Difference between revisions of "Sequence-Based Predictions Hemochromatosis"

From Bioinformatikpedia
(GO Terms)
(GO Terms)
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== GO Terms ==
 
== GO Terms ==
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For the last part of this task we used [http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.startthis?SIMGO=w2h.welcome&INTRA_CONTINUE=1 GOPET] and [http://www.cbs.dtu.dk/services/ProtFun/ ProtFun] to make a GO term prediction for the HFE protein (Q30201). The results were then compared to [http://pfam.sanger.ac.uk/ Pfam] and [http://www.ebi.ac.uk/QuickGO/GProtein?ac=Q30201 QuickGO].
   
 
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Revision as of 13:15, 19 May 2012

Hemochromatosis>>Task 3: Sequence-based predictions

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Don't google it... but a hint: Caesar would solve it ;)


Short Task Description

Detailed description: Sequence-Based Predictions

Protocol

Protocol

Secondary Structure


Disorder

<figtable id="iupred">

Q30201
P10775
Q08209
Q9X0E6
Table XXX: IUPred predictions for Q30201, P10775, Q08209, and Q9X0E6. The figures show the disorder probability predicted for each amino acid residue (green line) and the 50% threshold (red line).

</figtable>


Transmembrane Helices

<figtable id="tmh_q30201">

Q30201 TMH 1
PolyPhobius 306-329
UniProt 307-330
OPM no entry
PDBTM no entry
Table XXX: TMH predictions and annotations for Q30201. There were no entries for either of the two PDB IDs (1A6Z, 1DE4) in OPM or PDBTM.

</figtable>


<figtable id="tmh_p35462">

P35462 (3PBL) TMH 1 TMH 2 TMH 3 TMH 4 TMH 5 TMH 6 TMH 7
PolyPhobius 30-55 66-88 105-126 150-170 188-212 329-352 367-386
UniProt 33-55 66-88 105-126 150-170 188-212 330-351 367-388
OPM 34-52 67-91 101-126 150-170 187-209 330-351 363-386
PDBTM 35-52 68-84 109-123 152-166 191-206 334-347 368-382
Table XXX: TMH predictions and annotations for P35462 (PDB ID: 3PBL).

</figtable>


<figtable id="tmh_p47863">

P47863 (2D57) TMH 1 TMH 2 TMH 3 TMH 4 TMH 5 TMH 6 TMH 7 TMH 8
PolyPhobius 34-58 70-91 115-136 156-177 188-208 231-252
UniProt 37-57 65-85 116-136 156-176 185-205 232-252
OPM 34-56 70-88 98-107 112-136 156-178 189-203 214-223 231-252
PDBTM 39-55 72-89 95-106* 116-133 158-177 188-205 209-222* 231-248
Table XXX: TMH predictions and annotations for P47863 (PDB ID: 2D57). TMH3 and TMH7 (marked with *) are listed as "Membrane Loop" in PDBTM.

</figtable>


<figtable id="tmh_q9ydf8">

Q9YDF8 (1ORQ/1ORS) TMH 1 TMH 2 TMH 3 TMH 4 TMH 5 TMH 6 TMH 7 TMH 8
PolyPhobius 42-60 68-88 108-129 137-157 163-184 196-213 224-244
UniProt 39-63 68-92 97-105* 109-125 129-145 160-184 196-208* 222-253
OPM (1ORS) 38-59 68-91 99-110 113-120 130-161
OPM (1ORQ) 166-185 196-208 220-238
PDBTM (1ORS) 40-63 68-88 101-120 131-155
PDBTM (1ORQ) 34-65 70-93 164-184 197-213* 222-249
Table XXX: TMH predictions and annotations for Q9YDF8 (PDB IDs: 1ORQ, 1ORS). Residue positions are adjusted for the PDB sequence's 13AA shift. TMH3 is annotated as "Intramembrane, Helical" in UniProt, TMH7 as "Intramembrane, Pore-Forming". TMH7 is additionally marked as "Membrane Loop" in PDBTM.

</figtable>


Signal Peptides

<figtable id="signalp">

Q30201
P47863
P11279
P02768
Table XXX: SignalP predictions for Q30201, P47863, P11279, and P02768. Each figure shows the C-score, S-score, and Y-score per residue position for the corresponding protein.

</figtable>


GO Terms

For the last part of this task we used GOPET and ProtFun to make a GO term prediction for the HFE protein (Q30201). The results were then compared to Pfam and QuickGO.


GOPET

<figtable id="gopet">

GOid Aspect Confidence Go term
GO:0004872 F (Molecular Function Ontology) 91% receptor activity
GO:0030106 F (Molecular Function Ontology) 88% MHC class I receptor activity
Table XXX: GO term prediction with GOPET for Q30201.

</figtable>


ProtFun

<figtable id="protfun">

Functional category Probability Odds
Biosynthesis of cofactors 0.105 1.452
Cell envelope* 0.633* 10.377*
Cellular processes 0.095 1.297
Central intermediary metabolism 0.231 3.663
Fatty acid metabolism 0.016 1.265
Purines and pyrimidines 0.583 2.400
Translation 0.079 1.801
Transport and binding 0.732 1.785
Enzyme/nonenzyme
Enzyme 0.208 0.727
Nonenzyme* 0.792* 1.110*
Enzyme class
Hydrolase 0.135 0.425
Lyase 0.049 1.054
Gene Ontology category
Signal transducer 0.201 0.939
Receptor 0.353 2.076
Stress response 0.274 3.108
Immune response* 0.381* 4.486*
Table XXX: GO term prediction with ProtFun for Q30201. Entries marked with asterisks (*) had been deemed "true" by ProtFun. Results with a probability below 0.1 and odds below 1.0 are not shown.

</figtable>


Pfam