An example of using PSI-BLAST
A paper by Holm & Sander (1997) demonstrated the similarity between histidine triad proteins (HIT) and galactose-1-phosphate uridyltransferase (GalT) protein by superimposing their three-dimensional structures.
However, when we look at their sequence similarity it looks very weak and a standard BLAST search using a HIT sequence reveals no significant hits to GalT sequences.
See if you can establish a relationship between HIT protein and GalT using PSI-BLAST.
Here is the HIT sequence:
>gi|1706794|sp|P49789|FHIT_HUMAN
BIS(5'-ADENOSYL)-TRIPHOSPHATASE
MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVE
KHFHGTSLTFSMQDGPEAGQTVKHVHVHVLPRKAGDFHRNDSIYEELQKHDKEDFPASWRSEEEMAAEAA
ALRVYFQ
You can get to PSI-BLAST here.
Hints
i) Change the database to SwissProt to keep search times low
ii) Switch on the low complexity filter to remove regions of low complexity
iii) Switch off the graphical overview
iv) Try an inclusion threshold of around 0.001
v) Keep your eyes open for GalT hits.