D-I-TASSER Q8N9I9

D-I-TASSER results for Q8N9I9

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

Summary of the Protein

Uniprot ID: Q8N9I9
Protein Name: Probable E3 ubiquitin-protein ligase DTX3
Gene Name: DTX3

Input Sequence in FASTA format

>Q8N9I9 (347 residues)
MSFVLSRMAACGGTCKNKVTVSKPVWDFLSKETPARLARLREEHRVSILIDGETSDIYVL
QLSPQGPPPAPPNGLYLARKALKGLLKEAEKELKKAQRQGELMGCLALGGGGEHPEMHRA
GPPPLRAAPLLPPGARGLPPPPPPLPPPLPPRLREEAEEQESTCPICLGEIQNAKTLEKC
RHSFCEGCITRALQVKKACPMCGRFYGQLVGNQPQNGRMLVSKDATLLLPSYEKYGTIVI
QYVFPPGVQGAEHPNPGVRYPGTTRVAYLPDCPEGNKVLTLFRKAFDQRLTFTIGTSMTT
GRPNVITWNDIHHKTSCTGGPQLFGYPDPTYLTRVQEELRAKGITDD

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	Q8N9I9-D1	1-148	148		MSFVLSRMAACGGTCKNKVTVSKPVWDFLSKETPARLARLREEHRVSILIDGETSDIYVLQLSPQGPPPAPPNGLYLARKALKGLLKEAEKELKKAQRQGELMGCLALGGGGEHPEMHRAGPPPLRAAPLLPPGARGLPPPPPPLPPP
2	Q8N9I9-D2	149-347	199		LPPRLREEAEEQESTCPICLGEIQNAKTLEKCRHSFCEGCITRALQVKKACPMCGRFYGQLVGNQPQNGRMLVSKDATLLLPSYEKYGTIVIQYVFPPGVQGAEHPNPGVRYPGTTRVAYLPDCPEGNKVLTLFRKAFDQRLTFTIGTSMTTGRPNVITWNDIHHKTSCTGGPQLFGYPDPTYLTRVQEELRAKGITDD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.53

(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	6y22A	0.54	1.60	0.404	0.565	model1_6y22A.pdb.gz
2	6y5nA	0.52	1.94	0.345	0.556	model1_6y5nA.pdb.gz
3	6b434	0.44	6.78	0.034	0.744	model1_6b434.pdb.gz
4	6w2dJ	0.43	6.68	0.046	0.715	model1_6w2dJ.pdb.gz
5	6g2dC	0.42	6.95	0.043	0.735	model1_6g2dC.pdb.gz
6	5cskA	0.42	6.51	0.042	0.680	model1_5cskA.pdb.gz
7	5tj6A	0.42	6.90	0.068	0.723	model1_5tj6A.pdb.gz
8	6v22A	0.40	7.02	0.060	0.712	model1_6v22A.pdb.gz
9	3p8cB	0.40	7.05	0.048	0.695	model1_3p8cB.pdb.gz
10	4o9xA	0.39	6.87	0.027	0.683	model1_4o9xA.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	0.90	catalytic activity
GO:0016740	0.81	transferase activity
GO:0004842	0.80	ubiquitin-protein transferase activity
GO:0061630	0.68	ubiquitin protein ligase activity
GO:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	organic cyclic compound binding
GO:0043169	0.56	cation binding
GO:0097367	0.51	carbohydrate derivative binding
GO:0035639	0.50	purine ribonucleoside triphosphate binding
GO:0032555	0.50	purine ribonucleotide binding
GO:0032550	0.50	purine ribonucleoside 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	0.89	cellular process
GO:0071704	0.82	organic substance metabolic process
GO:0044237	0.82	cellular metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0044238	0.81	primary metabolic process
GO:0019538	0.74	protein metabolic process
GO:0065007	0.61	biological regulation
GO:0050789	0.60	regulation of biological process
GO:0044267	0.59	cellular protein metabolic process
GO:0043412	0.59	macromolecule modification
GO:0006464	0.58	cellular protein modification process
GO:0050794	0.57	regulation of cellular process
GO:0070647	0.56	protein modification by small protein conjugation or removal
GO:0016567	0.55	protein ubiquitination
GO:1901575	0.52	organic substance catabolic process
GO:0051603	0.52	proteolysis involved in cellular protein catabolic process
GO:0044248	0.52	cellular catabolic process
GO:0043161	0.51	proteasome-mediated ubiquitin-dependent protein catabolic 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:0044424	0.99	intracellular part
GO:0043226	0.77	organelle
GO:0044446	0.76	intracellular organelle part
GO:0043229	0.76	intracellular organelle
GO:0044444	0.74	cytoplasmic part
GO:0043227	0.74	membrane-bounded organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0032991	0.61	macromolecular complex
GO:0005737	0.61	cytoplasm
GO:0043234	0.57	protein complex
GO:0005634	0.55	nucleus
GO:0016020	0.53	membrane

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	2rhqB	0.323	7.37	0.040	0.597	6.1.1.20	196
2	0.060	1sj2A	0.212	6.45	0.010	0.343	1.11.1.6 1.11.1.7	255
3	0.060	2pffD	0.280	6.71	0.011	0.470	2.3.1.86	NA
4	0.060	3b2vA	0.190	6.78	0.032	0.329	2.7.10.1	167,170,185,188
5	0.060	2qf7B	0.368	7.43	0.042	0.683	6.4.1.1	287

	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	3bg5C	0.333	7.51	0.037	0.631	0.14	ATP	complex1.pdb.gz	210,211,249,255,257
2	0.01	3ho8A	0.348	7.18	0.043	0.625	0.22	COA	complex2.pdb.gz	248,249,257
3	0.01	3bg5A	0.342	7.32	0.054	0.631	0.15	ATP	complex3.pdb.gz	203,205,206,211
4	0.01	3hb9B	0.288	7.69	0.036	0.548	0.17	BTI	complex4.pdb.gz	247,248,249
5	0.01	3ho8A	0.348	7.18	0.043	0.625	0.18	COA	complex5.pdb.gz	194,195,308
6	0.01	3ho8C	0.349	7.08	0.044	0.620	0.13	COA	complex6.pdb.gz	203,209,211,284
7	0.01	2cg9A	0.374	6.85	0.049	0.637	0.11	ATP	complex7.pdb.gz	247,257,258,260,291
8	0.01	3hb9A	0.363	6.80	0.030	0.617	0.13	ADP	complex8.pdb.gz	211,249,255
9	0.01	2iopD	0.326	6.69	0.036	0.550	0.14	ADP	complex9.pdb.gz	170,171,172,184
10	0.01	2iopA	0.352	6.59	0.021	0.585	0.13	ADP	complex10.pdb.gz	212,247,248

	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.