Canavan Task 3 - Sequence-based predictions
From Bioinformatikpedia
Oh, I would sing of mackerel skies, And why the sea is wet, Of jelly-fish and conger-eels, And things that I forget. (taken from "The Cumberbunce" by Paul West)
Contents
Protocol
Commands, Source Code and other methodocial issues are kept in the protocoll.
Secondary Structure Prediction
Information on Proteins
//TODO: picsPrediction of disordered regions
Transmembrane Helix Prediction
Information on Proteins
TM prediction of our Protein yielded the expected prediction of only cytoplasmic residues.
P35462
Polyphobius found 7 TMH for P35462. This is in accordance with the annotation for transmembrane regions in UniProt. There is only one structure listed for P35462: 3pbl. The annotation for TMH for this structure found in PDBTM and OPM also agrees with the Polyphobius result.
In figure ??? the length distribution for the predicted and annotated TMH is depicted. One can see that PDBTM in general finds shorter TMH, whereas Polyphobius and OPM find longer helices.
Signal Peptide Prediction
Information on Proteins
GO terms and Pfam
Pfam
AstE_AspA family: Succinylglutamate desuccinylase / Aspartoacylase family