BIOC0016

Indentifying the protein

First, let us identify what the protein is and which species it comes from.

Handy hint:

To make it easier to follow these notes and look at the Web pages mentioned at the same time, always click on the relevant links using the left mouse button. Every external link will open in the same window/tab so your screen doesn't get cluttered with many windows. You can flip between the external link and the practical as required.

Search for the sequence using either the EBI or NCBI BLAST servers using the links and instructions given below. As there will be many of you using these servers, pick one at random to spread the load a little and save you having to wait too long. The searches can take several minutes.

In each case you will need to paste the protein sequence, given in the first page into the appropriate box in the EBI or NCBI window.

EBI - European Bioinformatics Institute

  1. Go to the EBI BLAST server.
  2. Under STEP 1 - Select your databases, select UniProtKB/Swiss-Prot (The manually annotated section of UniProtKB)
  3. Paste the mystery protein sequence into the big box.
  4. Leave all the other boxes and parameter settings on the page exactly as they are.
  5. Click on the Submit button below the box where you pasted the sequence. Wait patiently ...

NCBI - National Center for Biotechnology Information

  1. Go to the NCBI BLAST server.
  2. Click on Protein BLAST.
  3. Paste the mystery protein sequence into the big box.
  4. Change the Database option from Non-redundant protein sequences(nr) to UniProtKB/Swiss-Prot(swissprot). (This will restrict the search to just the UniProtKB/Swiss-Prot protein sequence database).
  5. Leave all the other boxes and parameter settings on the page exactly as they are.
  6. Click on the BLAST button below the box where you pasted the sequence. Wait patiently ...

For whichever server you used, record the following information:

For the top hit:

For the second hit:

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