D-I-TASSER P78560

D-I-TASSER results for P78560

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

Summary of the Protein

Uniprot ID: P78560
Protein Name: Death domain-containing protein CRADD
Gene Name: CRADD

Input Sequence in FASTA format

>P78560 (199 residues)
MEARDKQVLRSLRLELGAEVLVEGLVLQYLYQEGILTENHIQEINAQTTGLRKTMLLLDI
LPSRGPKAFDTFLDSLQEFPWVREKLKKAREEAMTDLPAGDRLTGIPSHILNSSPSDRQI
NQLAQRLGPEWEPMVLSLGLSQTDIYRCKANHPHNVQSQVVEAFIRWRQRFGKQATFQSL
HNGLRAVEVDPSLLLHMLE

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	P78560-D1	1-99	99		MEARDKQVLRSLRLELGAEVLVEGLVLQYLYQEGILTENHIQEINAQTTGLRKTMLLLDILPSRGPKAFDTFLDSLQEFPWVREKLKKAREEAMTDLPA
2	P78560-D2	100-199	100		GDRLTGIPSHILNSSPSDRQINQLAQRLGPEWEPMVLSLGLSQTDIYRCKANHPHNVQSQVVEAFIRWRQRFGKQATFQSLHNGLRAVEVDPSLLLHMLE

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	6rkoA	0.47	5.02	0.062	0.734	model1_6rkoA.pdb.gz
2	7khbD	0.46	5.70	0.067	0.809	model1_7khbD.pdb.gz
3	6c84A	0.46	5.32	0.102	0.779	model1_6c84A.pdb.gz
4	2of5B	0.45	0.51	1.000	0.457	model1_2of5B.pdb.gz
5	4bedA	0.45	5.68	0.025	0.799	model1_4bedA.pdb.gz
6	3p23A	0.45	5.07	0.030	0.739	model1_3p23A.pdb.gz
7	4fxqA	0.45	4.77	0.050	0.709	model1_4fxqA.pdb.gz
8	1i6vD	0.45	5.80	0.075	0.819	model1_1i6vD.pdb.gz
9	1lnsA	0.45	5.56	0.069	0.764	model1_1lnsA.pdb.gz
10	1jqoA	0.45	5.17	0.062	0.719	model1_1jqoA.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:0019899	0.47	enzyme binding
GO:0003824	0.47	catalytic activity
GO:0019904	0.45	protein domain specific binding
GO:0060090	0.44	binding, bridging
GO:0002020	0.44	protease binding
GO:0070513	0.43	death domain binding
GO:0030674	0.43	protein binding, bridging
GO:0016787	0.36	hydrolase activity
GO:0070011	0.35	peptidase activity, acting on L-amino acid peptides
GO:0008234	0.33	cysteine-type peptidase activity
GO:0004175	0.32	endopeptidase activity
GO:0004197	0.31	cysteine-type endopeptidase 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:0065007	0.98	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0048522	0.95	positive regulation of cellular process
GO:0042981	0.94	regulation of apoptotic process
GO:0009987	0.77	cellular process
GO:0043065	0.69	positive regulation of apoptotic process
GO:0007165	0.69	signal transduction
GO:0050896	0.68	response to stimulus
GO:0035556	0.66	intracellular signal transduction
GO:0006950	0.66	response to stress
GO:0033554	0.65	cellular response to stress
GO:0006974	0.64	cellular response to DNA damage stimulus
GO:0080090	0.62	regulation of primary metabolic process
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0051246	0.60	regulation of protein metabolic process
GO:0065009	0.59	regulation of molecular function
GO:0030162	0.58	regulation of proteolysis
GO:0043281	0.57	regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0031323	0.53	regulation of cellular metabolic process
GO:0048519	0.52	negative regulation of biological process
GO:0048523	0.51	negative regulation of cellular process
GO:0022402	0.51	cell cycle process
GO:0032268	0.50	regulation of cellular protein metabolic process
GO:0031325	0.50	positive regulation of cellular metabolic process
GO:0010604	0.50	positive regulation of macromolecule metabolic process
GO:0006977	0.50	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest

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	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0005737	0.76	cytoplasm
GO:0044444	0.71	cytoplasmic part
GO:0005829	0.57	cytosol
GO:0043229	0.51	intracellular organelle
GO:0043227	0.50	membrane-bounded organelle

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	2h2qA	0.430	5.85	0.040	0.764	2.1.1.45 1.5.1.3	NA
2	0.060	1l5jA	0.412	4.69	0.061	0.613	4.2.1.3	117,148
3	0.060	1zcjA	0.358	5.69	0.063	0.638	1.1.1.35	NA
4	0.060	2zicA	0.388	5.21	0.061	0.638	3.2.1.70	NA
5	0.060	2agsA	0.408	5.61	0.034	0.714	3.2.1.18	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	2a6hD	0.362	5.60	0.067	0.638	0.52	STD	complex1.pdb.gz	136,139,140,171
	2	0.01	2onk2	0.216	5.65	0.019	0.372	0.85	III	complex2.pdb.gz	130,131,133,134,135,136,137,138,139,140,141,142,144,148

	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.