BCB 444/544X
Lab 6 Answer Key
Microarray analysis
1b-3d worth ½ pt. each.
3j worth 2 pts.
3k worth 3 pts.
1b) How many structure hits were found by this query?
16
1c) How many structures were found by this query?
6
1e) How many structures are found by this query?
2915
1f) How many structures would be returned using only this subquery?
42668
1g) How many structures were found?
2037
1h) How many structures were left?
606
2a) How many other proteins are defined as having the molecular function
, “actin binding”?
126
2b) What secondary structure is most prevalent in dystrophin?

-helix
2c) Open the file, then copy and paste the FASTA sequence for chain B only, including the comment line into your lab exercise document.
>1DXX:B|PDBID|CHAIN|SEQUENCE
MLWWEEVEDSYEREDVQKKTFTKWVNAQFSKFGKQHIENLFSDLQDGRRLLDLLEGLTGQKLPKEKGSTRVHALNNVNKA
LRVLQNNNVDLVNIGSTDIVDGNHKLTLGLIWNIILHWQVKNVMKNIMAGLQQTNSEKILLSWVRQSTRNYPQVNVINFT
TSWSDGLALNALIHSHRPDLFDWNSVVSQQSATQRLEHAFNIARYQLGIEKLLDPEDVDTTYPDKKSILMYITSLFQVLP
QQVSIE

3d) Under the File menu at the top of the page, select “Save Image”, and include this file as an attachment with your assignment .

3j)
Save a copy of your working session by selecting “Save Session” under the file menu, and include it with your assignment.
Your session should look more or less like this:
3k) Save this file as dystrophin.pml and submit it along with your assignment .
select water, resn hoh remove water show cartoon hide lines select cd, chain c or chain d ('chain c | chain d' is also acceptable) remove cd select abs1, resi 17-26 ('17:26' is also acceptable) select abs2, resi 88-116 select abs3, resi 131-148 color red, abs1 color blue, abs2 color yellow, abs3 select abs, abs1 or abs2 or abs3 show spheres, abs