D-I-TASSER Q9Y4K0-D7

D-I-TASSER results for Q9Y4K0-D7

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

Input Sequence in FASTA format

>Q9Y4K0 (72 residues)
VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH
FSGLLNNQLSPQ

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEHFSGLLNNQLSPQ
Prediction	CCCCSSSSSSSSCCCCSCCCCCCCCCSSSSSSSSCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCC
Confidence	999508999996898412434664755999999868399998343588756789999998554553246679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEHFSGLLNNQLSPQ
Prediction	664441202020247351453435322030304244430303413335414661454156354245543468
	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

                   |                   |                   |

SS
Seq

CCCCSSSSSSSSCCCCSCCCCCCCCCSSSSSSSSCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCC
VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEHFSGLLNNQLSPQ

5ze3A3

1.00

0.83

23.33

1.71

SPARKS-K

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

5ze3A3

1.00

0.83

23.33

1.47

MUSTER

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

5ze3A3

1.00

0.83

23.33

1.91

HHsearch

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

5ze3A3

1.00

0.83

23.33

1.01

FFAS-3D

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

5ze3A

1.00

0.83

23.33

1.67

CNFpred

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

5ze3A

1.00

0.83

23.33

1.53

SPARKS-K

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

5ze3A

1.00

0.83

23.33

1.27

MUSTER

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

5ze3A

1.00

0.83

23.33

1.32

HHsearch

VPPGDYLFQVVINPNFEVAESDYSNNIMKCRSRYDGHRIWMYNCHIGGSFSEETEKKFEH------------

3r74A

0.03

1.62

0.83

DEthreader

----PCFALIARS-TG--SA-GERAMIDVFAGAVSYVAITCDEHETVSAAAIP-DAALVFVTFVGTIAALSA

6tkuA

0.10

3.61

0.65

SPARKS-K

TERNRYVGVLRVGATAVGTIKFEDNLLFACEGLIAGGIVVSRGNVNNQGSATTAIKQF-TNTSSKLCKLERV

(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	0.6097

(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	6pqnA	0.56	3.57	0.044	0.889	model1_6pqnA.pdb.gz
2	2d0cA	0.54	3.28	0.000	0.889	model1_2d0cA.pdb.gz
3	1c0mC	0.54	3.29	0.032	0.847	model1_1c0mC.pdb.gz
4	6x67C	0.54	3.70	0.030	0.875	model1_6x67C.pdb.gz
5	4a5bA	0.54	3.62	0.134	0.903	model1_4a5bA.pdb.gz
6	3agrA	0.54	3.60	0.119	0.903	model1_3agrA.pdb.gz
7	3ecpA1	0.54	3.39	0.029	0.861	model1_3ecpA1.pdb.gz
8	3l2rA	0.52	2.93	0.067	0.806	model1_3l2rA.pdb.gz
9	1ex4A	0.50	3.42	0.070	0.778	model1_1ex4A.pdb.gz
10	3hpgB2	0.49	3.16	0.053	0.778	model1_3hpgB2.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:0016641	0.95	oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
GO:0004720	0.92	protein-lysine 6-oxidase activity
GO:0070492	0.64	oligosaccharide binding
GO:0044877	0.51	macromolecular complex 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	0.97	single-organism process
GO:0044767	0.92	single-organism developmental process
GO:0009987	0.80	cellular process
GO:0009653	0.76	anatomical structure morphogenesis
GO:0044763	0.74	single-organism cellular process
GO:0065007	0.69	biological regulation
GO:0050789	0.67	regulation of biological process
GO:0016043	0.65	cellular component organization
GO:0050794	0.64	regulation of cellular process
GO:0048869	0.60	cellular developmental process
GO:0030198	0.59	extracellular matrix organization
GO:0048523	0.58	negative regulation of cellular process
GO:0080090	0.57	regulation of primary metabolic process
GO:0060255	0.57	regulation of macromolecule metabolic process
GO:0031323	0.57	regulation of cellular metabolic process
GO:0050896	0.56	response to stimulus
GO:0006355	0.55	regulation of transcription, DNA-templated
GO:0031324	0.54	negative regulation of cellular metabolic process
GO:0010605	0.54	negative regulation of macromolecule metabolic process
GO:0045892	0.53	negative regulation of transcription, DNA-templated
GO:0008152	0.53	metabolic process
GO:0001837	0.53	epithelial to mesenchymal transition
GO:0030199	0.51	collagen fibril organization
GO:0071704	0.50	organic substance metabolic process
GO:0051239	0.50	regulation of multicellular organismal process
GO:0048518	0.50	positive regulation of biological process
GO:0044238	0.50	primary metabolic process

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:0044421	0.90	extracellular region part
GO:0044464	0.74	cell part
GO:0005604	0.71	basement membrane
GO:0044424	0.68	intracellular part
GO:0043226	0.66	organelle
GO:0043227	0.65	membrane-bounded organelle
GO:0043229	0.57	intracellular organelle
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0005615	0.53	extracellular space
GO:0005634	0.52	nucleus

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	3f9mA	0.562	3.04	0.067	0.806	2.7.1.2	NA
2	0.060	1c0mA	0.544	3.29	0.032	0.847	2.7.7.49	4,36
3	0.060	1o4zB	0.475	3.74	0.043	0.847	3.2.1.81	36
4	0.060	2ac1A	0.472	4.06	0.029	0.778	3.2.1.26	NA
5	0.060	3hpgB	0.493	3.10	0.053	0.778	2.7.7.49	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:

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	3o5bB	0.514	2.99	0.102	0.750	0.28	BGC	complex1.pdb.gz	5,38,39
2	0.01	3l2wA	0.515	2.86	0.102	0.806	0.26	ELV	complex2.pdb.gz	5,36,65
3	0.01	3s3mA	0.522	2.81	0.102	0.806	0.14	DLU	complex3.pdb.gz	5,8,37
4	0.01	3oyaA	0.520	2.93	0.067	0.806	0.30	RLT	complex4.pdb.gz	2,3,33,34,36,37
5	0.01	1c6v1	0.267	4.09	0.073	0.528	0.15	III	complex5.pdb.gz	34,35,36
6	0.01	1czbA	0.495	3.63	0.048	0.833	0.35	EPE	complex6.pdb.gz	36,38,39
7	0.01	3s3oA	0.517	3.39	0.081	0.847	0.15	DLU	complex7.pdb.gz	5,8,37
8	0.01	3e54A	0.517	3.19	0.015	0.819	0.22	QNA	complex8.pdb.gz	5,6,8,9,10,11,12,26,59,62,63
9	0.01	3mipA	0.513	3.20	0.030	0.778	0.12	QNA	complex9.pdb.gz	7,10,33,35,36

	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.