Sequence-Based Predictions Hemochromatosis

Hemochromatosis>>Task 3: Sequence-based predictions

Short Task Description

Detailed description: Sequence-Based Predictions

In this part of the wiki we present our results on different sequence based prediction methods.

These cover the prediction of secondary structure, disordered regions, transmembrane helices, signal peptides and GO annotations.

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

Secondary Structure

In the following the secondary structure predictions were evaluated against the DSSP data. The DSSP data was parsed so that only H(helix), E(sheet) and C(coil) are existant. Nonanalyzed positions that exists in the (for DSSP) used sequence were denoted as "*" in the sequence and (from us) predicted as coil.

Afterwards Q3 and SOV scores were evaluated, where Q3 denotes the percentage of right assigned secondary structures. The SOV is a scoring to calculate how good single secondary structure fragments are approximated. This means

CCCCCHHHHHHHHHCCCCC
CCCCCHCHCHCHCHCCCCC

gets a much lower score than

CCCCCHHHHHHHHHCCCCC
CCCCCCCHHHHHCCCCCCC

although their Q3 scores dont differ. The maximum score is here also 100%. this gives some more insight about the predictions.

The Q3E, Q3H and Q3C score denote the percentage amount of correctly predicted E/H/C secondary structures.

The used Sequences for this were the "aligned" secondary structure sequences.

1KR4

DSSPSQ: ALYFXGHXILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIFTLKVENILTEYXNWLRESVLGS
PsiPSQ:        MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVL
RPRFSQ:        MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVL
DSSPSS: CCEECCCEEEEEEEECCHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCEEEEEEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCEEEECCCCEEHHHHHHHHHHCCCC
PsiPSS:        CEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCCEEECCEEEEEEECCCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHCC
RPRFSS:        CEEEEECCCCHHHHHHHHHHHHHHHHHHHHCHCHHHCCCEEECEEECCHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHEHHHHHHHHHHHHHHHHHHCC

<figtable id="Q3SOV1KR4">

Table 1: Q3- and SOV-Scores of the predictions with ReProf and PSIPred (PDBID: 1KR4).

Scoring method	PsiPred	ReProf
Q3	85.15	57.43
Q3E	76.19	26.19
Q3H	91.89	97.30
Q3C	90.91	50.00
SOV	82.61	60.37

</figtable>

1AUI

DSSPSQ: **************TDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYP
PsiPSQ:  MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYP
RPRFSQ:  MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYP
DSSPSS: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCECHHHHECCCCCECHHHHHHHHHCCCCECHHHHHHHHHHHHHHHHCCCCEEEECCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHCC
PsiPSS:  CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC
RPRFSS:  CCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCCEEEEEHHHECCCCCCCEEEEEEEEECCCCEEECCCCCCCCCCCEEEEECCCCHHHHHHEEEEECCCCCCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCC
        --------------------------------------------------------------------------------------------------------------------------------------
DSSPSQ: KTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEA
PSIPSQ: KTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEA
RPRFSQ: KTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEA
DSSPSS: CCEEECCCCCCCHHHHHHCCHHHHHHHHCCHHHHHHHHHHHCCCCCEEEECCCEEEECCCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHCEECCCCCCCCCCCCEEECCCCCCCEEECHHHHHHHHHHCCCCEEEECCCC
PsiPSS: CCEEEECCCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHCCCCHHHHHCCCCEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCHHHHHHHHHHCCCCHHHHHHHH
RPRFSS: CEEEEEECCCCCCEEEEEEEEEEEEEEEEECHHHHHHHHHCCCCCHHHHHCCCEEEEECCCCCCCCCHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCECCCCCECCEEEEECCCCEEEEHCCCCHHHHEHHHCC
        ----------------------------------------------------------------------------------------------------------------------------------------------
DSSPSQ: QDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICS****************************************************
PsiPSQ: QDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKIRAIGKMARVFSVLREESESVLTLKG
RPRFSQ: QDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKIRAIGKMARVFSVLREESESVLTLKG
DSSPSS: CCCCEEECCECCCCCCECEEEECCCCCHHHCCCCCEEEEEEECCEEEEEEECCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
PSIPSS: HHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
RPRFSS: CCCCEEEEEECCCCCCCEEEEEEECCCEEEEECCCEEEEEECCCEEEEEEECCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCHHEEEEEEEECCCCCEEEEEC
        ----------------------------------------------------------------------------------------------------------------------------------------------
DSSPSQ: *******************************************SFEEAKGLDRINERMPPR
PsiPSQ: LTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRINERMPPRRDAMPSDANLNSINKALTSETNGTDSNGSNSSNIQ
RPRFSQ: LTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRINERMPPRRDAMPSDANLNSINKALTSETNGTDSNGSNSSNIQ
DSSPSS: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC
PSIPSS: CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
RPRFSS: CCCCCCCCCCEECCCCEEEEEEEEEEECCHHHHCCCCCCCEEEEHHHHCCCCHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCC

<figtable id="Q3SOV1AUI">

Table 2: Q3- and SOV-Scores of the predictions with ReProf and PSIPred (PDBID: 1AUI).

