Coding

Part:BBa_K1159109

Designed by: Dong-Jiunn Jeffery TRUONG   Group: iGEM13_TU-Munich   (2013-09-16)
Revision as of 19:45, 8 October 2013 by JohannaB (Talk | contribs)

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Micrococcal nuclease (Thermonuclease) with N-terminal SV40 NLS in RFC[25]

This part encodes a micrococcal nuclease (Thermonuclease) with N-terminal SV40 Nuclear Localization Signal (SV40 NLS). Thermonuclease degrades ssDNA/dsDNA/ssRNA/dsRNA. This part is flanked by RFC[25] pre- and suffix for further protein fusions.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
 ATGGCCGGCGCGGAATTA ... TCAGGTCAAACCGGT
 ORF from nucleotide position -8 to 516 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 		MAGAELIPEPPKKKRKVELGTATGATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEF
DKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
SV40 nuclear localization sequence: 11 to 17
RFC25 scar (shown in bold): 23 to 24
Amino acid composition:
Ala (A)17 (9.7%)
Arg (R)6 (3.4%)
Asn (N)6 (3.4%)
Asp (D)8 (4.6%)
Cys (C)0 (0.0%)
Gln (Q)6 (3.4%)
Glu (E)15 (8.6%)
Gly (G)14 (8.0%)
His (H)4 (2.3%)
Ile (I)6 (3.4%)
Leu (L)13 (7.4%)
Lys (K)27 (15.4%)
Met (M)5 (2.9%)
Phe (F)3 (1.7%)
Pro (P)9 (5.1%)
Ser (S)5 (2.9%)
Thr (T)13 (7.4%)
Trp (W)1 (0.6%)
Tyr (Y)7 (4.0%)
Val (V)10 (5.7%)
Amino acid counting
Total number:175
Positively charged (Arg+Lys):33 (18.9%)
Negatively charged (Asp+Glu):23 (13.1%)
Aromatic (Phe+His+Try+Tyr):15 (8.6%)
Biochemical parameters
Atomic composition:C864H1405N241O259S5
Molecular mass [Da]:19473.4
Theoretical pI:9.56
Extinction coefficient at 280 nm [M-1 cm-1]:15930 / 15930 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.77)good (0.80)excellent (0.80)good (0.80)good (0.72)good (0.61)
Alignments (obtained from PredictProtein.org)
SwissProt:P00644 (98% identity on 153 AAs), Q5HHM4 (97% identity on 153 AAs)
TrEML:A3QSR2 (97% identity on 143 AAs), A3QSR3 (97% identity on 143 AAs)
PDB:1ey0 (100% identity on 136 AAs), 1eyd (100% identity on 136 AAs), 1nsn (100% identity on 138 AAs), 1snc (100% identity on 135 AAs), 1sta (100% identity on 135 AAs), 1stb (100% identity on 136 AAs), 1stg (100% identity on 136 AAs), 1sth (100% identity on 136 AAs), 1stn (100% identity on 136 AAs), 1sty (100% identity on 136 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:secreted (45%)
Eukarya:cytosol (26%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0030541 (28%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
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Categories
Parameters
None