D-I-TASSER Q0VDG4

D-I-TASSER results for Q0VDG4

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

Summary of the Protein

Uniprot ID: Q0VDG4
Protein Name: Secernin-3
Gene Name: SCRN3

Input Sequence in FASTA format

>Q0VDG4 (424 residues)
MEPFSCDTFVALPPATVDNRIIFGKNSDRLYDEVQEVVYFPAVVHDNLGERLKCTYIEID
QVPETYAVVLSRPAWLWGAEMGANEHGVCIGNEAVWGREEVCDEEALLGMDLVRLGLERA
DTAEKALNVIVDLLEKYGQGGNCTEGRMVFSYHNSFLIADRNEAWILETAGKYWAAEKVQ
EGVRNISNQLSITTKIAREHPDMRNYAKRKGWWDGKKEFDFAAAYSYLDTAKMMTSSGRY
CEGYKLLNKHKGNITFETMMEILRDKPSGINMEGEFLTTASMVSILPQDSSLPCIHFFTG
TPDPERSVFKPFIFVPHISQLLDTSSPTFELEDLVKKKSHFKPDRRHPLYQKHQQALEVV
NNNEEKAKIMLDNMRKLEKELFREMESILQNKHLDVEKIVNLFPQCTKDEIQIYQSNLSV
KVSS

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	Q0VDG4-D1	1-319	319		MEPFSCDTFVALPPATVDNRIIFGKNSDRLYDEVQEVVYFPAVVHDNLGERLKCTYIEIDQVPETYAVVLSRPAWLWGAEMGANEHGVCIGNEAVWGREEVCDEEALLGMDLVRLGLERADTAEKALNVIVDLLEKYGQGGNCTEGRMVFSYHNSFLIADRNEAWILETAGKYWAAEKVQEGVRNISNQLSITTKIAREHPDMRNYAKRKGWWDGKKEFDFAAAYSYLDTAKMMTSSGRYCEGYKLLNKHKGNITFETMMEILRDKPSGINMEGEFLTTASMVSILPQDSSLPCIHFFTGTPDPERSVFKPFIFVPHIS
2	Q0VDG4-D2	320-424	105		QLLDTSSPTFELEDLVKKKSHFKPDRRHPLYQKHQQALEVVNNNEEKAKIMLDNMRKLEKELFREMESILQNKHLDVEKIVNLFPQCTKDEIQIYQSNLSVKVSS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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	5iauA	0.83	2.66	0.135	0.910	model1_5iauA.pdb.gz
2	4wl2A	0.56	4.05	0.117	0.674	model1_4wl2A.pdb.gz
3	2iwmA	0.55	4.04	0.120	0.665	model1_2iwmA.pdb.gz
4	5x8zA	0.55	4.05	0.102	0.667	model1_5x8zA.pdb.gz
5	2oqcA	0.54	3.86	0.126	0.649	model1_2oqcA.pdb.gz
6	3fgwA	0.54	3.97	0.067	0.653	model1_3fgwA.pdb.gz
7	2rf8B	0.54	4.05	0.137	0.649	model1_2rf8B.pdb.gz
8	4wl3A	0.53	4.09	0.124	0.639	model1_4wl3A.pdb.gz
9	3hbcA	0.53	4.02	0.113	0.634	model1_3hbcA.pdb.gz
10	5hkeA	0.52	3.77	0.129	0.618	model1_5hkeA.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	0.76	catalytic activity
GO:0016787	0.67	hydrolase activity
GO:0016810	0.52	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds

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:0006887	1.00	exocytosis

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:0043227	1.00	membrane-bounded organelle
GO:0044464	0.94	cell part
GO:0016020	0.80	membrane
GO:0044424	0.79	intracellular part
GO:0044446	0.61	intracellular organelle part
GO:0043229	0.59	intracellular organelle
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0044428	0.54	nuclear part
GO:0044421	0.53	extracellular region part
GO:0070062	0.52	extracellular exosome
GO:0031090	0.52	organelle membrane
GO:0005634	0.52	nucleus
GO:0044425	0.50	membrane part
GO:0031965	0.50	nuclear 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	0.066	2hf0A	0.518	3.69	0.118	0.618	3.5.1.24	NA
2	0.060	1d7fA	0.383	7.37	0.037	0.665	2.4.1.19	NA
3	0.060	1qhoA	0.392	7.60	0.040	0.698	3.2.1.133	NA
4	0.060	2oqcA	0.544	3.86	0.126	0.649	3.5.1.11	NA
5	0.060	2x1cA	0.527	2.58	0.142	0.576	2.3.1.164	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	0.15	1pnlB	0.516	3.92	0.115	0.613	0.28	PAC	complex1.pdb.gz	23,24,88,89,90
2	0.05	2x1eA	0.518	2.78	0.146	0.571	0.34	X1E	complex2.pdb.gz	23,24,25,183
3	0.05	2x1dD	0.518	2.84	0.146	0.573	0.24	D1D	complex3.pdb.gz	22,23,26
4	0.03	1ai7B	0.516	3.92	0.115	0.613	0.29	IPH	complex4.pdb.gz	23,25,158
5	0.03	1fxvB	0.517	3.90	0.111	0.613	0.31	PNN	complex5.pdb.gz	25,82,83,88
6	0.03	3srcB	0.526	4.01	0.105	0.632	0.27	28N	complex6.pdb.gz	9,88,89,296
7	0.02	1gm8B	0.517	3.91	0.111	0.613	0.28	SOX	complex7.pdb.gz	88,89,91
8	0.01	2z71A	0.545	3.98	0.111	0.653	0.27	PNV	complex8.pdb.gz	25,27,166
9	0.01	1jvzB	0.523	3.70	0.104	0.620	0.19	CEN	complex9.pdb.gz	24,81,82
10	0.01	2ya1A	0.419	6.83	0.052	0.682	0.39	GLC	complex10.pdb.gz	21,23,285

	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.