Sequence-based analyses Gaucher Disease

Secondary structure

Knowing the secondary structure of a protein can shed light on its function since structure implies function. If the structure of a protein is known, secondary structure elements (helix, sheet, coiled) can be assigned to its residues depending on their affinity to form hydrogen bonds. DSSP <ref name="DSSP">Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers</ref> is the most common method to perform such secondary structure assignments. If the structure of a protein is unknown, secondary structure elements be be predicted by tools like PSIPRED <ref name="PSIPRED">Liam J. McGuffin, Kevin Bryson, and David T. Jones (2000). "The PSIPRED protein structure prediction server". Bioinformatics</ref> or Reprof<ref name="Reprof">B Rost, C Sander (1993). "Prediction of protein secondary structure at better than 70% accuracy". J. Mol. Bio.</ref>. The aim of this task was to analyse the secondary structure of different proteins and the compare the secondary structure predictions of PSIPRED and Reprof with the DSSP secondary structure assignments. Following sequences were taken into account: <figtable id="tab:ss_sequences">

NAME	UniProtKB	PDB
Glucosylceramidase	P04062	1OGS
Ribonuclease inhibitor	P10775	1DFJ
Divalent-cation tolerance protein CutA	Q9X0E6	1KR4
Serine/threonine-protein phosphatase	Q08209	1AUI

</figtable> Information about program calls and implementation details can be found in our protocol.

Predictions

For being able to better compare the different output formats, we mapped the secondary structure definitions of all three methods onto the three letters H (helix), E (sheet), and C (coiled) according to table <xr id="tab:ss_mapping"/>. Regions of the UniProt sequences which were not present in the PDB file as well as regions where no DSSP assignment was possible were ignored. <figtable id="tab:ss_mapping">

Method	H	E	C
DSSP	H,G,I	E,B	T,S,' '
PSIPRED	H	E	C
Reprof	H	E	L

</figtable>

P04062

Glycosylcermidase (P04062) is located the the membrane of lysosomes. It exhibits two domains which belong to the (1) glycosyl hydrolase domain fold and (2) the TIM beta/alpha-barrel fold. Both domains have hydrophobic beta sheets which anchor the protein in the membrane. <xr id="fig:ss_P04062"/> depicts the secondary structure elements of the corresponding crystal structure which coincide with the DSSP assignments. The following section shows the secondary structure annotations of the different methods: The PSIPRED predictions better coincide with the DSSP assigments than the Reprof predictions do. Reprof predicts sheets instead of helices in several regions. The residues of the beta-barell sheets (the tube in the middle of <xr id="fig:ss_P04062"/>) are marked by asterisks.

</figure>

Crsytal structure of 1OGS (P04062). Red: alpha-helix, yellow: beta-sheet, green: coiled.

40 ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKG Reprof CCCCCCCCCCCEEEEEEECCEECCCCCCCCCCCCCEEEEEEECCCCCEEEEECCCEECCCCCCEEEEEECCCCEEEEEEC PSIPRED CCCCCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCEEEEEEECCCCCCHHCCCCCCCCCCCCCCCEEEECCCCCCEEEEE DSSP CECCCEEECCCCCEEEEEECCCCCECCCCCCCCCCEEEEEEEECCCCCCEEEEEECECCCCCCCEEEEEEEEEEEEECCE 120 FGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPL Reprof CCCCCCHHHHHEEEEECCCCCCEEEEEEECCCCCEEEEEEECCCCCCEEEEEEEECCCCCCCEEEEECCCCCCCCCEEEE PSIPRED EEEEHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH DSSP EEEECCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCHHHH 200 IHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL Reprof EEHHHHHCCCCCEEEECCCCCCCEEEECCCECCCEECCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCCE PSIPRED HHHHHHHHCCCEEEEEEECCCCHHEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCC DSSP HHHHHHHCCCCCEEEEEECCCCHHHECCCCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCHHH ****** *** 280 LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPA Reprof ECCCCEEEECCCCCCCCCEEEECCCCCCCCCCCCEEEEEEECCCCEECCCEEEEEECCCCCCEEEEEEEEEEEEEECCCC PSIPRED CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHCCHHHHHHCCEEEEECCCCCCCCH DSSP CCCCCCCCCECCHHHHHHHHHHCHHHHHHCCCCCCCEEEEEEEEHHHCCHHHHHHHCCHHHHCCCCEEEEEEECCCCCCH ******** ******* 360 KATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDS Reprof CCECCCCCECCCCCEEEECCCCCCCEEEEEEEEECCCCCCCEEECEHHHHEEEEEEECCCCEEEECCCCCCEEEEECCCC PSIPRED HHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHEEEEEEEEECCCCCCCCCCCCCCC DSSP HHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCEEEEEEEECCECCCCCCCCCCCCCCC ******** ******** 440 PIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL Reprof CEEEEECCCCCCCCCEEEECCCEEEECCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEECCCCCCEEEECCCCEEEE PSIPRED CEEEECCCCEEEECHHHHHHHHHHHHCCCCCEEEEEECCCCCCEEEEEEECCCCCEEEEEEECCCCCEEEEEEECCCEEE DSSP CEEEEHHHCEEEECHHHHHHHHHHCCCCCCCEEEEEEECCCCCEEEEEEECCCCCEEEEEEECCCCCEEEEEEECCCEEE 520 ETISPGYSIHTYLWRRQ Reprof EEECCCCEEEEEEEECC PSIPRED EEECCCCEEEEEEEECC DSSP EEEECCCEEEEEEECCC

