Protein function prediction - answers

The goal of this exercise was to use web based tools for protein sequence analysis
  • Blasts with the truncated sequence yields quite different results than blasts with the complete sequence. For example, Myosin sequences, which have nothing to do with an outer membrane protein (which is our protein), appear only with the complete Q9X252 sequence. This is due to the coiled-coil (110-358) region that can match to any coiled-coil containing protein. The coils filter in the Blast avoid such problem by masking the coiled-coil domain.
  • SignalP predicts a signal peptide, but it is difficult to set the correct cleavage site, because this protein originates from an archean organism.
  • TMPred also predicts 2 TM regions, the first one being the signal peptide (1-20) and the second one from 380 to 402.
  • There are thousands of antigenic peptides and PTMs...
  • Interpro and other domain predictors predict an SLH domain (21-63).
  • Q9WZH0 is a hypothetical protein from Thermotoga Maritima. Tropomyosin is only found in eukaryotes (see the prosite entry PS00326), yet that TrEMBL entry contains a PRINTS tropomyosin annotation. When we go on the PRINTS site and search for tropomyosin by PRINTS code, Q9WZH0 doesn't appear.
    The reason for this is that in TrEMBL, the annotation is automatic, whereas in the PRINTS site, that error was manually corrected.
    A possible explanation for the error is that, as we have seen previously, our protein has a coiled-coils region myosin-like, and tropomyosin is a two-stranded alpha-helical rod.