Scoring method	PsiPred	ReProf
Q3	72.84	56.58
Q3E	52.46	67.21
Q3H	77.30	34.04
Q3C	75.00	65.49
SOV	51.99	28.89

</figtable>

2BNH

DSSPSQ: *MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVL
PsiPSQ:  MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVL
RPRFSQ:  MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVL
DSSPSS: CCECCEECCCCCHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHCHHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCEHHHHHHHHHHHHHCCCCCEEECCCCECHHHHHHHH
PsiPSS:  CEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHH
RPRFSS:  CCCCECHHCCCCCHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHEEEHCCCCCCCCEEEEECCCCCCCCHCCCCCCHHHHCHCHHHHHHCCCCCCCCHHHHHHHHHCCCCCHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
DSSPSQ: GQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLCESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLC
PsiPSQ: GQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLCESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLC
RPRFSQ: GQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLCESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLC
DSSPSS: HHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEECCCCCCEHHHHHHHHHHHHHCCCCCEEECCCCECHHHHHHHHHHHCCCCCCCCCEEE
PsiPSS: HHHCCCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHHCCCCCCCEEEEE
RPRFSS: CCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHCHCCHHHCCCCCCCCCHHHHHHHCCCCCCCHHHHCHHEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCEEEEEE
        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
DSSPSQ: LGDCEVTNSGCSSLASLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
PsiPSQ: LGDCEVTNSGCSSLASLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
RPRFSQ: LGDCEVTNSGCSSLASLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
DSSPSS: CCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCEEEC
PsiPSS: CCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCEECC
RPRFSS: ECCCCCCCCCHHHHHHHHHHHCCHHHHCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCECC

<figtable id="Q3SOV2BNH">

Table 3: Q3- and SOV-Scores of the predictions with ReProf and PSIPred (PDBID: 2NBH).

Scoring method	PsiPred	ReProf
Q3	91.89	60.96
Q3E	85.96	21.05
Q3H	90.31	71.94
Q3C	95.07	61.58
SOV	95.47	66.03

</figtable>

1A6Z

DSSPSQ:                      ****RSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGaEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKI
PsiPSQ: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKI
RPRFSQ: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKI
DSSPSS:                      CCCCCCEEEEEEEEEEECCCCCCECCEEEEEECCEEEEEEECCCCCEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEECCEEEEEEEHHHCEEEECCHHHHHHHHHHHCCCH
PsiPSS: CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEECCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCEECCCCCCCCEEEECCCCCCCCCCCCCCCCEECCCCHHHHHHHHHHHHHH
RPRFSS: CCCCCCHHHHHHHHHHHHHHCCCEEHHCCCEEEEECCCCHCCCCHHHHHHCCCCCEEEEEECCCCCCCCCCCCCECCCCCHHHHHHHHHCCCCCCCEEEEEHEEEHCCCCCCCCCCEEEEEEEEEECCCCCCCCEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCHHHHEE
        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
DSSPSQ: RARQNRAYLERDaPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRbRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTbQVEHPGLDQPLIVIW
PsiPSQ: RARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPSPSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
RPRFSQ: RARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPSPSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
DSSPSS: HHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCECCEEEEEEEECCCCEEEEEEEEEEECCCCEEEEEECCEECCHHHCCCCEEEECCCCCEEEEEEEEECCCHHHHEEEEEECCCCCCCEEEEC
PsiPSS: HHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCCCCEECCCCCCEEEEEEEECCCCCCCEEEEEECCCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
RPRFSS: EEECCCHCCCCCCHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCEEEEEEEECCCCCCCEEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHHHHEECCCCCCCCCEEEEEECCC

<figtable id="Q3SOV1A6Z">

Table 4: Q3- and SOV-Scores of the predictions with ReProf and PSIPred (PDBID: 1A6Z).

