Coding

Part:BBa_K1159105

Designed by: Dong-Jiunn Jeffery TRUONG   Group: iGEM13_TU-Munich   (2013-09-14)

Mature Nuclease NucA from Staphylococcus aureus (Thermonuclease) in RFC[25]

Thermonuclease is a endo-exonuclease from Staphylococcus aureus that degrades dsDNA, ssDNA, dsRNA and ssRNA. This part is coding the mature form of the nuclease, also called NucA. 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)
 ATGGCCGGCGCAACTTCA ... TCAGGTCAAACCGGT
 ORF from nucleotide position -8 to 453 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

101 
MAGATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGK
MVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)15 (9.7%)
Arg (R)5 (3.2%)
Asn (N)6 (3.9%)
Asp (D)8 (5.2%)
Cys (C)0 (0.0%)
Gln (Q)6 (3.9%)
Glu (E)12 (7.8%)
Gly (G)12 (7.8%)
His (H)4 (2.6%)
Ile (I)5 (3.2%)
Leu (L)11 (7.1%)
Lys (K)23 (14.9%)
Met (M)5 (3.2%)
Phe (F)3 (1.9%)
Pro (P)6 (3.9%)
Ser (S)5 (3.2%)
Thr (T)11 (7.1%)
Trp (W)1 (0.6%)
Tyr (Y)7 (4.5%)
Val (V)9 (5.8%)
Amino acid counting
Total number:154
Positively charged (Arg+Lys):28 (18.2%)
Negatively charged (Asp+Glu):20 (13.0%)
Aromatic (Phe+His+Try+Tyr):15 (9.7%)
Biochemical parameters
Atomic composition:C763H1231N213O230S5
Molecular mass [Da]:17228.8
Theoretical pI:9.48
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 (0.79)excellent (0.83)excellent (0.82)excellent (0.81)good (0.72)acceptable (0.60)
Alignments (obtained from PredictProtein.org)
SwissProt:P00644 (99% identity on 150 AAs), Q5HHM4 (98% identity on 150 AAs), Q6GB41 (98% identity on 150 AAs), Q6GIK1 (98% identity on 150 AAs), Q7A6P2 (98% identity on 150 AAs), Q8NXI6 (98% identity on 150 AAs), Q99VJ0 (98% identity on 150 AAs)
TrEML:A3QSR2 (98% identity on 140 AAs), A3QSR3 (98% identity on 140 AAs), A3QSR6 (98% identity on 140 AAs), A5A513 (98% identity on 148 AAs), A5A520 (98% identity on 148 AAs), A5A523 (98% identity on 148 AAs), A5IQZ5 (98% identity on 150 AAs), A6QFA0 (98% identity on 150 AAs), A6TZS0 (98% identity on 150 AAs), A7WZZ3 (98% identity on 150 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 (55%)
Eukarya:cytosol (24%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0030541 (28%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
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[edit]
Categories
//chassis/prokaryote/lactobacillus
//collections/probiotics
//collections/probiotics/biocontainment
Parameters
None