D-I-TASSER P08138

D-I-TASSER results for P08138

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

Summary of the Protein

Uniprot ID: P08138
Protein Name: Tumor necrosis factor receptor superfamily member 16
Gene Name: NGFR

Input Sequence in FASTA format

>P08138 (427 residues)
MGAGATGRAMDGPRLLLLLLLGVSLGGAKEACPTGLYTHSGECCKACNLGEGVAQPCGAN
QTVCEPCLDSVTFSDVVSATEPCKPCTECVGLQSMSAPCVEADDAVCRCAYGYYQDETTG
RCEACRVCEAGSGLVFSCQDKQNTVCEECPDGTYSDEANHVDPCLPCTVCEDTERQLREC
TRWADAECEEIPGRWITRSTPPEGSDSTAPSTQEPEAPPEQDLIASTVAGVVTTVMGSSQ
PVVTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSCKQNKQGANSRPVNQTPPPEGEK
LHSDSGISVDSQSLHDQQPHTQTASGQALKGDGGLYSSLPPAKREEVEKLLNGSAGDTWR
HLAGELGYQPEHIDSFTHEACPVRALLASWATQDSATLDALLAALRRIQRADLVESLCSE
STATSPV

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	P08138-D1	1-427	427		MGAGATGRAMDGPRLLLLLLLGVSLGGAKEACPTGLYTHSGECCKACNLGEGVAQPCGANQTVCEPCLDSVTFSDVVSATEPCKPCTECVGLQSMSAPCVEADDAVCRCAYGYYQDETTGRCEACRVCEAGSGLVFSCQDKQNTVCEECPDGTYSDEANHVDPCLPCTVCEDTERQLRECTRWADAECEEIPGRWITRSTPPEGSDSTAPSTQEPEAPPEQDLIASTVAGVVTTVMGSSQPVVTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSCKQNKQGANSRPVNQTPPPEGEKLHSDSGISVDSQSLHDQQPHTQTASGQALKGDGGLYSSLPPAKREEVEKLLNGSAGDTWRHLAGELGYQPEHIDSFTHEACPVRALLASWATQDSATLDALLAALRRIQRADLVESLCSESTATSPV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3984

(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	6w1sR	0.38	6.68	0.028	0.595	model1_6w1sR.pdb.gz
2	7bwmA	0.35	7.09	0.074	0.593	model1_7bwmA.pdb.gz
3	6mixA	0.35	7.71	0.034	0.614	model1_6mixA.pdb.gz
4	6rutB1	0.34	7.17	0.055	0.571	model1_6rutB1.pdb.gz
5	6ar6A	0.34	7.57	0.023	0.600	model1_6ar6A.pdb.gz
6	6r9tA	0.34	7.10	0.032	0.562	model1_6r9tA.pdb.gz
7	6eojA	0.33	6.79	0.039	0.536	model1_6eojA.pdb.gz
8	6um1A	0.33	6.83	0.052	0.539	model1_6um1A.pdb.gz
9	5nrlA	0.33	7.26	0.039	0.569	model1_5nrlA.pdb.gz
10	6rw8A	0.33	7.19	0.041	0.555	model1_6rw8A.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:0005031	0.95	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:0050896	0.94	response to stimulus
GO:0044699	0.93	single-organism process
GO:0043207	0.93	response to external biotic stimulus
GO:0042981	0.93	regulation of apoptotic process
GO:1901700	0.92	response to oxygen-containing compound
GO:0042127	0.92	regulation of cell proliferation
GO:0033993	0.92	response to lipid
GO:0006952	0.92	defense response
GO:0032496	0.91	response to lipopolysaccharide
GO:0006954	0.91	inflammatory response
GO:0002376	0.91	immune system process
GO:0007165	0.90	signal transduction
GO:0006955	0.90	immune response
GO:0097190	0.88	apoptotic signaling pathway
GO:0048518	0.86	positive regulation of biological process
GO:0048522	0.84	positive regulation of cellular process
GO:0080090	0.83	regulation of primary metabolic process
GO:0060255	0.83	regulation of macromolecule metabolic process
GO:0048583	0.83	regulation of response to stimulus
GO:0031323	0.82	regulation of cellular metabolic process
GO:0009893	0.82	positive regulation of metabolic process
GO:0051246	0.81	regulation of protein metabolic process
GO:0048584	0.81	positive regulation of response to stimulus
GO:0031325	0.81	positive regulation of cellular metabolic process
GO:0010604	0.81	positive regulation of macromolecule metabolic process
GO:0001934	0.80	positive regulation of protein phosphorylation
GO:0009966	0.79	regulation of signal transduction
GO:1902533	0.78	positive regulation of intracellular signal transduction
GO:0043410	0.77	positive regulation of MAPK cascade
GO:0009987	0.62	cellular process
GO:0032502	0.59	developmental process
GO:0044767	0.57	single-organism developmental process
GO:0048856	0.56	anatomical structure development
GO:0048519	0.55	negative regulation of biological process
GO:0048523	0.53	negative regulation of cellular process
GO:0044763	0.53	single-organism cellular process
GO:0044707	0.52	single-multicellular organism process
GO:0051239	0.51	regulation of multicellular organismal 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:0044464	1.00	cell part
GO:0044459	0.97	plasma membrane part
GO:0005887	0.95	integral component of plasma membrane
GO:0044424	0.77	intracellular part
GO:0043226	0.64	organelle
GO:0043229	0.62	intracellular organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0043231	0.60	intracellular membrane-bounded organelle
GO:0005634	0.53	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	1j0kA	0.303	7.14	0.025	0.506	3.2.1.135	NA
2	0.060	1qbaA	0.303	7.16	0.038	0.515	3.2.1.52	NA
3	0.060	1ea9C	0.292	7.17	0.040	0.487	3.2.1.54	NA
4	0.060	1x1nA	0.302	7.11	0.032	0.499	2.4.1.25	NA
5	0.060	1t3tA	0.308	6.88	0.053	0.499	6.3.5.3	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	2d0gA	0.314	7.38	0.048	0.546	0.56	UUU	complex1.pdb.gz	46,50,51,52,53,64

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.