D-I-TASSER P05106-D2

D-I-TASSER results for P05106-D2

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

Input Sequence in FASTA format

>P05106 (99 residues)
GWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECD
DFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| GWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCSSSSCCCCCCCSCCCCCSCCCCCCCCCCCCCCCCCCSSSCCSSSSCCCCSCCCCCCCCC
Confidence	987996606899867765655668999887689857939978808999885306884237862789998857998489099678489963588888488
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| GWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR
Prediction	846175440557434574445046675463022304043240314544436231530314434056474540233040544504357415174162448
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCSSSSCCCCCCCSCCCCCSCCCCCCCCCCCCCCCCCCSSSCCSSSSCCCCSCCCCCCCCC
GWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR

3k6sB3

0.40

11.91

3.41

SPARKS-K

GYIGKNCECQTQGRSSQELGSCRKDNNSIICSGLGDCVCGQCLCHTSDVKLIYGQYCECDTINCERYNGQVCGGRGLCFCGKCRCHPGFEGSACQCERT

3k6sB3

0.40

11.91

2.02

MUSTER

GYIGKNCECQTQGRSSELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVKLIYGQYCECDTINCERYNGQVCGGRGLCFCGKCRCHPGFEGSACQCERT

3k6sB

0.40

11.91

2.07

HHsearch

GYIGKNCECQTQGRSSELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDGKLIYGQYCECDTINCERYNGQVCGGRGLCFCGKCRCHPGFEGSACQCERT

3ijeB

1.00

28.00

4.45

CNFpred

GWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR

3fcsB2

0.32

0.27

8.21

0.83

DEthreader

RSSDFG-KITCECD-------SCVR-KGEMCSGHGQCSCGDCLCDSD----WTGYYCNCTTRT--DTMSLLCSGRGKCECGSCVCIPGSYGDTCEKCCP

4g1eB

0.98

0.94

26.32

3.35

SPARKS-K

GWLGSQCECSEE----DYQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR

4g1eB

0.84

23.64

0.84

MapAlign

CNCGPGWLGQCECSEEDYQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR

3k6sB3

0.39

11.64

0.72

CEthreader

GYIGKNCECQTQGRSSQEEGSCRKDNNSIICSGLGDCVCGQCLCHTSPGKLIYGQYCECDTINCERYNGQVCGGRGLCFCGKCRCHPGFEGSACQCERT

4g1eB

0.92

0.88

24.69

1.87

MUSTER

GWLGSQCECSEEDYQDECSPRE----GQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR

4g1eB

0.92

0.88

24.69

2.07

HHsearch

GWLGSQCECSEEDYQDECSPRE----GQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTR

(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	0.579

(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	3k6sB	0.96	0.83	0.414	1.000	model1_3k6sB.pdb.gz
2	3fcsB2	0.87	1.09	0.968	0.939	model1_3fcsB2.pdb.gz
3	4g1eB	0.86	1.42	0.958	0.960	model1_4g1eB.pdb.gz
4	1jkyA	0.48	4.31	0.043	0.879	model1_1jkyA.pdb.gz
5	3g5cA	0.47	3.58	0.162	0.667	model1_3g5cA.pdb.gz
6	6bxbA2	0.47	2.05	0.789	0.535	model1_6bxbA2.pdb.gz
7	2vzaA	0.47	4.79	0.042	0.929	model1_2vzaA.pdb.gz
8	6mgjA1	0.46	4.42	0.032	0.859	model1_6mgjA1.pdb.gz
9	6rc9A1	0.46	4.78	0.020	0.919	model1_6rc9A1.pdb.gz
10	4lgnA1	0.46	4.55	0.031	0.879	model1_4lgnA1.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:0050839	0.50	cell adhesion molecule binding
GO:0005102	0.46	receptor binding
GO:0044877	0.41	macromolecular complex binding
GO:0032403	0.40	protein complex binding
GO:0046983	0.32	protein dimerization activity
GO:0046982	0.31	protein heterodimerization activity

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	0.96	single-organism process
GO:0009987	0.94	cellular process
GO:0044763	0.93	single-organism cellular process
GO:0065007	0.84	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0016043	0.66	cellular component organization
GO:0050896	0.52	response to stimulus
GO:0032879	0.52	regulation of localization

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:0044464	0.93	cell part
GO:0044425	0.78	membrane part
GO:0044459	0.75	plasma membrane part
GO:0016020	0.75	membrane
GO:0044424	0.55	intracellular part

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	3c8xA	0.255	4.25	0.045	0.444	2.7.10.1	NA
2	0.060	1fohC	0.328	5.55	0.047	0.748	1.14.13.7	NA
3	0.060	1qksB	0.425	4.74	0.052	0.828	1.7.2.1	54
4	0.060	1aomB	0.422	4.73	0.052	0.818	1.7.99.1 1.7.2.1	NA
5	0.060	1zj8A	0.418	4.81	0.043	0.808	1.8.7.1	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	0.03	1jv2B	0.491	3.31	0.226	0.737	0.67	UUU	complex1.pdb.gz	71,72,73,75,87,91
2	0.03	1m1xB	0.487	3.15	0.226	0.727	0.52	UUU	complex2.pdb.gz	66,67,68,77,81
3	0.01	2z48A	0.363	4.24	0.026	0.646	0.50	A2G	complex3.pdb.gz	77,78,79,81,82
4	0.01	1fwxA	0.440	4.53	0.055	0.808	0.61	CUA	complex4.pdb.gz	83,85,91,94
5	0.01	2vdoB	0.288	5.03	0.014	0.586	0.51	III	complex5.pdb.gz	73,76,77,79,83

	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.