMMVGVKPV ADALGRVNKL EVIPLEELGR PRVDVVVNCS GVFRDLFVNQ MLLLDRAIKL AAEQDEPDEM NFVRKHAKQQ AAELGLQSLR
DAATRVFSNS SGSYSSNVNL AVENSSWSDE SQLQEMYLKR KSYAFNSDRP GAGGEMQRDV FETAMKTVDV TFQNLDSSEI SLTDVSHYFD SDPTKLVASL
RNDGRTPNAY IADTTTANAQ VRTLGETVRL DARTKLLNPK WYEGMLASGY EGVREIQKRM TNTMGWSATS GMVDNWVYDE ANSTFIEDAA MAERLMNTNP
NSFRKLVATF LEANGRGYWD AKPEQLERLR QLYMDVEDKI EGVE
References and documentation are available. Please note the modified algorithm for extinction coefficient.
Number of amino acids: 1344
Molecular weight: 148676.1
Theoretical pI: 5.33
Amino acid composition: Ala (A) 113 8.4% Arg (R) 68 5.1% Asn (N) 77 5.7% Asp (D) 81 6.0% Cys (C) 12 0.9% Gln (Q) 46 3.4% Glu (E) 91 6.8% Gly (G) 97 7.2% His (H) 14 1.0% Ile (I) 51 3.8% Leu (L) 141 10.5% Lys (K) 78 5.8% Met (M) 33 2.5% Phe (F) 49 3.6% Pro (P) 67 5.0% Ser (S) 84 6.2% Thr (T) 65 4.8% Trp (W) 14 1.0% Tyr (Y) 49 3.6% Val (V) 114 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): 172
Total number of positively charged residues (Arg + Lys): 146
Atomic composition:
Carbon C 6616 Hydrogen H 10441 Nitrogen N 1791 Oxygen O 2010 Sulfur S 45
Formula: C6616H10441N1791O2010S45 Total number of atoms: 20903
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 150760 Abs 0.1% (=1 g/l) 1.014, assuming all pairs of Cys residues form cystines
Ext. coefficient 150010
Abs 0.1% (=1 g/l) 1.009, assuming all Cys residues are reduced
Estimated half-life:
The N-terminal of the sequence considered is G (Gly).
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 32.91 This classifies the protein as stable.
Aliphatic index: 88.72
Grand average of hydropathicity (GRAVY): -0.257
Source
Chlamydomonas reinhardtii
===References===