D-I-TASSER O14579

D-I-TASSER results for O14579

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

Summary of the Protein

Uniprot ID: O14579
Protein Name: Coatomer subunit epsilon
Gene Name: COPE

Input Sequence in FASTA format

>O14579 (308 residues)
MAPPAPGPASGGSGEVDELFDVKNAFYIGSYQQCINEAQRVKLSSPERDVERDVFLYRAY
LAQRKFGVVLDEIKPSSAPELQAVRMFADYLAHESRRDSIVAELDREMSRSVDVTNTTFL
LMAASIYLHDQNPDAALRALHQGDSLECTAMTVQILLKLDRLDLARKELKRMQDLDEDAT
LTQLATAWVSLATGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGLLQ
EALDKDSGYPETLVNLIVLSQHLGKPPEVTNRYLSQLKDAHRSHPFIKEYQAKENDFDRL
VLQYAPSA

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	O14579-D1	1-67	67		MAPPAPGPASGGSGEVDELFDVKNAFYIGSYQQCINEAQRVKLSSPERDVERDVFLYRAYLAQRKFG
2	O14579-D2	68-143	76		VVLDEIKPSSAPELQAVRMFADYLAHESRRDSIVAELDREMSRSVDVTNTTFLLMAASIYLHDQNPDAALRALHQG
3	O14579-D3	144-215	72		DSLECTAMTVQILLKLDRLDLARKELKRMQDLDEDATLTQLATAWVSLATGGEKLQDAYYIFQEMADKCSPT
4	O14579-D4	216-308	93		LLLLNGQAACHMAQGRWEAAEGLLQEALDKDSGYPETLVNLIVLSQHLGKPPEVTNRYLSQLKDAHRSHPFIKEYQAKENDFDRLVLQYAPSA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.925

(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	3mkrA	0.94	0.59	0.938	0.945	model1_3mkrA.pdb.gz
2	3mv2B	0.76	2.68	0.196	0.877	model1_3mv2B.pdb.gz
3	8hmdC	0.71	4.29	0.094	0.929	model1_8hmdC.pdb.gz
4	5u1sA	0.70	4.10	0.070	0.925	model1_5u1sA.pdb.gz
5	4ui9X	0.69	4.39	0.107	0.919	model1_4ui9X.pdb.gz
6	8bdaE	0.69	4.48	0.115	0.916	model1_8bdaE.pdb.gz
7	8a3tJ	0.69	3.76	0.121	0.867	model1_8a3tJ.pdb.gz
8	5mz61	0.69	4.35	0.059	0.945	model1_5mz61.pdb.gz
9	7nj0A	0.69	4.82	0.098	0.974	model1_7nj0A.pdb.gz
10	4ui9J	0.69	3.83	0.070	0.864	model1_4ui9J.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:0005198	0.63	structural molecule activity
GO:0036094	0.59	small molecule binding
GO:0003824	0.59	catalytic activity
GO:0016740	0.54	transferase activity
GO:0033218	0.51	amide binding
GO:0016758	0.51	transferase activity, transferring hexosyl groups
GO:0008289	0.51	lipid binding
GO:1901981	0.50	phosphatidylinositol phosphate binding
GO:0030246	0.50	carbohydrate binding
GO:0010485	0.50	H4 histone acetyltransferase activity
GO:0008194	0.50	UDP-glycosyltransferase 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:0006891	1.00	intra-Golgi vesicle-mediated transport
GO:0006890	1.00	retrograde vesicle-mediated transport, Golgi to ER
GO:0006888	1.00	ER to Golgi vesicle-mediated transport

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:0044446	1.00	intracellular organelle part
GO:0044444	1.00	cytoplasmic part
GO:0044431	0.98	Golgi apparatus part
GO:0044425	0.98	membrane part
GO:0043234	0.98	protein complex
GO:0030126	0.97	COPI vesicle coat

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	1fo2A	0.495	4.88	0.060	0.711	3.2.1.113	181
2	0.060	1ojnA	0.431	5.78	0.072	0.692	4.2.2.1	NA
3	0.060	1rw9A	0.469	4.58	0.040	0.656	4.2.2.5	NA
4	0.060	1ut9A	0.479	4.81	0.048	0.666	3.2.1.4	NA
5	0.060	1i8qA	0.438	5.73	0.051	0.688	4.2.2.1	228

	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	3hymL	0.661	3.80	0.076	0.838	0.53	III	complex1.pdb.gz	151,154,157,169,181,185,188,217,220,221,224,227,254,255,258,261,262,266
2	0.05	3fp2A	0.601	5.02	0.085	0.841	0.54	III	complex2.pdb.gz	220,224,239,254,258
3	0.02	1hz40	0.637	4.73	0.086	0.883	0.62	III	complex3.pdb.gz	230,258,261
4	0.02	2j9q0	0.541	3.81	0.123	0.679	0.56	III	complex4.pdb.gz	228,230,261,262,290
5	0.01	1g6iA	0.499	4.88	0.057	0.714	0.51	UUU	complex5.pdb.gz	221,227,230,255,259
6	0.01	2axzC	0.464	4.36	0.079	0.617	0.51	III	complex6.pdb.gz	224,235,238,239
7	0.01	1dl2A	0.499	4.87	0.057	0.714	0.61	UUU	complex7.pdb.gz	221,224,225,228,255,258

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.