D-I-TASSER P50402

D-I-TASSER results for P50402

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

Summary of the Protein

Uniprot ID: P50402
Protein Name: Emerin
Gene Name: EMD

Input Sequence in FASTA format

>P50402 (254 residues)
MDNYADLSDTELTTLLRRYNIPHGPVVGSTRRLYEKKIFEYETQRRRLSPPSSSAASSYS
FSDLNSTRGDADMYDLPKKEDALLYQSKGYNDDYYEESYFTTRTYGEPESAGPSRAVRQS
VTSFPDADAFHHQVHDDDLLSSSEEECKDRERPMYGRDSAYQSITHYRPVSASRSSLDLS
YYPTSSSTSFMSSSSSSSSWLTRRAIRPENRAPGAGLGQDRQVPLWGQLLLFLVFVIVLF
FIYHFMQAEEGNPF

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	P50402-D1	1-254	254		MDNYADLSDTELTTLLRRYNIPHGPVVGSTRRLYEKKIFEYETQRRRLSPPSSSAASSYSFSDLNSTRGDADMYDLPKKEDALLYQSKGYNDDYYEESYFTTRTYGEPESAGPSRAVRQSVTSFPDADAFHHQVHDDDLLSSSEEECKDRERPMYGRDSAYQSITHYRPVSASRSSLDLSYYPTSSSTSFMSSSSSSSSWLTRRAIRPENRAPGAGLGQDRQVPLWGQLLLFLVFVIVLFFIYHFMQAEEGNPF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3536

(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	4adyA	0.46	5.82	0.048	0.756	model1_4adyA.pdb.gz
2	5xq3A	0.45	6.19	0.045	0.791	model1_5xq3A.pdb.gz
3	5mz9A	0.45	6.18	0.058	0.779	model1_5mz9A.pdb.gz
4	6rj1A	0.44	6.35	0.054	0.799	model1_6rj1A.pdb.gz
5	5mpbZ	0.44	5.70	0.050	0.721	model1_5mpbZ.pdb.gz
6	5awoA	0.44	5.73	0.047	0.724	model1_5awoA.pdb.gz
7	2b3yA	0.43	6.38	0.065	0.795	model1_2b3yA.pdb.gz
8	6dc6A3	0.43	5.86	0.044	0.717	model1_6dc6A3.pdb.gz
9	4k35A2	0.43	5.57	0.056	0.693	model1_4k35A2.pdb.gz
10	4cr2Z	0.43	5.56	0.036	0.693	model1_4cr2Z.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:0048487	0.97	beta-tubulin binding
GO:0003779	0.97	actin binding
GO:0098641	0.56	cadherin binding involved in cell-cell adhesion

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:0044763	0.99	single-organism cellular process
GO:0050794	0.80	regulation of cellular process
GO:0016043	0.80	cellular component organization
GO:0006998	0.77	nuclear envelope organization
GO:0048518	0.75	positive regulation of biological process
GO:0051716	0.74	cellular response to stimulus
GO:0048583	0.72	regulation of response to stimulus
GO:0031468	0.72	nuclear envelope reassembly
GO:0071363	0.69	cellular response to growth factor stimulus
GO:0060828	0.69	regulation of canonical Wnt signaling pathway
GO:0048147	0.69	negative regulation of fibroblast proliferation
GO:0046827	0.69	positive regulation of protein export from nucleus
GO:0035414	0.69	negative regulation of catenin import into nucleus
GO:1903047	0.56	mitotic cell cycle process
GO:0007077	0.50	mitotic nuclear envelope disassembly

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:0044428	1.00	nuclear part
GO:0043229	1.00	intracellular organelle
GO:0043227	0.88	membrane-bounded organelle
GO:0043231	0.87	intracellular membrane-bounded organelle
GO:0044444	0.83	cytoplasmic part
GO:0005783	0.78	endoplasmic reticulum
GO:0044425	0.77	membrane part
GO:0031965	0.76	nuclear membrane
GO:0005635	0.75	nuclear envelope
GO:0005640	0.51	nuclear outer membrane
GO:0005637	0.51	nuclear inner membrane
GO:0005634	0.51	nucleus

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	2ivfA	0.428	5.80	0.034	0.693	1.17.99.2	NA
2	0.060	5acnA	0.397	6.46	0.038	0.713	4.2.1.3	NA
3	0.060	1cygA	0.402	6.62	0.044	0.756	2.4.1.19	NA
4	0.060	1s6yA	0.409	6.31	0.075	0.724	3.2.1.86	NA
5	0.060	3ff6A	0.402	6.15	0.075	0.701	6.4.1.2 6.3.4.14	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:

Click to view	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	1v3mB	0.425	6.55	0.035	0.779	0.47	GAL	complex1.pdb.gz	5,25,29

	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.