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FAQ

close this sectionUse case A

When you search the public database, you will often encounter such a situation. Entries of public databases ,such as NCBI proteins and Uniprot, are mainly composed of registered information to INSDC. Description of each entries varies by the submitter.
DoBISCUIT is a database specified to biosynthesis clusters of secondary metabolites. Each CDS registered in DoBISCUIT is described in the same manner and controlled vocabulary. You can easily know what is the pikAV and how pikAV will function in biosynthesis of pikromycin.
  1. Enter 'pikAV' into simple text search area displayed upper-right and press 'enter'.
  2. You will find the search results which shows hit to Pikromycin cluster. If you are interested in whole biosynthesis cluster of Pikromycin, follow the hyperlink to Pikromycin cluster. If you °∆d like to know what pikAV is, tick cluster list box and switch to CDS tab. Now you will find PikAV is described as 'thioesterase II'. For more details, follow the hyperlink to Pikro_00070.
  3. In the annotation section of the CDS information page, you can know pikAV acts as typeII thioesterase and you can also related references about pikAV. From the reference digest (sorry, Japanese text only), deletion of pikAV does not affect polyketide production and purified recombinant pikAV can hydrolize acyl-ACP thioesters.

close this sectionUse case B

  1. First, you are better to start out from domain identification of the sequence. There are many domain identification services such as PKS/NRPS analysis, mapsiTools and antiSMASH. You can easily find the domain composition of your sequence there.
  2. Click the identified domains in the order of appearance at domain selection box of Module search menu and press 'Checked modules' button.
  3. You can see the checked domain compositions in upper section. Select the domain composition which is identical to your sequence and press Search button.
  4. You can see the search results which shows two CDSs have the identical domain composition. In this case, Pikro_00060 is more likely because AT domain in this sequence is predicted to catalyze methylmalonyl-CoA.
    You can follow the hyperlink and get information about this similar CDS.

close this sectionUse case C

  1. We recommend to execute BLAST search using your sequence as a query. Functionally classified CDS database will help you to know what kinds of CDS are encoded in your sequence.
    Copy and paste your sequence in textbox, select CDS database and push °∆search°« button.
  2. The list part of BLAST search result is colored depending on the functional categories. You can easily see the CDSs related to modification of sugar units are listed. So the query sequence contains CDSs involved in modification of sugar units.
  3. You can follow the hyperlink of CDS to retrieve more detailed information.

close this sectionUse case D

  1. Suppose, you are planning to introduce extra methyl group into your investigating compound. Category list of our database will help you.
  2. Open the category list and click the category '3.2 modification methylation'. You can find methyltransferases encoded in various biosynthesis clusters.. You can follow the hyperlink of CDS to retrieve more detailed information.
  3. May be you can express plasmid constructed methyltransferase gene in vivo, or you can treat recombinant methyltransferase protein in vitro. In either case, you can use DoBISCUIT as a candidate gene list. Using DoBISCUIT, you may have a chance to success much faster than searching, selecting one by one methyltransferase.