<figure id="fig:ss_P04062">

P10775

<xr id="fig:ss_P10775"/> depicts the crystal structure 1DFJ which refers to P10775. It has two domains: d1dfji_ is a repeat domain consisting of altering alpha-helices and parallel beta-sheets. d1dfje_ contains long curved antiparallel beta-sheets and three alpha-helices. The alternating HHH and EEE regions in the following secondary structure annotations suit well with repetitive structure shown in <xr id="fig:ss_P10775"/>. Again, the PSIPRED predictions better match the DSSP assignments than Reprof.

</figure>

Crsytal structure of 1DFJ (P10775). Red: alpha-helix, yellow: beta-sheet, green: coiled.

1 MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTC Reprof CCCCECHHCCCCCHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHEEEHCCCCCCCC PSIPRED CEEECCCCCCCHHHHHHHHHHHCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHHHCCC DSSP CECCCECCCCCHHHHHHHHHHHCCCCEEECECCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHCCCCC 81 KIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASV Reprof EEEEECCCCCCCCHCCCCCCHHHHCHCHHHHHHCCCCCCCCHHHHHHHHHCCCCCHCCHHHHHHHHHHCCCCCCHHHHHH PSIPRED CCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHH DSSP CCCEEECCCCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHH 161 LRATRALKELTVSNNDIGEAGARVLGQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIA Reprof HHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHCHCCHHHCCCCCCCCCHHHHH PSIPRED HHHCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHH DSSP HHHCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCHHHHHH 241 ELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLCESLLQPGCQLESLWVKSCSL Reprof HHCCCCCCCHHHHCHHEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHCHH PSIPRED HHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEECCCCCC DSSP HHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCC 321 TAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDL Reprof HHHHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHCCHHHHCC PSIPRED CHHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEC DSSP EHHHHHHHHHHHHHCCCCCEEECCCCECHHHHHHHHHHHHHCCCCCCCEEECCCCCCEHHHHHHHHHHHHHCCCCCEEEC 401 SNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS Reprof CCCCCCCHHHHHHHCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCECC PSIPRED CCCCCCHHHHHHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCEECC DSSP CCCECCHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCEEEC

<figure id="fig:ss_P10775">

Q9X0E6

<xr id="fig:ss_Q9X0E6"/> depicts the d1kr4a_ domain of 1KR4 which is made of three alpha-helices interrupted by beta-sheets. Reprof predicts too long helices.

</figure>

Crsytal structure of 1KR4 (Q9X0E6). Red: alpha-helix, yellow: beta-sheet, green: coiled.

2 ILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIF Reprof EEEEECCCCHHHHHHHHHHHHHHHHHHHHCHCHHHCCCEEECEEECCHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHE PSIPRED EEEEEECCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEECCCEEEEEEEEEEECCCHHHHHHHHHHHHHHCCCCCCEEE DSSP EEEEEEECCHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCEEEEEEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCEE 82 TLKVENVLTEYMNWLRESVL Reprof HHHHHHHHHHHHHHHHHHCC PSIPRED EEECCCCCHHHHHHHHHHCC DSSP EECCCCEEHHHHHHHHHHCC

<figure id="fig:ss_Q9X0E6">

Q08209

Q08209 contains the domain d1auib_ and d1auia_ which are mainly assembled of alpha-helices (<xr id="fig:ss_Q08209"/>). PSIPRED predicts these alpha-helices considerably better than Reprof which suggests beta-sheets in some regions.

