D-I-TASSER Q9GZR2

D-I-TASSER results for Q9GZR2

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

Summary of the Protein

Uniprot ID: Q9GZR2
Protein Name: RNA exonuclease 4
Gene Name: REXO4

Input Sequence in FASTA format

>Q9GZR2 (422 residues)
MGKAKVPASKRAPSSPVAKPGPVKTLTRKKNKKKKRFWKSKAREVSKKPASGPGAVVRPP
KAPEDFSQNWKALQEWLLKQKSQAPEKPLVISQMGSKKKPKIIQQNKKETSPQVKGEEMP
AGKDQEASRGSVPSGSKMDRRAPVPRTKASGTEHNKKGTKERTNGDIVPERGDIEHKKRK
AKEAAPAPPTEEDIWFDDVDPADIEAAIGPEAAKIARKQLGQSEGSVSLSLVKEQAFGGL
TRALALDCEMVGVGPKGEESMAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPEN
LKQGEELEVVQKEVAEMLKGRILVGHALHNDLKVLFLDHPKKKIRDTQKYKPFKSQVKSG
RPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLYVMVKKEWESMARDRRPLLTAPDHCSD
DA

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	Q9GZR2-D1	1-422	422		MGKAKVPASKRAPSSPVAKPGPVKTLTRKKNKKKKRFWKSKAREVSKKPASGPGAVVRPPKAPEDFSQNWKALQEWLLKQKSQAPEKPLVISQMGSKKKPKIIQQNKKETSPQVKGEEMPAGKDQEASRGSVPSGSKMDRRAPVPRTKASGTEHNKKGTKERTNGDIVPERGDIEHKKRKAKEAAPAPPTEEDIWFDDVDPADIEAAIGPEAAKIARKQLGQSEGSVSLSLVKEQAFGGLTRALALDCEMVGVGPKGEESMAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRILVGHALHNDLKVLFLDHPKKKIRDTQKYKPFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLYVMVKKEWESMARDRRPLLTAPDHCSDDA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5566

(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	6uebA	0.40	7.32	0.030	0.687	model1_6uebA.pdb.gz
2	5xjcQ	0.40	7.11	0.023	0.668	model1_5xjcQ.pdb.gz
3	7alpU2	0.38	7.21	0.043	0.649	model1_7alpU2.pdb.gz
4	6l42A	0.38	7.29	0.054	0.642	model1_6l42A.pdb.gz
5	4kmqA	0.36	7.10	0.043	0.607	model1_4kmqA.pdb.gz
6	5b7iA	0.36	7.14	0.033	0.609	model1_5b7iA.pdb.gz
7	6gykB	0.36	7.63	0.042	0.640	model1_6gykB.pdb.gz
8	6ysgA	0.36	7.02	0.051	0.590	model1_6ysgA.pdb.gz
9	5fvmA	0.36	7.02	0.071	0.590	model1_5fvmA.pdb.gz
10	3ba6A	0.36	7.29	0.045	0.609	model1_3ba6A.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	0.84	catalytic activity
GO:0004518	0.81	nuclease activity
GO:0004527	0.80	exonuclease activity
GO:1901363	0.72	heterocyclic compound binding
GO:0097159	0.72	organic cyclic compound binding
GO:0008408	0.72	3'-5' exonuclease activity
GO:0000175	0.67	3'-5'-exoribonuclease activity
GO:0004535	0.57	poly(A)-specific ribonuclease activity
GO:0003676	0.55	nucleic acid binding
GO:0003723	0.51	RNA binding

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	0.96	cellular process
GO:0008152	0.90	metabolic process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0044237	0.89	cellular metabolic process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0034641	0.88	cellular nitrogen compound metabolic process
GO:0090304	0.87	nucleic acid metabolic process
GO:0016070	0.86	RNA metabolic process
GO:0006401	0.70	RNA catabolic process
GO:0016071	0.66	mRNA metabolic process
GO:0000289	0.65	nuclear-transcribed mRNA poly(A) tail shortening

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	0.97	intracellular organelle
GO:0043232	0.91	intracellular non-membrane-bounded organelle
GO:0044444	0.67	cytoplasmic part
GO:0044446	0.65	intracellular organelle part
GO:0032991	0.63	macromolecular complex
GO:0044428	0.59	nuclear part
GO:0043234	0.59	protein complex
GO:0030529	0.57	intracellular ribonucleoprotein complex
GO:0031251	0.54	PAN complex
GO:0000932	0.54	cytoplasmic mRNA processing body
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	2fh7A	0.313	7.18	0.059	0.524	3.1.3.48	NA
2	0.060	2hpiA	0.283	7.09	0.048	0.474	2.7.7.7	NA
3	0.060	2nlkA	0.325	6.65	0.023	0.514	3.1.3.48	NA
4	0.060	1w36B	0.318	7.52	0.036	0.552	3.1.11.5	NA
5	0.060	1eulA	0.300	6.77	0.070	0.476	3.6.3.8	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	2oa0A	0.326	7.17	0.050	0.543	0.20	CZA	complex1.pdb.gz	272,323,394
2	0.01	3namA	0.299	7.23	0.041	0.507	0.18	OTK	complex2.pdb.gz	265,344,392
3	0.01	2easA	0.327	7.11	0.051	0.545	0.14	CZA	complex3.pdb.gz	271,272,324,325
4	0.01	2dqsA	0.302	7.10	0.044	0.502	0.17	ACP	complex4.pdb.gz	324,325,327
5	0.01	2c88A	0.301	7.20	0.038	0.507	0.15	ACP	complex5.pdb.gz	271,318,324,325
6	0.01	3fgoA	0.323	6.89	0.048	0.524	0.17	CZA	complex6.pdb.gz	267,268,385
7	0.01	3ar9A	0.282	6.90	0.044	0.465	0.17	TM1	complex7.pdb.gz	249,277,330,389,390,391

	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.