Difference between revisions of "Part:BBa K1080002:Design"

Latest revision as of 02:28, 26 September 2013

ChlD

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NotI site found at 1334
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 2039
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 614
Illegal NgoMIV site found at 1433
Illegal NgoMIV site found at 1975
1000
COMPATIBLE WITH RFC[1000]

Design Notes

Incorporated sequence overlap for Gibson assembly and no GC rich region or restriction site in sequence

ChlD Clone: DNA sequence from translation start site:

Amino acid sequence:

MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG
TAKSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI
DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID
AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR
AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP
PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR
AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV
QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV
VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT
ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY

References and documentation are available. Please note the modified algorithm for extinction coefficient.

Number of amino acids: 707

Molecular weight: 76420.1

Theoretical pI: 5.23

Amino acid composition: Ala (A) 88 12.4% Arg (R) 47 6.6% Asn (N) 14 2.0% Asp (D) 51 7.2% Cys (C) 7 1.0% Gln (Q) 31 4.4% Glu (E) 55 7.8% Gly (G) 51 7.2% His (H) 6 0.8% Ile (I) 40 5.7% Leu (L) 60 8.5% Lys (K) 43 6.1% Met (M) 20 2.8% Phe (F) 12 1.7% Pro (P) 50 7.1% Ser (S) 42 5.9% Thr (T) 24 3.4% Trp (W) 1 0.1% Tyr (Y) 16 2.3% Val (V) 49 6.9% 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): 106 Total number of positively charged residues (Arg + Lys): 90

Atomic composition:

Carbon C 3333 Hydrogen H 5435 Nitrogen N 949 Oxygen O 1047 Sulfur S 27

Formula: C3333H5435N949O1047S27 Total number of atoms: 10791

Extinction coefficients:

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

Ext. coefficient 29715 Abs 0.1% (=1 g/l) 0.389, assuming all pairs of Cys residues form cystines

Ext. coefficient 29340 Abs 0.1% (=1 g/l) 0.384, 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 45.56 This classifies the protein as unstable.

