Revisiting old friends - BLAST, Prosite, InterPro, SMART and Pfam
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In this section, we will revisit using BLAST, Prosite, InterPro, SMART and Pfam.
If you get stuck, or can't remember how to do some of these searches, or interpret the results, then revisit the second year training material. (Don't forget that the second year training material index is a good place to look for the specific pages you need.)
You have been given a protein sequence:
MDAKHKNSTILGPIKADKVSKNALGLYHDIQVQHREYIVPISFLSILALILLTLGNFVYTFVWMLVAFKLSDVLDDVLFLRRLEKITSNVHALASNAYKTLTVKIISARNLPKAMADKVSKNALGLDPYVKVSHREYIVKTKVVKKTLSGFNPVWNEESETFEFEVPPVAFSALEIEVYDKFLRRLDFIGRVTIPPNNAHQHSADGLIHLSELLTGGRHPKLQVLEESIAVESELYARFPHGEDSKQIAQIANKKKIDRWYLLDVSFRVKDKWHKKQGDM
(To copy the sequence highlight it by double click on it, and then use the copy command)
What can you find out about it?
Suggested course of action:
Don't forget the second year training material, and remember that you can easily find pages in the second year material by using the second year training material index.
  1. Perform a BLAST search (a HUGE hint to help with the result!) - Link to BLAST - http://www.ncbi.nlm.nih.gov/blast/.
  2. Perform a Prosite search - http://prosite.expasy.org.
  3. Perform an Interpro search - http://www.ebi.ac.uk/interpro/search/sequence-search.
  4. Carry out a SMART analysis - http://smart.embl-heidelberg.de/.
  5. Carry out a Pfam analysis - http://pfam.xfam.org.
1) How many transmembrane domain(s) does the protein have?
One answer only.
   0
   1
   2
   3
   4
   5
   6
2) If a transmembrane domain is present it is between amino acids:
One answer only.
   No domain present
   10 - 30
   41 - 63
   60 - 80
   87 - 107
   115 - 135
   157 - 190
3) Which of the following domains may the protein contain?
One answer only.
   No domain present
   ATP binding site
   N-Glycosylation site
   O-Glycosylation site
   Protein Kinase A phosphorylaion site
   ADP ribosylation site
   None of the above
4) The protein may contain which of the following domains:
One answer only.
   A C2 domain
   A C3PO domain
   A PTB domain
   A 14.3.3 domain
   A VWD domain
   A R2D2 domain
5) A C2 domain is:
One answer only.
   The first part of the C2C bike route between Tynemouth and the west coast (further information)
   A Ca2+/lipid binding motif
   A prototype of the Sinclair C5 (further information)
   A Ca4+/lipid binding motif
   A Fe2+/lipid binding motif
   A Mg2+/lipid binding motif
6) If the protein contains a C2 domain it can be found between amino acids (data from SMART):
One answer only.
   Does not contain the domain
   1 - 99
   100 - 222
   250 - 370
   The full length of the protein
7) If the protein contains a C3PO domain it can be found between amino acids:
One answer only.
   1 - 100
   100 - 250
   150 - 300
   C3PO is a fictional character in Star Wars
   C3PO is robot in a galaxy far far away
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