Sequence-based predictions TSD

Thor: He's my brother

Natasha Romanoff: He killed 80 people in 2 days

Thor: ...He's adopted

If not noted otherwise, the sequence for all predictions is the HEXA Reference sequence (Uniprot P06865). A protocol for this task can be found here.

Secondary structure

Proteins: Ribonuclease inhibitor P10775 , CutA Q9X0E6 , CAM-PRP catalytic subunit Q08209
Ribonuclease inhibitor and CutA are located in the cytoplasm whereas the CAM-PRP catalytic subunit is located in the nucleus.

Transmembrane helices

Proteins: Dopamine D3 receptor P35462 , KvAP Q9YDF8 , AQP-4 P47863
Dopamine D3 receptor, KvAP and AQP-4 are multi-pass membrane proteins. <figtable id="tab:gopetgo">

Positions of transmembrane helices
Drd3	33–35	66–88	105–126	150–170	188–212	330–351	367–388
KvAP	39–63	68–92	109–125	129–145	160–184	222–253
AQP-4	37–57	65–85	116–136	156–176	185–205	232–252

Table TODO: Assigned transmembrane regions in Uniprot </figtable>

Signal peptides

Proteins: Serum albumin P02768, LAMP-1 P11279, AQP-4 P47863
HEXA LAMP-1 and Serum albumin contain a signal peptide. HEXA has an assigned peptide between position 1 and 22, LAMP-1 between 1 and 28 and Serum albumin between position 1 and 18.
LAMP-1 is a membrane protein which passes the membrane with one helix. Serum albumin, the main protein of plasma, is a secreted extracellular protein. AQP-4 is a multi-pass membrane protein which forms a waterspecific channel and functions in transport.

The prediction of the displayed results was performed with SignalP version 4.0.
SignalP employs 3 main scores for the prediction of signal peptides, C, S and Y. The S-score stands for the actual signal peptide prediction, with high scores indicating that the corresponding amino acid is part of a signal peptide, and low scores indicating that the amino acid is part of a mature protein. The C-score is the cleavage score, which indicates the best cleavage cite when significantly high. (When a cleavage site position is referred to by a single number, the number indicates the first residue in the mature protein.) Y-max is a derivative of the C-score combined with the S-score calculated to give a better cleavage site prediction than the raw C-score alone.
There are two additional scores reported in the SignalP output, namely the S-mean and the D-score. The S-mean is the average of the S-score, ranging from the N-terminal amino acid to the amino acid assigned with the highest Y-max score. The D-score is implemented as a weighted average of the S-mean and the Y-max scores.
For non-secretory proteins all scores are supposed to be very low.

<figtable id="tbl:signalp">

	Table : Signal peptide predictions.

</figtable>

The <xr id="tbl:signalp"/> displays the results of the SignalP predictions. The additional scores can be viewed here. HEXA, LAMP-1 and Serum albumin are correctly predicted one signal peptide at the beginning of the sequence and AQP-4 is identified as a mature protein.

GO terms

GOpet

<figtable id="tab:gopetgo">

GO-Term ID	Type	Confidence	GO-Term description	Validation
GO:0003824	Molecular function	97%	catalytic activity	true
GO:0004563	Molecular function	96%	beta-N-acetylhexosaminidase activity	true
GO:0015929	Molecular function	96%	hexosaminidase activity	false
GO:0016787	Molecular function	96%	hydrolase activity	true
GO:0016798	Molecular function	96%	hydrolase activity acting on glycosyl bonds	true
GO:0004553	Molecular function	96%	hydrolase activity hydrolyzing O-glycosyl compounds	true
GO:0016799	Molecular function	77%	hydrolase activity hydrolyzing N-glycosyl compounds	false
GO:0046982	Molecular function	61%	protein heterodimerization activity	true

Table TODO: GO term prediction. </figtable>