Aliphatic index: 87.71

Grand average of hydropathicity (GRAVY): -0.337

@@ Line 1: / Line 1: @@
 __NOTOC__
 <partinfo>BBa_K1080002 short</partinfo>
@@ Line 12: / Line 11: @@
 ChlD 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
-Note: No XbaI, EcoRI, PstI or SpeI sites
-<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>
-<br><br>
-CTGCGCGCCATGAAGGTGTCTGAGGAGGACTCCAAGGGCTTCGATGCGGATGTGTCGACCCGCCTGGCCCGCTCG TACCCTCTGGCGGCCGTGGTGGGCCAGGACAACATCAAGCAGGCGCTGCTGCTGGGCGCCGTGGACACCGGGCTG
-GGCGGCATCGCCATCGCCGGTCGCCGCGGTACCGCCAAGTCCATCATGGCTCGCGGCCTGCACGCTCTGCTGCCG
-CCCATTGAGGTGGTGGAGGGCAGCATCTGCAACGCCGACCCCGAGGACCCCCGCTCCTGGGAGGCTGGCCTGGCTGAGAAGTATGCGGGCGGCCCTGTGAAGACCAAGATGCGCTCGGCGCCGTTTGTGCAGATCCCTCTGGGTGTGACTGAGGACCGCTTGGTGGGCACTGTGGACATTGAGGCGTCCATGAAGGAGGGCAAGACTGTGTTCCAGCCCGGCCTGCTGGCTGAGGCGCACCGCGGCATCCTGTACGTGGACGAGATCAACCTGCTGGATGACGGCATTGCCAACCTGCTGCTGTCCATCCTGTCGGACGGAGTCAACGTGGTGGAGCGCGAGGGCATCTCCATCAGCCACCCCTGCCGGCCGCTGCTGATTGCCACCTACAACCCCGAGGAGGGCCCTCTGCGTGAGCACCTGCTGGACCGCATCGCCATTGGCCTCAGCGCCGACGTCCCCAGCACCAGCGACGAGCGCGTCAAGGCCATTGACGCAGCCATCCGCTTCCAGGACAAGCCGCAGGACACTATTGACGACACCGCGGAGCTCACCGACGCCCTGCGCACCTCGGTCATCCTGGCTCGCGAGTACCTGAAGGACGTGACCATCGCGCCGGAGCAGGTGACCTACATTGTGGAGGAGGCGCGCCGCGGCGGAGTCCAGGGGCACCGCGCGGAGCTGTACGCGGTCAAGTGTGCCAAGGCGTGTGCGGCTCTGGAGGGCCGTGAGCGTGTGAACAAGGATGACCTGCGCCAGGCCGTGCAGCTGGTCATCCTGCCGCGCGCCACCATCCTGGACCAGCCCCCGCCCGAGCAGGAGCAGCCCCCGCCGCCGCCCCCGCCCCCTCCCCCGCCGCCGCCGCAGGACCAAATGGAGGACGAGGACCAGGAGGAGAAGGAGGACGAGAAGGAGGAGGAGGAGAAGGAGAACGAGGACCAGGACGAGCCCGAGATCCCTCAGGAGTTCATGTTTGAGTCCGAGGGCGTCATCATGGACCCCTCCATCCTCATGTTCGCGCAGCAGCAGCAGCGCGCGCAGGGCCGCTCCGGCCGCGCCAAGACGCTCATCTTCAGCGACGACCGCGGCCGCTACATCAAGCCCATGCTGCCCAAGGGTGACAAGGTCAAGCGCCTGGCAGTGGACGCCACGCTTCGCGCCGCCGCGCCCTACCAGAAGATTCGCCGGCAGCAGGCCATCAGCGAGGGCAAGGTGCAGCGCAAGGTGTACGTGGACAAGCCAGACATGCGCTCCAAGAAGCTGGCCCGCAAGGCCGGTGCGCTGGTGATTTTTGTTGTGGACGCGTCCGGCTCCATGGCTCTGAACCGCATGAGCGCCGCCAAGGGCGCCTGCATGCGCCTGCTGGCTGAGTCGTACACCAGCCGCGACCAGGTGTGCCTCATCCCCTTCTACGGCGACAAGGCCGAGGTGCTGCTGCCGCCCTCCAAGTCCATCGCCATGGCCCGCCGCCGCCTGGACTCGCTGCCCTGCGGCGGCGGCTCGCCCCTTGCGCACGGCCTGTCCACGGCGGTACGTGTGGGCATGCAGGCCAGCCAGGCGGGCGAGGTGGGCCGCGTCATGATGGTGCTCATCACGGACGGCCGCGCCAACGTCAGCCTGGCCAAGTCCAACGAGGACCCCGAGGCGCTCAAGCCCGACGCGCCCAAGCCCACCGCCGACTCGCTGAAGGACGAGGTGCGCGACATGGCCAAGAAGGCCGCGTCCGCCGGCATCAACGTGCTTGTCATTGACACGGAGAACAAGTTCGTGAGCACCGGCTTTGCGGAGGAGATCTCCAAGGCAGCGCAGGGCAAGTACTACTACCTGCCCAACGCCAGCGACGCCGCCATCGCGGCGGCCGCGTCCGGCGCCATGGCCGCGGCCAAGGGCGGCTACTAGGTGCCGAGTGACTGAGGTGGCAAGGTGCAGTGGCGGCGGAGGCAGTTGTGCTGGGGTGGCAAGGCGGACAGGCGAAGCTGGTGGGTTGCGACGAGGAGGAGGTGCACGTGCACGCGTAACATAAGAAGAACAGTGGGAGGACAGGTAGCGTGACTTGACTGGGACGAGGAGCGTACTGATGTGTGGCGTGTGTTGGTATGTGAGCGTTACCCCTCC
-Protein sequence:
-         20         30         40         50         60
-MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDHPFTLRAM KVSEEDSKGF DADVSTRLAR
-         80         90        100        110        120
-SYPLAAVVGQ DNIKQALLLG AVDTGLGGIA IAGRRGTAKS IMARGLHALL PPIEVVEGSI
-        140        150        160        170        180
-CNADPEDPRS WEAGLAEKYA GGPVKTKMRS APFVQIPLGV TEDRLVGTVD IEASMKEGKT
-        200        210        220        230        240
-VFQPGLLAEA HRGILYVDEI NLLDDGIANL LLSILSDGVN VVEREGISIS HPCRPLLIAT
-        260        270        280        290        300
-YNPEEGPLRE HLLDRIAIGL SADVPSTSDE RVKAIDAAIR FQDKPQDTID DTAELTDALR
-        320        330        340        350        360
-TSVILAREYL KDVTIAPEQV TYIVEEARRG GVQGHRAELY AVKCAKACAA LEGRERVNKD
-        380        390        400        410        420
-DLRQAVQLVI LPRATILDQP PPEQEQPPPP PPPPPPPPPQ DQMEDEDQEE KEDEKEEEEK
-        440        450        460        470        480
-ENEDQDEPEI PQEFMFESEG VIMDPSILMF AQQQQRAQGR SGRAKTLIFS DDRGRYIKPM
-        500        510        520        530        540
-LPKGDKVKRL AVDATLRAAA PYQKIRRQQA ISEGKVQRKV YVDKPDMRSK KLARKAGALV
-        560        570        580        590        600
-IFVVDASGSM ALNRMSAAKG ACMRLLAESY TSRDQVCLIP FYGDKAEVLL PPSKSIAMAR
-        620        630        640        650        660
