Gaucher Disease: Task 03 - Sequence-based predictions
Contents
Secondary Structure
TODO: What features are predicted? Discuss the results for your protein and the example proteins. Using the predictions, what could you learn about your protein and the example proteins? Compare to the available knowledge in UniProt, PDB, DisProt, OPM, PDBTM, Pfam...
Disorder
Transmembrane Helices
Four Proteins, including the Gaucher's disease causing Protein, where analysed under reference by transmembrane helices. The used prediction tools differ in their analysing features. While Polyphobius only differs between residues being part of a transmembrane helix or being inside/outside of the cytoplama, Memsat-SVM also predicts re-entrant helices and pore-linig helices. Due to the fact that pore-lining helices are also transmembrane helices, this kind of helices is detected of both prediction tools. In case of re-entrant helices both programms differ. Polyphobius takes this helix as a membrane helix, but Memsat-SVM predicts a re-entrant helix outside the membrane. Therefore the number of the transmembrane hlices, predicted by the tools, differ from each other. In this case also the C-terminal or the N-terminal may be predicted in a different area because of an additional helix.
Comparison of TMH for P04062 | ||||
---|---|---|---|---|
Prediction | Assignment | |||
Memsat SVM | Polyphobius | OPM | PDMTM | |
# of TMH | 1 | - | ||
TMH Topology | 456-471 | - | ||
N-terminal | extracellular | extracellular | ||
C-terminal | cytoplasmic | extracellular | ||
Signal peptide | 1-34 | 1-40 | ||
Re-entrant Helix | - | - | ||
Pore-lining Helix | 1 | - | ||
Graphical position | ||||
more information | MemsatSVM |
Comparison of TMH for Q9YDF8 | ||||
---|---|---|---|---|
Prediction | Assignment | |||
Memsat SVM | Polyphobius | OPM | PDMTM | |
# of TMH | 6 | 7 | 5 | 4 |
TMH Topology | 43-59 72-90 101-118 128-143 163-184 221-245 |
42-60 68-88 108-129 137-157 163-184 196-213 224-244 |
25-46 55-78 86-97 100-107 117-148 |
27-50 55-75 88-107 118-142 |
N-terminal | cytoplasmic | extracellular | cytoplasmic | extracellular |
C-terminal | cytoplasmic | cytoplasmic | cytoplasmic | extracellular |
Signal peptide | - | - | ||
Re-entrant Helix | 188-217 | - | ||
Pore-lining Helix | 1 | - | ||
Graphical position | ||||
more information | MemsatSVM | 1ORS | 1ORS |
Comparison of TMH for P4 | ||||
---|---|---|---|---|
Prediction | Assignment | |||
Memsat SVM | Polyphobius | OPM | PDMTM | |
# of TMH | - | |||
TMH Topology | ||||
N-terminal | ||||
C-terminal | ||||
Signal peptide | ||||
Re-entrant Helix | ||||
Pore-lining Helix | ||||
Graphical position | ||||
more information |
Comparison of TMH for P3 | ||||
---|---|---|---|---|
Prediction | Assignment | |||
Memsat SVM | Polyphobius | OPM | PDMTM | |
# of TMH | - | |||
TMH Topology | ||||
N-terminal | ||||
C-terminal | ||||
Signal peptide | ||||
Re-entrant Helix | ||||
Pore-lining Helix | ||||
Graphical position | ||||
more information |
Signal Peptides
GO Terms
Discussion
Other available methods
Prediction of | Tool | Information |
---|---|---|
secondary structure | GOR | http://gor.bb.iastate.edu/ |
disorder | DISOPRED2 | http://bioinf.cs.ucl.ac.uk/psipred/ |
transmembrane helices | MEMSAT3 | http://bioinf.cs.ucl.ac.uk/psipred/ |
TMHMM | http://www.cbs.dtu.dk/services/TMHMM/ | |
signal peptides | ||
GO terms |
What else can/is be predicted from protein sequence alone
- Fold recognition (profile based pGenTHREADER and rapid GenTHREADER)
- Fold domain recognition (pDomTHREADER)
- Protein domain prediction (DomPred)
- Homology modelling (BioSerf v2.0)
- Function prediction (eukaryotic function: FFPred v2.0)
- Prediction of TM topology and helix packing (SVM-based MEMPACK)
http://bioinf.cs.ucl.ac.uk/psipred/