Canavan Task 3 - Sequence-based predictions

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Revision as of 18:51, 13 May 2012 by Vorbergs (talk | contribs) (P35462)
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)

Protocol

Commands, Source Code and other methodocial issues are kept in the protocoll.


Secondary Structure Prediction

Information on Proteins

//TODO: pics
Identifier P10775 Q08209 Q9X0E6
Protein Ribonuclease inhibitor Serine/threonine phosphatase (alt. name:Calcineurin Divalent-cation tolerance protein
Organism Sus scrofa (pig) Homo Sapiens Thermotoga maritima
Sequence length 456 521 101
Subcellular location Cytoplasm Nucleus Cytoplasm
PDB Identifier 2BNH 1AUI 1O5J
Structure CD 3PBL.jpg CD 1ORQ.jpg CD 2D57.jpg

Prediction of disordered regions

Transmembrane Helix Prediction

Information on Proteins

Identifier P35462 Q9YDF8 P47863
Protein D(3) dopamine receptor Voltage-gated potassium channel Aquaporin-4
Organism Homo sapiens (Human) Aeropyrum pernix Rattus norvegicus (Rat)
Sequence length 400 295 323
Subcellular location Cell membrane; Multi-pass membrane protein Cell membrane; Multi-pass membrane protein Membrane; Multi-pass membrane protein
PDB Identifier 3PBL 1ORQ 2D57
Structure CD 3PBL.jpg CD 1ORQ.jpg CD 2D57.jpg

TM prediction of our Protein yielded the expected prediction of only cytoplasmic residues.


P35462

id=CD_tm_3pbl

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 <xr id="CD_tm_3pbl"/> 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

Identifier P02768 P11279 P47863
Protein Serum albumin Lysosome-associated membrane glycoprotein 1 Aquaporin-4
Organism Homo sapiens (Human) Homo sapiens (Human) Rattus norvegicus (Rat)
Sequence length 609 417 323
Subcellular location Secreted Lysosome membrane, Single-pass type I membrane protein Membrane; Multi-pass membrane protein
PDB Identifier 1E7I - 2D57
Structure CD 1E7I.jpg CD 2D57.jpg


GO terms and Pfam

Pfam

AstE_AspA family: Succinylglutamate desuccinylase / Aspartoacylase family