Prediction of transmembrane alpha-helices and signal peptides INSL5 HUMAN

TMHMM

First, we used TMHMM to predict the transmembrane helices in this protein.

Figure 1: Prediction of TMHMM for the transmembrane helices of INSL5_HUMAN

start position	end position	location
1	135	outside

TMHMM predicts no transmembrane helices, which can be seen on Figure 1. The whole protein is located at the extracellular space.

Comparison with the real structure of the protein:

Figure 2: Comparison between real occurring transmembrane helices and the TMHMM result.

The TMHMM prediction is again completely right (compare Figure 2).

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Phobius and PolyPhobius

Next, we used Phobius and PolyPhobius to predict again the transmembrane helices and also the signal peptide of this protein.

Figure 3: Prediction of Phobius for the transmembrane helices and signal peptides of INSL5_HUMAN

Figure 4: Prediction of PolyPhobius for the transmembrane helices and signal peptides of INSL5_HUMAN

Phobius			PolyPhobius
start position	end position	prediction	start position	end position	prediction
Signal peptide prediction
1	5	N-Region	1	4	N-Region
6	17	H-Region	5	16	H-Region
18	22	C-Region	17	22	C-Region
Summary signal peptide
1	22	Secretory signal peptide	1	22	Secretoy signal peptide
Transmembrane helices prediction
23	135	outside	23	135	outside

Both methods predict a signal peptide for the secretory pathway and both prediction results are totally equal, which can be seen on Figure 3 and Figure 4.

Comparison with the real structure of the protein:

Figure 5: Comparison between the prediction of Phobius and the real protein

Figure 6: Comparison between the prediction of PolyPhobius and the real protein

The complete prediction is correct, which can be seen on Figure 5 and Figure 6.

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OCTOPUS and SPOCTOPUS

As next tools we used OCTOPUS and SPOCTOPUS which can predict transmembrane helices and also signal peptides.

Figure 7: Prediction of OCTOPUS for the transmembrane helices of INSL5_HUMAN

Figure 8: Prediction of SPOCTOPUS for the transmembrane helices of INSL5_HUMAN

OCTOPUS			SPOCTOPUS
start position	end position	prediction	start position	end position	prediction
1	1	inside	1	5	N-terminal of a signale peptide
2	32	TM helix	6	23	signal peptide
33	135	outside	24	135	outside

As we can seen on Figure 7 and Figure 8 the prediction of both methods is similar, but not identical.

Comparison with the real structure of the protein:

Figure 9: Comparison between the prediction of OCTOPUS and the real protein

Figure 10: Comparison between the prediction of SPOCTOPUS and the real protein

As we already have seen before, OCTOPUS predicts a transmembrane helix (Figure 9), whereas SPOCTOPUS predicts this region as signal peptide (Figure 10), which is correct.

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TargetP

All of our proteins are proteins from human and archaea, so therefore we only use the non-plant option of TargetP.

Location	Probability
mitochondrial targeting SP	0.074
secretory pathway SP	0.899
other	0.037

As before, TargetP predicts a secretory pathway signal peptide, which is again correct.

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SignalP

For our analysis we used the Hidden Markov Model based and also the neuronal network based prediction.
The prediction with the Hidden Markov Model used three different scores. The S-score which is the score for the signal peptide, the C-score which is the score for the cleavage site and the Y-score which is a combination of the S-score and the C-score and is used to predict the cleavage site, because the Y-score is more precise than the C-score.



Result of the neuronal network

Signal peptide		Cleavage site
start position	end position	start position	end position	prediction
1	22	22	23	signal peptide

Result of the Hidden Markov Model

prediction	signal peptide probability	signal anchor probability	cleavage site start	cleavage site end
signal peptide	0.999	0.000	22	23

Figure 11: Result of the SignalP method based on the neuronal network for INSL5_HUMAN

Figure 12: Result of the SignalP method based on the Hidden Markov Model for INSL5_HUMAN

Both methods predict a signal peptide for INSL5_HUMAN (compare Figure 11 and Figure 12), which is correct.

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