Coding

Part:BBa_K1159315

Designed by: TU Munich 2013   Group: iGEM13_TU-Munich   (2013-09-16)

TMD of SERK Receptor from Physcomitrella patens with C-terminal GFP fusion in RFC[25]

This part codes for the Transmembrane Domain of SERK Receptor from Physcomitrella patens with a C-terminal (intracellular) GFPmut1 fusion; SERK TMD and GFPmut1 are seperated by a middle long linker. Still, a signal peptide is needed for membrane integration. 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
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 863

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)
 ATGGCCGGCCCTGGACAA ... CTCTACAAAACCGGT
 ORF from nucleotide position -8 to 939 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

101 
201 
301 
MAGPGQPPFPPPPPFTPPPPQTPNGASGENSTGAIAGGVAAGAALLFAAPAIGFAWWRRRRPIEATGGGSGGGSGTGSKGEELFTGVVPILVELDGDVNG
HKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIE
LKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLSPDNHYLSTQSALSKDPNEKRDHMVLLEFV
TAAGITHGMDELYKTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 66 to 67, 76 to 77
Amino acid composition:
Ala (A)21 (6.6%)
Arg (R)10 (3.2%)
Asn (N)15 (4.7%)
Asp (D)18 (5.7%)
Cys (C)2 (0.6%)
Gln (Q)10 (3.2%)
Glu (E)18 (5.7%)
Gly (G)40 (12.7%)
His (H)10 (3.2%)
Ile (I)15 (4.7%)
Leu (L)21 (6.6%)
Lys (K)20 (6.3%)
Met (M)6 (1.9%)
Phe (F)16 (5.1%)
Pro (P)25 (7.9%)
Ser (S)15 (4.7%)
Thr (T)22 (7.0%)
Trp (W)3 (0.9%)
Tyr (Y)11 (3.5%)
Val (V)18 (5.7%)
Amino acid counting
Total number:316
Positively charged (Arg+Lys):30 (9.5%)
Negatively charged (Asp+Glu):36 (11.4%)
Aromatic (Phe+His+Try+Tyr):40 (12.7%)
Biochemical parameters
Atomic composition:C1531H2342N414O462S8
Molecular mass [Da]:34196.4
Theoretical pI:5.93
Extinction coefficient at 280 nm [M-1 cm-1]:32890 / 33015 (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 (0.73)good (0.75)good (0.76)excellent (0.84)excellent (0.81)good (0.71)
Alignments (obtained from PredictProtein.org)
SwissProt:P42212 (98% identity on 238 AAs), Q9U6Y3 (25% identity on 217 AAs)
TrEML:Q71RY9 (98% identity on 238 AAs), B6F2F5 (97% identity on 241 AAs)
PDB:1gfl (98% identity on 229 AAs), 2y0g (98% identity on 226 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:secreted (100%)
Bacteria:secreted (74%)
Eukarya:cytosol (44%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0018298 (44%), GO:0008218 (31%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices:37 to 54 going inwards
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[edit]
Categories
//chassis/eukaryote/ppatens
Parameters
None