Difference between revisions of "Task 3: Sequence-based predictions"

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(Task 3.4: Prediction of GO terms)
(Task 3.3: Prediction of transmembrane alpha-helices and signal peptides)
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== Task 3.3: Prediction of transmembrane alpha-helices and signal peptides ==
 
== Task 3.3: Prediction of transmembrane alpha-helices and signal peptides ==
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=== General Questions to prediction of transmembrane alpha-helices and signal peptides ===
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==== Why is the prediction of transmembrane helices and signal peptides grouped together here? ====
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==== Description of different signal peptides ====
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===== Signalpeptides for the import to the endoplasmic reticulum (ER) =====
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The import to the ER is usually required for the secretory pathway (to export proteins out of a cell). The import process can occur either co-translational (the nascent protein chain is translocated together with the ribosome) or post-translational (only the fully synthesized protein is transported to the ER). However, for both cases the SEC-pathway is mostly used.
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The co-translational transport to the ER is done by the signal recognition particle (SRP). This particle recognizes the N-terminal signal-sequence of the nascent polypeptide chain and then transports it to the ER membrane where the complex, consisting of SRP, polypeptide chain and ribosome, is recognized by the ER membrane bound signal recognition particle receptor (SR). After this recognition the polypeptide chain is imported into the ER lumen via the SEC channel in a ATP dependent process.
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===== Signalpeptides for the import to the mitochondrion =====
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===== Signalpeptides for the import to the chloroplast =====
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===== Signalpeptides for the import to the
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=== TMHMM ===
 
=== TMHMM ===

Revision as of 16:56, 25 May 2011

Task description

The full description of this task can be found here.


Task 3.1: Secondary structure prediction

Task 3.2: Prediction of disordered regions

Task 3.3: Prediction of transmembrane alpha-helices and signal peptides

General Questions to prediction of transmembrane alpha-helices and signal peptides

Why is the prediction of transmembrane helices and signal peptides grouped together here?

Description of different signal peptides

Signalpeptides for the import to the endoplasmic reticulum (ER)

The import to the ER is usually required for the secretory pathway (to export proteins out of a cell). The import process can occur either co-translational (the nascent protein chain is translocated together with the ribosome) or post-translational (only the fully synthesized protein is transported to the ER). However, for both cases the SEC-pathway is mostly used.

The co-translational transport to the ER is done by the signal recognition particle (SRP). This particle recognizes the N-terminal signal-sequence of the nascent polypeptide chain and then transports it to the ER membrane where the complex, consisting of SRP, polypeptide chain and ribosome, is recognized by the ER membrane bound signal recognition particle receptor (SR). After this recognition the polypeptide chain is imported into the ER lumen via the SEC channel in a ATP dependent process.



Signalpeptides for the import to the mitochondrion
Signalpeptides for the import to the chloroplast

===== Signalpeptides for the import to the


TMHMM

Phobius and PolyPhobius

OCTOPUS and SPOCTOPUS

SignalP

TargetP

Task 3.4: Prediction of GO terms

GOPET

Pfam

ProtFun 2.2