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3. Secondary structure prediction

APVKSQESIN QKLALVIKSG KYTLGYKSTV KSLRQGKSKL IIIAANTPVL
RKSELEYYAM LSKTKVYYFQ GGNNELGTAV GKLFRVGVVS ILEAGDSDIL
TTLA
 

1. Go to the Jpred2 server

 

2. Press the 'Submit a sequence' button.

 

3. Enter your email address in Box 1.

 

4. Copy the query sequence and paste it into the window:


APVKSQESIN QKLALVIKSG KYTLGYKSTV KSLRQGKSKL IIIAANTPVL
RKSELEYYAM LSKTKVYYFQ GGNNELGTAV GKLFRVGVVS ILEAGDSDIL
TTLA


 

5. Click the option to bypass an automatic scan of the current Brookhaven Protein Database.

You need to do this because the three-dimensional structure of the ribosomal protein L30 is known. By default, Jpred will not perform any secondary structure prediction unless you force it to do so.

 

6. Press the "Run secondary structure prediction" button.

The prediction takes very long to run. To save time, the instructor have run the prediction for you and you can view the result here.
 

7. Scroll the result window until you see:


Alpha-helices are represented by the letter 'H' while beta-strands are represented by the letter 'E'. The prediction suggested the ribosomal protein consists of 5 alpha-helices and 4 beta-strands.

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