</figure>

Crsytal structure of 1AUI (Q08209). Red: alpha-helix, yellow: beta-sheet, green: coiled.

14 TDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHG Reprof CCCEEEEECCCCCCCEEEEEEECCCCCCEEEEEHHHECCCCCCCEEEEEEEEECCCCEEECCCCCCCCCCCEEEEECCCC PSIPRED CCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCEEEECCCEEEECCCCC DSSP CCCCCCCCCCCCCCCECHHHHECCCCCECHHHHHHHHHCCCCECHHHHHHHHHHHHHHHHCCCCEEEECCCEEEECCCCC 94 QFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSER Reprof HHHHHHEEEEECCCCCCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCEEEEEECCCCCCEEEEEEEEEEEEEEEEECH PSIPRED HHHHHHHHHHHCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHCCCCHHHHHHHHCCHH DSSP CHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCEEECCCCCCCHHHHHHCCHHHHHHHHCCHH 174 VYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTV Reprof HHHHHHHHCCCCCHHHHHCCCEEEEECCCCCCCCCHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCECCCCCE PSIPRED HHHHHHHHHCCCHHHHHCCCCEEEECCCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCC DSSP HHHHHHHHHCCCCCEEEECCCEEEECCCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHCEECCCCCCCCCCCCEEECCC 254 RGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQ Reprof CCEEEEECCCCEEEEHCCCCHHHHEHHHCCCCCCEEEEEECCCCCCCEEEEEEECCCEEEEECCCEEEEEECCCEEEEEE PSIPRED CCCCCCCCHHHHHHHHHHCCCCEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCEEEEEEECCCCCEEEE DSSP CCCCEEECHHHHHHHHHHCCCCEEEECCCCCCCCEEECCECCCCCCECEEEECCCCCHHHCCCCCEEEEEEECCEEEEEE 334 FNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICSSFEEAKGLDRINERMPPR Reprof ECCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHEECCEHHHHCCCCHHCCCCCCC PSIPRED ECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCC DSSP ECCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCC

<figure id="fig:ss_Q08209">

Prediction accuracy/precision

We compared the prediction performance of PSIPRED and Reprof via the Q3 score and the precision of the three secondary structure states H,E, and C. The Q3 score is identical to the accuracy, i.e. the number of correctly predicted states divided by the length of the protein. The precision of state X is the fraction of correct predictions of X, formally precision(X)=TP(X)/(TP(X)+FP(X)). <xr id="ss_acc"/> shows the results: PSIPRED clearly outperforms Reprof in all for cases. PSIPRED achieves an average accuracy of 87% which is significantly higher than 58% in case of Reprof. <figtable id="ss_acc">

Method	Q3	Precision H	Precision E	Precision C
P04062
PSIPRED	0.831	0.830	0.872	0.810
Reprof	0.553	1.000	0.455	0.592
P10775
PSIPRED	0.941	0.959	0.960	0.919
Reprof	0.603	0.589	0.417	0.644
Q9X0E6
PSIPRED	0.890	1.000	0.895	0.720
Reprof	0.580	0.562	0.917	0.458
Q08209
PSIPRED	0.833	0.842	0.902	0.812
Reprof	0.579	0.762	0.293	0.743

</figtable>

Disorder

Disordered regions are regions with a varying three-dimensional structure. Nevertheless, such regions can be functionally highly important: regulation, signalling, and flexible ligand binding are only some examples. DisProt<ref name="DisProt">Vucetic S, Obradovic Z, Vacic V, et al. (2005). "DisProt: a database of protein disorder". Bioinformatics</ref> is a curated databases of proteins with experimentally determined disordered regions. IUPred<ref name="IUPred">Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon (2005). "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins". J. Mol. Biol.</ref> is a method for predicting disordered regions ab-initio, i.e. based solely on the protein sequence. We compared the predictions of IUPred with the annotations in the DisProt database for all four example proteins. IUPred was called to predict long, global disorder regions (confer the protocol for details). Residues involved in disordered regions were defined as those with a probability of at least 50%. These residues were compared to the DisProt annotations: either by the UniProt entry itself if available, or by a significant homolog (e-value < 1e-3) for which a DisProt entry existed. We measured the performance of IUPred via the precision (TP/(TP+FP)), sensitivity (TP/(TP+FN)), and specificity (TN/(TN+FP)).

