D-I-TASSER Q07011

D-I-TASSER results for Q07011

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

Summary of the Protein

Uniprot ID: Q07011
Protein Name: Tumor necrosis factor receptor superfamily member 9
Gene Name: TNFRSF9

Input Sequence in FASTA format

>Q07011 (255 residues)
MGNSCYNIVATLLLVLNFERTRSLQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQR
TCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQDCKQGQELTKKGCKDC
CFGTFNDQKRGICRPWTNCSLDGKSVLVNGTKERDVVCGPSPADLSPGASSVTPPAPARE
PGHSPQIISFFLALTSTALLFLLFFLTLRFSVVKRGRKKLLYIFKQPFMRPVQTTQEEDG
CSCRFPEEEEGGCEL

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

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q07011-D1	1-104	104		MGNSCYNIVATLLLVLNFERTRSLQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ
2	Q07011-D2	105-176	72		DCKQGQELTKKGCKDCCFGTFNDQKRGICRPWTNCSLDGKSVLVNGTKERDVVCGPSPADLSPGASSVTPPA
3	Q07011-D3	177-255	79		PAREPGHSPQIISFFLALTSTALLFLLFFLTLRFSVVKRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.44

(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	6bwvD	0.45	2.62	0.963	0.529	model1_6bwvD.pdb.gz
2	5wi8A	0.45	2.80	0.644	0.529	model1_5wi8A.pdb.gz
3	6rw9A	0.44	5.93	0.042	0.729	model1_6rw9A.pdb.gz
4	5yz0A	0.43	6.33	0.044	0.776	model1_5yz0A.pdb.gz
5	1vw1A	0.43	5.65	0.043	0.706	model1_1vw1A.pdb.gz
6	6rw8A	0.43	5.88	0.035	0.710	model1_6rw8A.pdb.gz
7	6ar6A	0.42	6.66	0.039	0.796	model1_6ar6A.pdb.gz
8	2pffB	0.41	6.13	0.077	0.722	model1_2pffB.pdb.gz
9	6u5vB	0.41	6.42	0.042	0.729	model1_6u5vB.pdb.gz
10	7cunB	0.41	6.48	0.053	0.733	model1_7cunB.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:0038023	0.97	signaling receptor activity
GO:0005031	0.96	tumor necrosis factor-activated receptor 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:0050794	0.99	regulation of cellular process
GO:0042981	0.94	regulation of apoptotic process
GO:0043207	0.93	response to external biotic stimulus
GO:0042127	0.92	regulation of cell proliferation
GO:0007165	0.92	signal transduction
GO:0006952	0.92	defense response
GO:0010033	0.91	response to organic substance
GO:0002376	0.91	immune system process
GO:0032496	0.90	response to lipopolysaccharide
GO:0006954	0.90	inflammatory response
GO:0097190	0.89	apoptotic signaling pathway
GO:0006955	0.89	immune response
GO:0044699	0.88	single-organism process
GO:0032502	0.86	developmental process
GO:0048856	0.85	anatomical structure development
GO:0044767	0.83	single-organism developmental process
GO:0044707	0.78	single-multicellular organism process
GO:0007275	0.77	multicellular organism development
GO:0048518	0.70	positive regulation of biological process
GO:0048522	0.66	positive regulation of cellular process
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0051246	0.62	regulation of protein metabolic process
GO:0048583	0.62	regulation of response to stimulus
GO:0031323	0.62	regulation of cellular metabolic process
GO:0048584	0.61	positive regulation of response to stimulus
GO:0032268	0.60	regulation of cellular protein metabolic process
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0032270	0.59	positive regulation of cellular protein metabolic process
GO:0031399	0.59	regulation of protein modification process
GO:0019220	0.59	regulation of phosphate metabolic process
GO:0001934	0.58	positive regulation of protein phosphorylation
GO:0009966	0.57	regulation of signal transduction
GO:1902533	0.56	positive regulation of intracellular signal transduction
GO:0043410	0.54	positive regulation of MAPK cascade

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	1.00	cell part
GO:0044459	0.96	plasma membrane part
GO:0031226	0.93	intrinsic component of plasma membrane
GO:0016021	0.93	integral component of membrane
GO:0005887	0.92	integral component of plasma membrane

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	3d8vA	0.295	6.50	0.039	0.537	2.7.7.23 2.3.1.157	NA
2	0.060	1w36C	0.283	6.40	0.026	0.510	3.1.11.5	67
3	0.060	3h09B	0.305	6.52	0.040	0.561	3.4.21.72	NA
4	0.060	2gblA	0.261	6.67	0.018	0.498	2.7.11.1	4
5	0.060	2pffB	0.252	5.96	0.026	0.412	2.3.1.86	10,13,36

	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	1utcA	0.212	5.73	0.024	0.341	0.19	III	complex1.pdb.gz	4,8,10
2	0.01	1utcB	0.176	5.71	0.034	0.286	0.19	III	complex2.pdb.gz	4,11,67
3	0.01	1w7j3	0.269	6.08	0.067	0.478	0.13	III	complex3.pdb.gz	66,73,89,90
4	0.01	1w7jA	0.269	6.08	0.067	0.478	0.14	UUU	complex4.pdb.gz	6,71,72,73,74,90

	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.