Coding

Part:BBa_K1159009

Designed by: Louise FUNKE   Group: iGEM13_TU-Munich   (2013-09-15)

Secretory Erythromycin Esterase Type II (SERK-SigP_EreB) in RFC[25] N-Part

Erythromycin esterase type II (EreB) is fused with a N-terminal signal peptide for secretion (Signal peptide from SERK Receptor of Physcomitrella patens). This construct is flanked by RFC[25] N-part prefix and suffix. Note: This means only protein fusions to the C-terminus of this part is possible, adding promoters (typically RFC[10]) into the prefix or terminators/IRES (typically RFC[10]) into the suffix of this part is nevertheless possible.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 295
    Illegal XhoI site found at 705
    Illegal XhoI site found at 1295
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 422

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25 N-Part using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)
 AACAATGCCTGGT ... GTTTATGAAACCGGT
 ORF from nucleotide position 5 to 1366 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 
401 		MPGEVAWWRPLFLIALMPIGVLSNAEGDALNTTGRFEEWVKDKHIPFKLNHPDDNYDDFKPLRKIIGDTRVVALGENSHFIKEFFLLRHTLLRFFIEDLG
FTTFAFEFGFAEGQIINNWIHGQGTDDEIGRFLKHFYYPEELKTTFLWLREYNKAAKEKITFLGIDIPRNGGSYLPNMEIVHDFFRTADKEALHIIDDAF
NIAKKIDYFSTSQAALNLHELTDSEKCRLTSQLARVKVRLEAMAPIHIEKYGIDKYETILHYANGMIYLDYNIQAMSGFISGGGMQGDMGAKDKYMADSV
LWHLKNPQSEQKVIVVAHNAHIQKTPILYDGFLSCLPMGQRLKNAIGDDYMSLGITSYSGHTAALYPEVDTKYGFRVDNFQLQEPNEGSVEKAISGCGVT
NSFVFFRNIPEDLQSIPNMIRFDSIYMKAELEKAFDGIFQIEKSSVSEVVYETG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 33 to 34
Amino acid composition:
Ala (A)30 (6.6%)
Arg (R)17 (3.7%)
Asn (N)22 (4.8%)
Asp (D)30 (6.6%)
Cys (C)3 (0.7%)
Gln (Q)14 (3.1%)
Glu (E)32 (7.0%)
Gly (G)34 (7.5%)
His (H)15 (3.3%)
Ile (I)38 (8.4%)
Leu (L)39 (8.6%)
Lys (K)29 (6.4%)
Met (M)13 (2.9%)
Phe (F)32 (7.0%)
Pro (P)17 (3.7%)
Ser (S)23 (5.1%)
Thr (T)21 (4.6%)
Trp (W)6 (1.3%)
Tyr (Y)19 (4.2%)
Val (V)20 (4.4%)
Amino acid counting
Total number:454
Positively charged (Arg+Lys):46 (10.1%)
Negatively charged (Asp+Glu):62 (13.7%)
Aromatic (Phe+His+Try+Tyr):72 (15.9%)
Biochemical parameters
Atomic composition:C2361H3588N606O678S16
Molecular mass [Da]:51823.1
Theoretical pI:5.42
Extinction coefficient at 280 nm [M-1 cm-1]:61310 / 61498 (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 (0.74)good (0.76)good (0.74)excellent (0.81)good (0.77)good (0.66)
Alignments (obtained from PredictProtein.org)
SwissProt:P05789 (100% identity on 418 AAs), P07684 (24% identity on 381 AAs)
TrEML:Q2V0Y9 (100% identity on 418 AAs), Q8RTE6 (100% identity on 165 AAs)
PDB:2qgm (20% identity on 379 AAs), 2rad (19% identity on 386 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (99%)
Bacteria:cytosol (94%)
Eukarya:cytosol (50%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0046677 (51%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.


[edit]
Categories
Parameters
None