Scoring method	PsiPred	ReProf
Q3	76.09	61.59
Q3E	61.47	60.55
Q3H	74.29	31.428
Q3C	93.81	84.54
SOV	71.38	50.40

</figtable>

You can see, that the PsiPred Q3Score is for these proteins in a range from 72 to 92% and the SOV-score is in a range from 52 to 96%. As here are only four proteins this probably does not reflect the general performance of the prediction, but one can gain insight from this. When just looking at the annotated "aligned" secondary structure sequences, it looks like a fairly good prediction (also when looking at the protein 1AUI although the SOV is quite low. This is very likely caused by the fact that many short H/E sequences are not correctly predicted). Another problem occurs at the regions without DSSP-data. Because this is a disordered region the results my be viewed in addition to a disorder prediction. This could give additional informations for both secondary structure and disorder.

This means the predictions should be reliable to gain more insight of the proteins secondary structure.

The ReProf predictions do not get such good results. The Q3Score ranges from 56 to 62%, the SOVScore from 29 to 66%. This means that this prediction is far less reliable than the PsiPred predictions, which should be preferred. This may due to the use of only four sequences not reflect the general performance, and this prediction method may therefore be better on other proteins.

Disorder

<figtable id="iupred">

Table 5: 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>

<figure id="map92">

Figure 1: DisProt map with ordered (blue) and disordered (red) regions for Q08209 (DP00092).

</figure>

IUPred was employed to find disordered regions within HFE (Q30201), RNH1 (P10775), PPP3CA (Q08209), and cutA (Q9X0E6). The results are shown in <xr id="iupred"/>. DisProt was used to validate the predictions.

As shown in the upper left figure (<xr id="iupred"/>) Q30201 has two small regions (around residue 250 and 285) where it might be disordered. There is no entry for Q30201 in DisProt that would suggest that this is true and a sequence search (PsiBlast) against DisProt did not yield any significant results.

For P10775 no disordered regions are predicted (upper right figure in <xr id="iupred"/>). There is also no entry in DisProt. A PsiBlast search results in one significant hit (DP00554), but the alignment does not include the hit's disordered region (31-50).

DisProt does have an entry for Q08209 (DP00092). A PsiBlast search also results in an additional significant hit (DP00365), but the alignment does not contain the disordered region (19-147), so it can be discarded. A comparison between the DisProt Map (<xr id="map92"/>) and the IUPred prediction (lower left figure in <xr id="iupred"/>) shows that the general predictions are true, although IUPred inserts a small ordered region at the end of the protein (about 374-425) which should be disordered. The disordered regions from residue 374-486 are known to make a disorder-order transition which might cause IUPred's vague prediction within this section.

Neither IUPred (lower right figure in <xr id="iupred"/>) nor DisProt suggest any disordered regions for Q9X0E6.

IUPred seems to be quite accurate in predicting completely ordered proteins (P10775, Q9X0E6, and with the exception of the small peak in Q30201), but it seems to have problems with disordered regions where a disorder-order transition occurs.

Transmembrane Helices

Transmembrane helices were predicted with PolyPhobius for HFE (Q30201), DRD3 (P35462), Aquaporin-4 (P47863), and KvAP (Q9YDF8). The results were compared to OPM, PDBTM, and UniProt. The PDB IDs for OPM and PDBTM were chosen based on the following criteria:

• wildtype over mutant
• higher coverage
• better resolution

UniProt -> PDB mapping:

• P35462 -> 3PBL
• P47863 -> 2D57
• Q9YDF8 -> 1ORQ/1ORS

Q30201

PolyPhobius predicts only one transmembrane helix for Q30201 (see <xr id="tmh_q30201"/>). There is no entry in OPM or PDBTM for either of its PDB IDs, but UniProt lists a TMH which almost exactly matches the predicted one (1-residue-shift).

<figtable id="tmh_q30201">

Table 6: 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>

P35462

For P35462 all methods list 7 transmembrane helices (<xr id="tmh_p35462"/>) which are consistent (regarding their positions) throughout all methods.

<figtable id="tmh_p35462">

Table 7: 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>

P47863

PolyPhobius, UniProt, and PDBTM list 6 TMHs for P47863, OPM lists two additional TMHs (see <xr id="tmh_p47863"/>). These two regions are listed as "Membrane Loop" in PDBTM which might be the cause for the false entries in OPM.

<figtable id="tmh_p47863">

Table 8: 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>

Q9YDF8

Q9YDF8 seems to be the hardest one to predict TMHs for (cf. <xr id="tmh_q9ydf8"/>). PolyPhobius predicts an additional TMH (compared to UniProt); OPM and PDBTM need two PDB IDs to identify all (and "false") TMHs. Both PDB entries were adjusted for an AA shift of 13 residues. It should also be noted that PsiBlast didn't find any hits for Q9YDF8, so no homology information could be used for PolyPhobius.

PolyPhobius predicted a region (TMH7), labeled as "Intramembrane - Pore-Forming" in UniProt, as a (false) TMH. OPM also included this region and an additional one labeled as "Intramembrane - Helical" in UniProt. PDBTM lists TMH7 as "Membrane Loop".

