D-I-TASSER Q8WXH2-D2

D-I-TASSER results for Q8WXH2-D2

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>Q8WXH2 (121 residues)
IRSPLRTSINSLRSEHTNGTALHPDASPAVAGSPAVSRGGFVLVAHSDSEILKSKKKGLF
RRSLLSGLKLRKSESKSSLASQRSKQSSFRSEAGMSTVSSTASDIHSTISLGEAEAELAV
I

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| IRSPLRTSINSLRSEHTNGTALHPDASPAVAGSPAVSRGGFVLVAHSDSEILKSKKKGLFRRSLLSGLKLRKSESKSSLASQRSKQSSFRSEAGMSTVSSTASDIHSTISLGEAEAELAVI
Prediction	CCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCSSSHHHHCHHHHCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9985322112114578999879987776678998777651588613785322445566322012211023214565663344455422540676543333444444543224567777889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| IRSPLRTSINSLRSEHTNGTALHPDASPAVAGSPAVSRGGFVLVAHSDSEILKSKKKGLFRRSLLSGLKLRKSESKSSLASQRSKQSSFRSEAGMSTVSSTASDIHSTISLGEAEAELAVI
Prediction	8644334314304354573433474447456553433200000204256753575443313413234342445645553555444443144544344344444444343442457473457
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCSSSHHHHCHHHHCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
IRSPLRTSINSLRSEHTNGTALHPDASPAVAGSPAVSRGGFVLVAHSDSEILKSKKKGLFRRSLLSGLKLRKSESKSSLASQRSKQSSFRSEAGMSTVSSTASDIHSTISLGEAEAELAVI

6z5rH

0.07

2.79

0.54

CEthreader

NVALTPAAPWPGAPFVPTGNPFADGVGPGSADVPELGLDNLPIIVPLRAAKGMFLDPRMPVVGCDGVVGGTVTEVWVDRAEVLARYLEVEVAKSRKRVLLPVPFALINDPFGKVSVDAIRG

6w2rA

0.05

2.34

0.48

EigenThreader

RALEIAAVKLALDVALRVAQEAAKRGNKDAIDEAAEVVVRIAALRVLEEIAKAVLKSEKAVKLVQEAYKAAQRAIEAAKRTGTAIKLAKLAARAALKKIVKAIQEAVESLREAEESARERV

6qp6A1

0.19

0.10

3.20

0.22

FFAS-3D

---------------NQQDFRTPEFEEFNGKPDSLFFTDGFILVYEDESKKGTNEKQKRKRQAYEHGLQLEATRSVSD-------------------------------------------

5jcss

0.11

3.88

0.97

SPARKS-K

RNRGVEIYIDELHSRSTAFDRLTLGFELGENIDFVSIDDGIKKIKLNEPDM--SIPLKHYVPSYLSRPCIFAQVHDILLLSDEEPIEESLAAVIPISHLGEVGKWANNVLNCTEYSEKKIA

3nrkA

0.11

0.02

0.89

0.36

CNFpred

--------------------------------------RYCILKIEGKRPTPMENLRGGIQNILY--------------------------------------------------------

3s4wA

0.03

0.02

1.60

0.83

DEthreader

TQSEEDGALRRYKIYSCCIQLVEASEIGLLMLEVHHFPGPLLVALILCVVAKVLTFVGIIFFEIIFSIASVGLIEFLIEILEQVLNVVLFLPQLDARKAGFL----QCTQS-IGVRY----

2pffB

0.07

2.77

0.71

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGRADNHFKDTYGFSILDIVINNPVNLTI--

6etxG

0.12

4.35

0.62

MUSTER

LSLKASYRLHQLRSWGAPEGESHQRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVL

1lf9A1

0.13

0.11

3.75

0.55

HHsearch

IDTADKETAIKVEKFTDKSLGY-------KLVN-TDKKGRYRITIFTDVKR----------NSLIMKAKFEALGSIHDYKKRDNVYTALSSNKQMTKHDSARGNIIEGAEIDLTKNEFIVL

2aw7C2

0.07

0.06

2.35

0.44

CEthreader

PELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLADIDYNTSEAHTTYGVIGVKVWIFKGEI--------------------------

