Coding

Part:BBa_K1159013

Designed by: TU Munich 2013   Group: iGEM13_TU-Munich   (2013-05-17)
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Secretory Human Protein Phosphatase 1 (SERK-SigP_PP1) in RFC[25] N-Part

This part encodes for the Human protein phosphatase 1, which binds the toxic oligopeptide produces by gree-blue algae, with a N-terminal signal peptdie 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 643
    Illegal BamHI site found at 107
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 1030

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 ... GCAAAGAAAACCGGT
 ORF from nucleotide position 5 to 1084 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 		MPGEVAWWRPLFLIALMPIGVLSNAEGDALNTTGGSADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDI
HGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIV
DEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVT
LFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKKTG*
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)20 (5.6%)
Arg (R)19 (5.3%)
Asn (N)15 (4.2%)
Asp (D)24 (6.7%)
Cys (C)13 (3.6%)
Gln (Q)13 (3.6%)
Glu (E)23 (6.4%)
Gly (G)28 (7.8%)
His (H)6 (1.7%)
Ile (I)23 (6.4%)
Leu (L)44 (12.2%)
Lys (K)23 (6.4%)
Met (M)8 (2.2%)
Phe (F)19 (5.3%)
Pro (P)20 (5.6%)
Ser (S)16 (4.4%)
Thr (T)13 (3.6%)
Trp (W)5 (1.4%)
Tyr (Y)12 (3.3%)
Val (V)16 (4.4%)
Amino acid counting
Total number:360
Positively charged (Arg+Lys):42 (11.7%)
Negatively charged (Asp+Glu):47 (13.1%)
Aromatic (Phe+His+Try+Tyr):42 (11.7%)
Biochemical parameters
Atomic composition:C1835H2865N485O524S21
Molecular mass [Da]:40778.1
Theoretical pI:5.79
Extinction coefficient at 280 nm [M-1 cm-1]:45380 / 46193 (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 (0.69)good (0.74)good (0.68)good (0.79)good (0.80)good (0.71)
Alignments (obtained from PredictProtein.org)
SwissProt:P36873 (100% identity on 322 AAs), P36874 (99% identity on 322 AAs), P61287 (99% identity on 322 AAs), P63087 (99% identity on 322 AAs), P63088 (99% identity on 322 AAs), Q6NVU2 (99% identity on 322 AAs), Q7SZ10 (99% identity on 322 AAs), Q8MJ46 (98% identity on 322 AAs)
TrEML:F6YKN7 (100% identity on 322 AAs), F7AYW3 (100% identity on 305 AAs), F7GFT6 (100% identity on 313 AAs), F7GFU1 (100% identity on 322 AAs), G3R7N4 (100% identity on 313 AAs), G5AWL7 (100% identity on 296 AAs), G7N5H3 (100% identity on 296 AAs), G7PI87 (100% identity on 296 AAs), H2NIN2 (100% identity on 313 AAs), H2Q6V8 (100% identity on 313 AAs)
PDB:1it6 (100% identity on 293 AAs), 1jk7 (100% identity on 294 AAs), 2bcd (100% identity on 293 AAs), 2bdx (100% identity on 293 AAs), 2o8a (100% identity on 295 AAs), 2o8g (100% identity on 295 AAs), 1u32 (98% identity on 293 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:cytosol (90%)
Eukarya:cytosol (38%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology:GO:0005515 (70%), GO:0004722 (70%)
Biological Process Ontology:GO:0051301 (28%), GO:0005977 (27%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices:190 to 207 going outwards
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