Lab Journal Task 3 Hemo

Secondary Structure Predictions

• reprof version 1.0.1
• psipred version 3.3

The PSSMs used for reprof were selected from the psiblast runs against big_80, SwissProt and PDB with standard parameters (2 iterations and e-value cutoff of 0.002) that were already performed in task2. Reprof was called using

reprof -i <input file>

The Psipred server was run only using the sequences and not with a multiple sequence alignment.

Output unification

DSSP, reprof and psipred all have different output types. In order to compare the results, the following mappings were performed

reprof

H helix

E extended

L loop -> C

DSSP

H = alpha helix -> H

B = residue in isolated beta-bridge -> C

E = extended strand, participates in beta ladder -> E

G = 3-helix (3/10 helix) -> H

I = 5 helix (pi helix) -> C

T = hydrogen bonded turn - C

S = bend -> C

psipred:

H helix

E sheet

C disordered

Disorder Prediction

The IUPred server was used to generate the corresponding predictions. But unfortunately, the server does not show a version number.

Metadisorder was called using the predictprotein command specified in the task description.

Transmembrane Helix Prediction

For running Polyphobius, the [polyphobius.pl] script was used in conjuntion with the swissprot database (May 7 2013).

Memsat-SVM was run using the web server.

voltage-gated potassium channel

The sequence of 1ORQ starts at position 30 of the Uniprot reference sequence Q9YDF8 and the sequence of 1ORS at position 33. However, the PDB file of 1ORQ contains a start annotation at position 18 and 1ORS a start at position 20. Thus, se added 12 to the positions in the pdb files to get the actual position in the reference sequence Q9YDF8.

Signal Peptides

signalP server Version 4.1

• Organism: Eukaryote
• D-cutoff values: default
• Input may include TM-helices: yes
• Restrictions: None

GO Terms

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