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.466

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5fq6B	0.47	4.74	0.066	0.860	model1_5fq6B.pdb.gz
2	7jptA	0.47	4.96	0.066	0.893	model1_7jptA.pdb.gz
3	4aipA	0.46	4.41	0.067	0.802	model1_4aipA.pdb.gz
4	4iglA	0.45	4.49	0.017	0.810	model1_4iglA.pdb.gz
5	6l7iF	0.45	4.50	0.084	0.793	model1_6l7iF.pdb.gz
6	3ir7A	0.45	4.96	0.025	0.835	model1_3ir7A.pdb.gz
7	7lhtA	0.45	4.57	0.033	0.802	model1_7lhtA.pdb.gz
8	6e4vA	0.44	4.80	0.050	0.818	model1_6e4vA.pdb.gz
9	2w78A2	0.44	4.63	0.058	0.818	model1_2w78A2.pdb.gz
10	4epaA	0.44	4.72	0.076	0.752	model1_4epaA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0043167	0.61	ion binding
GO:0099600	0.58	transmembrane receptor activity
GO:0005215	0.58	transporter activity
GO:0004871	0.58	signal transducer activity
GO:0022836	0.57	gated channel activity
GO:0005543	0.57	phospholipid binding
GO:0005262	0.57	calcium channel activity
GO:0004888	0.57	transmembrane signaling receptor activity
GO:0080025	0.56	phosphatidylinositol-3,5-bisphosphate binding
GO:0070300	0.56	phosphatidic acid binding
GO:0070273	0.56	phosphatidylinositol-4-phosphate binding
GO:0032266	0.56	phosphatidylinositol-3-phosphate binding
GO:0015278	0.56	calcium-release channel activity
GO:0010314	0.56	phosphatidylinositol-5-phosphate binding
GO:0005547	0.56	phosphatidylinositol-3,4,5-trisphosphate binding
GO:0005546	0.56	phosphatidylinositol-4,5-bisphosphate binding
GO:0001786	0.56	phosphatidylserine binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	1.00	single-organism process
GO:0065007	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0065008	0.89	regulation of biological quality
GO:0023051	0.88	regulation of signaling
GO:0010646	0.88	regulation of cell communication
GO:0065009	0.81	regulation of molecular function
GO:0051049	0.81	regulation of transport
GO:0048583	0.81	regulation of response to stimulus
GO:0060314	0.80	regulation of ryanodine-sensitive calcium-release channel activity
GO:0009987	0.76	cellular process
GO:0044763	0.69	single-organism cellular process
GO:0051480	0.61	regulation of cytosolic calcium ion concentration
GO:0007204	0.60	positive regulation of cytosolic calcium ion concentration
GO:0051234	0.53	establishment of localization
GO:0044765	0.52	single-organism transport
GO:0051649	0.51	establishment of localization in cell
GO:0006816	0.51	calcium ion transport
GO:0060402	0.50	calcium ion transport into cytosol

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044444	1.00	cytoplasmic part
GO:0044422	0.94	organelle part
GO:0016020	0.94	membrane
GO:0044446	0.86	intracellular organelle part
GO:0044425	0.84	membrane part
GO:0005789	0.82	endoplasmic reticulum membrane
GO:0043226	0.64	organelle
GO:0043229	0.63	intracellular organelle
GO:0031090	0.63	organelle membrane
GO:0098588	0.62	bounding membrane of organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0014701	0.61	junctional sarcoplasmic reticulum membrane
GO:0043234	0.59	protein complex
GO:0030314	0.54	junctional membrane complex
GO:0005783	0.51	endoplasmic reticulum

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2pdaA	0.299	4.68	0.035	0.545	1.2.7.1	NA
2	0.060	3b9jI	0.214	5.67	0.058	0.455	1.17.1.4 1.17.3.2	58
3	0.060	2nyfA	0.366	4.47	0.051	0.620	4.3.1.5	NA
4	0.060	1t9kD	0.379	4.44	0.070	0.628	5.3.1.23	NA
5	0.060	3b9jC	0.282	4.78	0.019	0.496	1.17.3.2 1.17.1.4	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1siwA	0.421	5.16	0.041	0.860	0.41	SF4	complex1.pdb.gz	3,6,7,10,39
	2	0.01	2ckjA	0.402	5.03	0.036	0.760	0.55	FES	complex2.pdb.gz	38,39,40,42

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.