Coding

Part:BBa_K4790108:Design

Designed by: Hongyan Jing   Group: iGEM23_NNU-CHINA   (2023-10-11)


ASR2(node 98)


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 472
    Illegal PstI site found at 928
    Illegal PstI site found at 1129
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 472
    Illegal PstI site found at 928
    Illegal PstI site found at 1129
    Illegal NotI site found at 758
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 336
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 472
    Illegal PstI site found at 928
    Illegal PstI site found at 1129
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 472
    Illegal PstI site found at 928
    Illegal PstI site found at 1129
    Illegal NgoMIV site found at 294
    Illegal NgoMIV site found at 1035
    Illegal NgoMIV site found at 1416
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Firstly, we use profile-HMM algorithm instead of BLAST local alignment algorithm. To obtain PETase-related protein sequences from all species, Pfam entries and HMMER web server were used to search Swiss-prot and NCBI public databases. Then we set up a database of PETase protein sequences by selecting relatively strict sequences according to e-value, and manually adding sequences identified by homology. Finally, the phylogenetic tree was established through the ML algorithm of fireprot server, and several ancestor sequences of PETase were obtained according to the evolved nodes, among which the most primitive sequence was node 98.


Source

It does not come from any genomic sequence.

References