D-I-TASSER Q9NT62

D-I-TASSER results for Q9NT62

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

Summary of the Protein

Uniprot ID: Q9NT62
Protein Name: Ubiquitin-like-conjugating enzyme ATG3
Gene Name: ATG3

Input Sequence in FASTA format

>Q9NT62 (314 residues)
MQNVINTVKGKALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEE
LKVKAYLPTGKQFLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNTGITGIT
EAVKEITLENKDNIRLQDCSALCEEEEDEDEGEAADMEEYEESGLLETDEATLDTRKIVE
ACKAKTDAGGEDAILQTRTYDLYITYDKYYQTPRLWLFGYDEQRQPLTVEHMYEDISQDH
VKKTVTIENHPHLPPPPMCSVHPCRHAEVMKKIIETVAEGGGELGVHMYLLIFLKFVQAV
IPTIEYDYTRHFTM

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	Q9NT62-D1	1-314	314		MQNVINTVKGKALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLPTGKQFLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNTGITGITEAVKEITLENKDNIRLQDCSALCEEEEDEDEGEAADMEEYEESGLLETDEATLDTRKIVEACKAKTDAGGEDAILQTRTYDLYITYDKYYQTPRLWLFGYDEQRQPLTVEHMYEDISQDHVKKTVTIENHPHLPPPPMCSVHPCRHAEVMKKIIETVAEGGGELGVHMYLLIFLKFVQAVIPTIEYDYTRHFTM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5609

(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	3vx8B	0.55	0.92	0.617	0.557	model1_3vx8B.pdb.gz
2	2dytA	0.55	2.28	0.422	0.586	model1_2dytA.pdb.gz
3	5fsaA	0.42	5.96	0.072	0.675	model1_5fsaA.pdb.gz
4	4uylA	0.42	6.11	0.063	0.678	model1_4uylA.pdb.gz
5	5tl8A	0.42	6.41	0.091	0.691	model1_5tl8A.pdb.gz
6	4k0fA	0.42	6.30	0.071	0.694	model1_4k0fA.pdb.gz
7	6mcwA	0.41	6.27	0.042	0.678	model1_6mcwA.pdb.gz
8	3na0A	0.41	6.36	0.049	0.681	model1_3na0A.pdb.gz
9	4dvqA	0.41	6.55	0.081	0.694	model1_4dvqA.pdb.gz
10	2ve3A	0.41	6.21	0.043	0.662	model1_2ve3A.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:0016740	0.99	transferase activity
GO:0019776	0.98	Atg8 ligase 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	1.00	cellular process
GO:0007005	0.99	mitochondrion organization
GO:0000045	0.99	autophagosome assembly
GO:0044699	0.98	single-organism process
GO:0006914	0.98	autophagy
GO:1902589	0.97	single-organism organelle organization
GO:0022411	0.97	cellular component disassembly
GO:0044804	0.96	nucleophagy
GO:0000422	0.96	mitophagy

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:0005829	1.00	cytosol
GO:0000153	0.99	cytoplasmic ubiquitin ligase complex

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	1w0eA	0.380	6.60	0.042	0.643	1.14.13.67 1.14.14.1	NA
2	0.060	2zy4F	0.400	6.24	0.047	0.653	4.1.1.12	NA
3	0.060	2q9fA	0.400	6.50	0.049	0.669	1.14.13.98	NA
4	0.060	2fr7A	0.390	6.37	0.040	0.646	1.14.-.-	NA
5	0.060	3e6iA	0.393	6.43	0.015	0.662	1.14.13.-	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	0.04	3l4dB	0.411	6.29	0.063	0.675	0.14	UUU	complex1.pdb.gz	26,32,287,291,292,293,296,297
2	0.04	3na0B	0.413	6.32	0.049	0.681	0.19	III	complex2.pdb.gz	33,39,43
3	0.01	1og2A	0.396	6.45	0.038	0.666	0.10	HEC	complex3.pdb.gz	39,43,251
4	0.01	1dt6A	0.406	6.39	0.033	0.675	0.12	HEM	complex4.pdb.gz	43,217,219
5	0.01	3p99B	0.414	6.10	0.047	0.666	0.18	LNP	complex5.pdb.gz	34,42,43,46,294
6	0.01	1og5A	0.396	6.56	0.034	0.672	0.10	SWF	complex6.pdb.gz	32,33,292
7	0.01	2j0dB	0.369	6.35	0.056	0.605	0.12	HEM	complex7.pdb.gz	39,43,50,251
8	0.01	3g1qC	0.411	6.23	0.038	0.672	0.17	HEM	complex8.pdb.gz	29,32,215,289,290,291,297,301
9	0.01	3n9zB	0.410	6.53	0.060	0.694	0.11	UUU	complex9.pdb.gz	47,281,285,311
10	0.01	3p99A	0.404	6.25	0.051	0.669	0.12	HEM	complex10.pdb.gz	37,40,258

	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.