-RRLDSLPCGG GSPLAHGLST AVRVGMQASQ AGEVGRVMMV LITDGRANVS LAKSNEDPEA
-        680        690        700        710        720
-LKPDAPKPTA DSLKDEVRDM AKKAASAGIN VLVIDTENKF VSTGFAEEIS KAAQGKYYYL
-        740
-PNASDAAIAA AASGAMAAAK GGY
-References and documentation are available.
+<FONT FACE="courier"> MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG<br> TAKSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI<br> DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID<br> AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR<br> AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP<br> PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR<br> AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV<br> QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV<br>   VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT<br> ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY </FONT>
+References and documentation are available.
 Please note the modified algorithm for extinction coefficient.
+--------------------------------------------------------------------------------
+Number of amino acids: 707
-Number of amino acids: 743
+Molecular weight: 76420.1
-Molecular weight: 80527.5
+Theoretical pI: 5.23
-Theoretical pI: 5.37
+Amino acid composition: Ala (A)  88	 12.4%
+Arg (R)  47	  6.6%
+Asn (N)  14	  2.0%
+Asp (D)  51	  7.2%
+Cys (C)   7	  1.0%
+Gln (Q)  31	  4.4%
+Glu (E)  55	  7.8%
+Gly (G)  51	  7.2%
+His (H)   6	  0.8%
+Ile (I)  40	  5.7%
+Leu (L)  60	  8.5%
+Lys (K)  43	  6.1%
+Met (M)  20	  2.8%
+Phe (F)  12	  1.7%
+Pro (P)  50	  7.1%
+Ser (S)  42	  5.9%
+Thr (T)  24	  3.4%
+Trp (W)   1	  0.1%
+Tyr (Y)  16	  2.3%
+Val (V)  49	  6.9%
+Pyl (O)   0	  0.0%
+Sec (U)   0	  0.0%
-Amino acid composition:
+ (B)   0	  0.0%
-Ala (A) 89 12.0% Arg (R) 49 6.6% Asn (N) 14 1.9% Asp (D) 57 7.7% Cys (C) 7 0.9% Gln (Q) 33 4.4% Glu (E) 55 7.4% Gly (G) 56 7.5% His (H) 13 1.7% Ile (I) 40 5.4% Leu (L) 62 8.3% Lys (K) 44 5.9% Met (M) 23 3.1% Phe (F) 13 1.7% Pro (P) 51 6.9% Ser (S) 44 5.9% Thr (T) 26 3.5% Trp (W) 1 0.1% Tyr (Y) 17 2.3% Val (V) 49 6.6% Pyl (O) 0 0.0% Sec (U) 0 0.0% (B) 0 0.0% (Z) 0 0.0% (X) 0 0.0%
+ (Z)   0	  0.0%
+ (X)   0	  0.0%
-Total number of negatively charged residues (Asp + Glu): 112
+Total number of negatively charged residues (Asp + Glu): 106
-Total number of positively charged residues (Arg + Lys): 93
+Total number of positively charged residues (Arg + Lys): 90
 Atomic composition:
-Carbon      C	      3504
+Carbon      C	      3333
-Hydrogen    H	      5684
+Hydrogen    H	      5435
-Nitrogen    N	      1008
+Nitrogen    N	       949
-Oxygen      O	      1102
+Oxygen      O	      1047
-Sulfur      S	        30
+Sulfur      S	        27
-Formula: C3504H5684N1008O1102S30
+Formula: C3333H5435N949O1047S27
-Total number of atoms: 11328
+Total number of atoms: 10791
 Extinction coefficients:
@@ Line 106: / Line 74: @@
 Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
-Ext. coefficient    31205
+Ext. coefficient    29715
-Abs 0.1% (=1 g/l)   0.388, assuming all pairs of Cys residues form cystines
+Abs 0.1% (=1 g/l)   0.389, assuming all pairs of Cys residues form cystines
-Ext. coefficient    30830
+Ext. coefficient    29340
-Abs 0.1% (=1 g/l)   0.383, assuming all Cys residues are reduced
+Abs 0.1% (=1 g/l)   0.384, assuming all Cys residues are reduced
 Estimated half-life:
@@ Line 117: / Line 85: @@
 The N-terminal of the sequence considered is M (Met).
-The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
+The estimated half-life is:
+hours (mammalian reticulocytes, in vitro).
                              >20 hours (yeast, in vivo).
                              >10 hours (Escherichia coli, in vivo).
@@ Line 124: / Line 93: @@
 Instability index:
-The instability index (II) is computed to be 44.71
+The instability index (II) is computed to be 45.56
 This classifies the protein as unstable.
-Aliphatic index: 84.64
+Aliphatic index: 87.71
-Grand average of hydropathicity (GRAVY): -0.392
-===Source===
-Chlamydomonas reinhardtii
-===References===
+Grand average of hydropathicity (GRAVY): -0.337