D-I-TASSER Q8WTP8

D-I-TASSER results for Q8WTP8

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

Summary of the Protein

Uniprot ID: Q8WTP8
Protein Name: Apoptosis-enhancing nuclease
Gene Name: AEN

Input Sequence in FASTA format

>Q8WTP8 (325 residues)
MVPREAPESAQCLCPSLTIPNAKDVLRKRHKRRSRQHQRFMARKALLQEQGLLSMPPEPG
SSPLPTPFGAATATEAASSGKQCLRAGSGSAPCSRRPAPGKASGPLPSKCVAIDCEMVGT
GPRGRVSELARCSIVSYHGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKE
ILKLLKGKVVVGHALHNDFQALKYVHPRSQTRDTTYVPNFLSEPGLHTRARVSLKDLALQ
LLHKKIQVGQHGHSSVEDATTAMELYRLVEVQWEQQEARSLWTCPEDREPDSSTDMEQYM
EDQYWPDDLAHGSRGGAREAQDRRN

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	Q8WTP8-D1	1-325	325		MVPREAPESAQCLCPSLTIPNAKDVLRKRHKRRSRQHQRFMARKALLQEQGLLSMPPEPGSSPLPTPFGAATATEAASSGKQCLRAGSGSAPCSRRPAPGKASGPLPSKCVAIDCEMVGTGPRGRVSELARCSIVSYHGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKGKVVVGHALHNDFQALKYVHPRSQTRDTTYVPNFLSEPGLHTRARVSLKDLALQLLHKKIQVGQHGHSSVEDATTAMELYRLVEVQWEQQEARSLWTCPEDREPDSSTDMEQYMEDQYWPDDLAHGSRGGAREAQDRRN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.608

(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	6r5kA	0.55	4.42	0.215	0.689	model1_6r5kA.pdb.gz
2	4q8hA	0.54	4.25	0.206	0.668	model1_4q8hA.pdb.gz
3	4czwA	0.54	4.08	0.204	0.652	model1_4czwA.pdb.gz
4	1wljA	0.50	1.47	0.494	0.517	model1_1wljA.pdb.gz
5	5z9xA	0.49	3.09	0.204	0.563	model1_5z9xA.pdb.gz
6	4q5vA	0.49	5.04	0.086	0.646	model1_4q5vA.pdb.gz
7	3d45A	0.48	4.01	0.121	0.591	model1_3d45A.pdb.gz
8	2p51A	0.46	3.43	0.105	0.541	model1_2p51A.pdb.gz
9	2gv9B	0.44	4.66	0.060	0.566	model1_2gv9B.pdb.gz
10	1s5jA	0.39	4.73	0.045	0.523	model1_1s5jA.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	0.95	catalytic activity
GO:0016788	0.94	hydrolase activity, acting on ester bonds
GO:0004527	0.93	exonuclease activity
GO:0008408	0.66	3'-5' exonuclease activity
GO:0004540	0.62	ribonuclease activity
GO:0000175	0.61	3'-5'-exoribonuclease activity
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	organic cyclic compound binding
GO:0004535	0.50	poly(A)-specific ribonuclease 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:0008152	0.82	metabolic process
GO:0071704	0.81	organic substance metabolic process
GO:0044238	0.80	primary metabolic process
GO:0044237	0.80	cellular metabolic process
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0034641	0.78	cellular nitrogen compound metabolic process
GO:0006139	0.77	nucleobase-containing compound metabolic process
GO:0090304	0.76	nucleic acid metabolic process
GO:0016070	0.75	RNA metabolic process
GO:0006401	0.61	RNA catabolic process
GO:0016071	0.56	mRNA metabolic process
GO:0000289	0.55	nuclear-transcribed mRNA poly(A) tail shortening
GO:0065007	0.50	biological regulation

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:0044424	1.00	intracellular part
GO:0043229	0.96	intracellular organelle
GO:0043232	0.90	intracellular non-membrane-bounded organelle
GO:0044422	0.65	organelle part
GO:0044446	0.64	intracellular organelle part
GO:0044444	0.62	cytoplasmic part
GO:0044428	0.58	nuclear part
GO:0032991	0.54	macromolecular complex
GO:0043234	0.51	protein complex
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	0.208	1wljA	0.496	1.47	0.494	0.517	3.1.13.1	116,253
2	0.122	2f96A	0.433	3.47	0.188	0.514	3.1.13.-	116,253
3	0.085	3cg7A	0.479	3.79	0.079	0.575	3.1.-.-	116,253
4	0.076	2gbzA	0.394	3.45	0.135	0.474	3.1.-.-	116,253
5	0.060	3ikmD	0.406	4.57	0.055	0.529	2.7.7.7	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	0.06	1wljA	0.496	1.47	0.494	0.517	0.17	U5P	complex1.pdb.gz	112,190,191
2	0.01	2a1rA	0.468	3.36	0.131	0.548	0.21	QNA	complex2.pdb.gz	114,115,116,117,158,192
3	0.01	2p5oA	0.465	4.75	0.057	0.609	0.21	QNA	complex3.pdb.gz	130,132,170
4	0.01	3taeD	0.464	4.82	0.061	0.609	0.17	QNA	complex4.pdb.gz	140,142,145
5	0.01	1clqA	0.459	4.74	0.068	0.603	0.14	GDP	complex5.pdb.gz	193,199,260,261,262
6	0.01	2p5oB	0.439	4.62	0.051	0.569	0.24	QNA	complex6.pdb.gz	232,233,234,235,246

	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.