P04062

Neither Glycosylceramidase (P04062) nor a homologous protein is annotated in DisProt. This might be due to lacking experimental data or, which is more likely, due to lacking disordered regions. The latter assumption is supported by the highly structured protein complex 1OGS (<xr id="fig:ss_P04062"/>). However, IUOred predicts some disordered residues with a probability >= 50%.

<figtable id="disorder_P04062">

Method	Disorder regions
IUPred	2, 3, 6, 90-93, 229-231, 235, 236
DisProt
Precision: 0%	Sensitivity: undef	Specificity: 98%

</figtable>

P10775

P10775 is not annotated in DisProt itself, but there is a significant homolog (DP00554) with a disordered region from 31 to 50. This region is, however, is not covered by the pairwise alignment of P10775 and DP00554. Hence, IUpred correctly did not predict any disordered region (Specificity=100%).

Q9X0E6

There is neither an entry in DisProt which suggests a disordered region in Q9X0E6 and nor does IUPred predict such a region.

Q08209

Five disordered regions are annotated in DisProt for Q08209. These regions mainly cover the C-terminal end which exhibits several rather arbitrarily arranged alpha-helices (<xr id="fig:ss_Q08209"/>). All residues predicted by IUPred with a probability >= 50% are covered by DisProt annotations (precision 100%), but IUpred predicts only about half of all disordered regions (sensitivity 52%).

</figure>

Disordered and ordered regions of Q08209 using the DisProt entry DP00092.

<figtable id="disorder_Q08209"> Method Disorder regions IUPred 1-6, 8, 383,384,424,425,432,434-439,443,445,448,449,455,458,463-521 DisProt 1-13,390-414,374-468,469-486,487-521 Precision: 100% Sensitivity: 52% Specificity: 100% </figtable>

<figure id="fig:disorder_Q08209">

Transmembrane helices

PolyPhobius was used to predict transmembrane helices for our protein P04062 and other three proteins P35462, Q9YDF8 and P47863. The scripts which were used to do the prediction can be found here [protocal]. The prediction results from PolyPhobius were then compared with the membrane assignment of the structures for these proteins in OPM and/or PDBTM. For that purpose, a corresponding pdb structure for each protein was needed and was taken from uniprot:

<figtable id="tab:ss_sequences_trans">

NAME	UniProtKB	PDB
Glucosylceramidase	P04062	1OGS
D(3) dopamine receptor	P35462	3PBL
DVoltage-gated potassium channel	Q9YDF8	1ORQ 1ORS
Aquaporin-4	P47863	2D57

</figtable>

P04062

Our protein Glucosylceramidase is located in the lysosome, therefore contains no transmembrane regions. As expected, PolyPhobius has not reported any transmembrane regions. Instead, the most regions were predicted lying in the non-cytoplam and a signal peptide was found. Compared with that in uniprot, PolyPhobius has returned correct prediction:

<figtable id="tab:P04062_trans">

P04062	Signal peptide	Others
PolyPhobius	1-39	40-536 NON CYTOPLASMIC
Uniprot	1-39	40–536 Chain

</figtable>

P35462

<figtable id="tab:P35462_trans">

P35462	TRANSMEM 1	TRANSMEM 2	TRANSMEM 3	TRANSMEM 4	TRANSMEM 5	TRANSMEM 6	TRANSMEM 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	3330-351	363-386
PDBTM	35-52	68-84	109-123	152-166	191-206	334-347	368-382

</figtable>

<figtable id="tab:P35462_trans_png">

Dopamine D3 receptor(P35462,3PBL) showing in OPM.

Dopamine D3 receptor(P35462,3PBL) showing in PDBTM.

</figtable>

Q9YDF8

<figtable id="tab:Q9YDF8_trans">

Q9YDF8	TRANSMEM_1	TRANSMEM_2	TRANSMEM_3	TRANSMEM_4	TRANSMEM_5	TRANSMEM_6	TRANSMEM_7	TRANSMEM_8
PolyPhobius	42-60	68-88	-	108-129	137-157	163-184	196-213	224-244
Uniprot	39–63	68–92	97–105(Intramembrane)	109–125	129–145	160–184	196–208(Intramembrane)	222 – 253
OPM_1ORQ	-	-	-	-	-	153-172	183-195	207-225
OPM_1ORS	25-46	55-78	86-97	100-107	117-148	-	-	-
PDBTM_1ORQ	21-52	57-80	-	-	151-171	-	-	209-236
PDBTM_1ORS	27-50	55-75	88-107	118-142	-	-	-	-

</figtable>

<figtable id="tab:Q9YDF8_trans_png">

Potassium channel KvAP(Q9YDF8,1ORQ) showing in OPM.

