D-I-TASSER Q13158

D-I-TASSER results for Q13158

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Summary of the Protein

Uniprot ID: Q13158
Protein Name: FAS-associated death domain protein
Gene Name: FADD

Input Sequence in FASTA format

>Q13158 (208 residues)
MDPFLVLLHSVSSSLSSSELTELKFLCLGRVGKRKLERVQSGLDLFSMLLEQNDLEPGHT
ELLRELLASLRRHDLLRRVDDFEAGAAAGAAPGEEDLCAAFNVICDNVGKDWRRLARQLK
VSDTKIDSIEDRYPRNLTERVRESLRIWKNTEKENATVAHLVGALRSCQMNLVADLVQEV
QQARDLQNRSGAMSPMSWNSDASTSEAS

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 AttentionPotential. 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	Q13158-D1	1-92	92		MDPFLVLLHSVSSSLSSSELTELKFLCLGRVGKRKLERVQSGLDLFSMLLEQNDLEPGHTELLRELLASLRRHDLLRRVDDFEAGAAAGAAP
2	Q13158-D2	93-208	116		GEEDLCAAFNVICDNVGKDWRRLARQLKVSDTKIDSIEDRYPRNLTERVRESLRIWKNTEKENATVAHLVGALRSCQMNLVADLVQEVQQARDLQNRSGAMSPMSWNSDASTSEAS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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 AttentionPotential, 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	5fx8A	0.50	5.29	0.065	0.808	model1_5fx8A.pdb.gz
2	2gf5A	0.49	2.98	0.574	0.572	model1_2gf5A.pdb.gz
3	1no3A	0.49	5.48	0.080	0.779	model1_1no3A.pdb.gz
4	3d3lA	0.48	5.20	0.085	0.755	model1_3d3lA.pdb.gz
5	2p0mA	0.48	5.27	0.065	0.760	model1_2p0mA.pdb.gz
6	3o8yA2	0.48	5.47	0.071	0.774	model1_3o8yA2.pdb.gz
7	2va8B	0.48	5.30	0.061	0.798	model1_2va8B.pdb.gz
8	4h3tA	0.48	4.99	0.066	0.740	model1_4h3tA.pdb.gz
9	3dy5A	0.48	5.32	0.080	0.764	model1_3dy5A.pdb.gz
10	4nreA2	0.48	5.28	0.065	0.750	model1_4nreA2.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:0003824	0.68	catalytic activity
GO:0016787	0.50	hydrolase 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:0009987	0.98	cellular process
GO:0044763	0.96	single-organism cellular process
GO:0065007	0.93	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0006915	0.79	apoptotic process
GO:0048518	0.75	positive regulation of biological process
GO:0048522	0.72	positive regulation of cellular process
GO:0048869	0.71	cellular developmental process
GO:0043067	0.70	regulation of programmed cell death
GO:0002521	0.70	leukocyte differentiation
GO:0042981	0.69	regulation of apoptotic process
GO:0048583	0.67	regulation of response to stimulus
GO:0048519	0.66	negative regulation of biological process
GO:0048523	0.65	negative regulation of cellular process
GO:0065008	0.64	regulation of biological quality
GO:0051239	0.64	regulation of multicellular organismal process
GO:0048584	0.64	positive regulation of response to stimulus
GO:0002682	0.64	regulation of immune system process
GO:0044767	0.63	single-organism developmental process
GO:0043069	0.63	negative regulation of programmed cell death
GO:0002376	0.63	immune system process
GO:0051240	0.62	positive regulation of multicellular organismal process
GO:0050776	0.62	regulation of immune response
GO:0048856	0.62	anatomical structure development
GO:0043066	0.62	negative regulation of apoptotic process
GO:0032879	0.62	regulation of localization
GO:0002684	0.62	positive regulation of immune system process
GO:0001817	0.62	regulation of cytokine production
GO:0050778	0.61	positive regulation of immune response
GO:0031343	0.61	positive regulation of cell killing
GO:0001819	0.61	positive regulation of cytokine production
GO:2000454	0.59	positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation
GO:0070236	0.59	negative regulation of activation-induced cell death of T cells
GO:0048538	0.59	thymus development
GO:0048536	0.59	spleen development
GO:0048535	0.59	lymph node development
GO:0043029	0.59	T cell homeostasis
GO:0042104	0.59	positive regulation of activated T cell proliferation
GO:0033077	0.59	T cell differentiation in thymus
GO:0032729	0.59	positive regulation of interferon-gamma production
GO:0001916	0.59	positive regulation of T cell mediated cytotoxicity

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:0044424	0.99	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0032991	0.81	macromolecular complex
GO:0043234	0.80	protein complex
GO:0097342	0.78	ripoptosome

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	2ch5A	0.439	5.64	0.089	0.760	2.7.1.59	NA
2	0.060	3c46B	0.435	5.39	0.041	0.750	2.7.7.6	NA
3	0.060	2p0mA	0.484	5.27	0.065	0.760	1.13.11.33	NA
4	0.060	1h2aL	0.430	5.67	0.072	0.769	1.12.2.1	NA
5	0.060	2fy3A	0.430	4.95	0.044	0.678	2.3.1.6	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	2ebhX	0.433	5.61	0.097	0.774	0.15	TRE	complex1.pdb.gz	50,55,57
2	0.01	1ik3A	0.350	5.31	0.027	0.553	0.14	13S	complex2.pdb.gz	56,79,82,87,91
3	0.01	1qmgA	0.435	5.95	0.068	0.779	0.13	APX	complex3.pdb.gz	114,174,175,177,178

	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.