<figtable id="tmh_q9ydf8">

Table 9: 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>

Comparison

PolyPhobius predicts the transmembrane helices very well. With the exception of TMH7 in Q9YDF8 it never predicts a false TMH nor misses a true one. Compared to UniProt and OPM it tends to shift the TMHs to the right, while it encloses PDBTM's helices. PolyPhobius, UniProt, and OPM annotate transmembrane helices with an average length of about 21, PDBTM has shorter TMHs with a mean of 18. So it seems that PDBTM is a little bit more cautious to annotate TMHs, while OPM doesn't distinguish between transmembrane helices and other (intra)membrane structures such as membrane loops and intramembrane helices. PolyPhobius' strength, the use of homology information, can be seen in the case of Q9YDF8 where PsiBlast didn't provide any hits, as there the deviation from the other annotations is the biggest.

The results suggest that PDBTM would be the best one to use if you want the least false positives, but compared to PolyPhobius it is quite limited in that you have to provide a PDB entry in the first place. When only sequence information is available PolyPhobius should provide reliable predictions, especially if there is homology information.

Signal Peptides

<figtable id="signalp">

Table 10: 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>

SignalP (Webserver 4.0) predictions were made for HFE (Q30201), Aquaporin-4 (P47863), Lysosome-associated membrane glycoprotein 1 (P11279), and Serum albumin (P02768) in order to find signal peptides within these sequences. The results are shown in <xr id="signalp"/> and were compared to the corresponding entries in UniProt. A high S-score indicates that an AA is part of the signal peptide, a low score that it is part of the mature protein. A possible cleavage site is represented by a high C-score. The Y-score is a combination of the other scores and a better indicator for the cleavage site than the C-score alone.

According to UniProt all four predictions are 100% precise:

• Q30201: signal peptide 1-22
• P47863: no signal peptide
• P11279: signal peptide 1-28
• P02768: signal peptide 1-18

This makes SignalP an excellent candidate for signal peptide predictions.

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). We did also search for Pfam families. The results were then compared to UniProt and QuickGO.

GOPET

GOPET predicts only two GO terms for our protein (see <xr id="gopet"/>) and even they are somewhat redundant (both are receptor activity). Although they do not match the QuickGO terms for HFE, they are eligible in that HFE has kind of a receptor activity when in complex with transferrin receptor (TFR).

<figtable id="gopet">

Table 11: 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

The results for the ProtFun prediction are shown in <xr id="protfun"/>. Predictions with a probability below 0.1 and odds below 1.0 are not shown to decrease the size of the table. ProtFun predicts "cell envelope" for the functional category. This is true as the HFE-TFR complex is located in the membrane. "Transport and binding" also has a high probability which corresponds with HFE's part in the iron transport within the body. HFE is categorized as "Nonenzyme" and no enzyme class was predicted. It is further predicted to be involved in "Immune response" as it is a protein of the major histocompatibility complex (MHC) class I.

<figtable id="protfun">

Table 12: 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>

Pfam

<figure id="pfam">

Figure 2: Pfam map for Q30201 with the two Pfam domains, the signal peptide (yellow), and the transmembrane helix (red) at the end.

</figure>

Pfam lists two significant results for Q30201 (cf. <xr id="pfam"/>):

• PF00129: MHC_I - Class I Histocompatibility antigen, domains alpha 1 and 2 (E-value 3.5e-43)
• PF07654: C1-set - Immunoglobulin C1-set domain (E-value 2.8e-18)

MHC class I proteins are cell surface receptors and involved in immune responses. UniProt also lists HFE in the MHC class I family and its structure (three extracellular domains, transmembrane region, cytoplasmic tail) fits. C1-set domains are associated with MHC class I proteins and HFE indeed contains such a domain (residues 207-298)

Comparison

Compared to QuickGO which lists 27 unique GO terms for Q30201, GOPET predicts only two. Both of them not included in QuickGO's list. These two also seem to fit the HFE-TFR complex better than HFE alone, but at least the MHC class I tag shows specificity to HFE.

ProtFun's prediction seems more accurate as it successfully identifies HFE's location within the membrane and lists "Transport and binding" as a good second result. "Immune response" is also in accordance to QuickGO's terms.

Pfam's two predicted families were both true positives and it was more informative that the other two methods.

Overall none of them did identify HFE's part in the iron transport.

Conclusion

All these methods can be used to extract more information from just the sequence. As most of it is reliable, these methods are able to generate additional info for further experiments, more insight on the structure of the protein and more, in very few time (compared to experimentally generated data).