Potassium channel KvAP(Q9YDF8,1ORS) showing in OPM.

Potassium channel KvAP(Q9YDF8,1ORQ) showing in PDBTM.

Potassium channel KvAP(Q9YDF8,1ORS) showing in PDBTM.

</figtable>

P47863

<figtable id="tab:P47863_trans">

P47863	TRANSMEM_1	TRANSMEM_2	TRANSMEM_3	TRANSMEM_4	TRANSMEM_5	TRANSMEM_6	TRANSMEM_7	TRANSMEM_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	-	116-133	158-177	188-205	-	231-248

</figtable>

<figtable id="tab:P47863_trans_png">

Aquaporin-4(P47863,2D57) showing in OPM.

Aquaporin-4(P47863,2D57) showing in PDBTM.

</figtable>

Signal peptides

The online server of SignalP with version 4.0 was used to predict signal peptides for our protein P04062 and other three proteins P02768, P47863 and P11279:

<figtable id="tab:ss_sequences_signa">

NAME	UniProtKB	PDB
Glucosylceramidase	P04062	1OGS
Serum albumin	P02768	1AO6
Aquaporin-4	P47863	2D57
Lysosome-associated membrane glycoprotein 1	P11279	-

</figtable>

<figtable id="tab:signa_png">

signal peptides prediction of Glucosylceramidase (P04062) by using SignalP.

signal peptides prediction of Serum albumin (P02768) by using SignalP.

signal peptides prediction of Aquaporin-4 (P47863) by using SignalP.

signal peptides prediction of Lysosome-associated membrane glycoprotein 1 (P11279) by using SignalP.

</figtable>

GO terms

GOPET

<figtable id="tab:ss_gopet">

GOid	Aspect	Confidence	GO term
GO:0016787	F	98%	hydrolase activity
GO:0004348	F	97%	glucosylceramidase activity
GO:0016798	F	97%	hydrolase activity acting on glycosyl bonds

</figtable>

ProtFun

<figtable id="tab:ss_protfun">

Functional category	Prob	Odds
Amino_acid_biosynthesis	0.035	1.593
Biosynthesis_of_cofactors	0.182	2.528
Cell_envelope	0.504	8.262
Cellular_processes	0.032	0.438
Central_intermediary_metabolism	0.382	6.063
Biosynthesis_of_cofactors	0.182	2.528
Energy_metabolism	0.067	0.740
Fatty_acid_metabolism	0.027	2.088
Purines_and_pyrimidines	0.538	2.213
Regulatory_functions	0.031	0.191
Replication_and_transcription	0.126	0.471
Translation	0.082	1.863
Transport_and_binding	0.560	1.365
Enzyme/nonenzyme	Prob	Odds
Enzyme	0.773	2.698
Nonenzyme	0.227	0.318
Enzyme class	Prob	Odds
Oxidoreductase (EC 1.-.-.-)	0.083	0.399
Transferase (EC 2.-.-.-)	0.228	0.660
Hydrolase (EC 3.-.-.-)	0.272	0.859
Lyase (EC 4.-.-.-)	0.045	0.961
Isomerase (EC 5.-.-.-)	0.011	0.345
Ligase (EC 6.-.-.-)	0.017	0.332
Gene Ontology category	Prob	Odds
Signal_transducer	0.054	0.251
Receptor	0.027	0.158
Hormone	0.001	0.206
Structural_protein	0.002	0.087
Transporter	0.024	0.222
Ion_channel	0.018	0.307
Voltage-gated_ion_channel	0.004	0.195
Cation_channel	0.012	0.268
Transcription	0.070	0.550
Transcription_regulation	0.030	0.237
Stress_response	0.085	0.962
Immune_response	0.153	1.804
Growth_factor	0.005	0.376
Metal_ion_transport	0.009	0.020

</figtable>

Pfam

<figure id="pfam_p94962">

One domain (green) was found by Pfam , the signal peptide (yellow) at the top (yellow).

</figure>

References

<references/>