Sequence-Based Predictions Hemochromatosis

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

Disorder

<figtable id="iupred">

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).

	Q30201	P10775
	Q08209	Q9X0E6

</figtable>

Transmembrane Helices

<figtable id="tmh_q30201">

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.

Q30201	TMH 1
PolyPhobius	306-329
UniProt	307-330
OPM	no entry
PDBTM	no entry

</figtable>

<figtable id="tmh_p35462">

Table XXX: TMH predictions and annotations for P35462 (PDB ID: 3PBL).

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

</figtable>

<figtable id="tmh_p47863">

Table XXX: TMH predictions and annotations for P47863 (PDB ID: 2D57). TMH3 and TMH7 (marked with *) are listed as "Membrane Loop" in PDBTM.

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

</figtable>

<figtable id="tmh_q9ydf8">

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.

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

</figtable>

Signal Peptides

<figtable id="signalp">

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.

	Q30201	P47863
	P11279	P02768

</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">

Table XXX: GO term prediction with GOPET for Q30201.

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

</figtable>

ProtFun

<figtable id="protfun">

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.

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*

</figtable>