D-I-TASSER Q8N4V2

D-I-TASSER results for Q8N4V2

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

Summary of the Protein

Uniprot ID: Q8N4V2
Protein Name: Synaptic vesicle 2-related protein
Gene Name: SVOP

Input Sequence in FASTA format

>Q8N4V2 (548 residues)
MEEDLFQLRQLPVVKFRRTGESARSEDDTASGEHEVQIEGVHVGLEAVELDDGAAVPKEF
ANPTDDTFMVEDAVEAIGFGKFQWKLSVLTGLAWMADAMEMMILSILAPQLHCEWRLPSW
QVALLTSVVFVGMMSSSTLWGNISDQYGRKTGLKISVLWTLYYGILSAFAPVYSWILVLR
GLVGFGIGGVPQSVTLYAEFLPMKARAKCILLIEVFWAIGTVFEVVLAVFVMPSLGWRWL
LILSAVPLLLFAVLCFWLPESARYDVLSGNQEKAIATLKRIATENGAPMPLGKLIISRQE
DRGKMRDLFTPHFRWTTLLLWFIWFSNAFSYYGLVLLTTELFQAGDVCGISSRKKAVEAK
CSLACEYLSEEDYMDLLWTTLSEFPGVLVTLWIIDRLGRKKTMALCFVIFSFCSLLLFIC
VGRNVLTLLLFIARAFISGGFQAAYVYTPEVYPTATRALGLGTCSGMARVGALITPFIAQ
VMLESSVYLTLAVYSGCCLLAALASCFLPIETKGRGLQESSHREWGQEMVGRGMHGAGVT
RSNSGSQE

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	Q8N4V2-D1	1-65	65		MEEDLFQLRQLPVVKFRRTGESARSEDDTASGEHEVQIEGVHVGLEAVELDDGAAVPKEFANPTD
2	Q8N4V2-D2	66-297	232		DTFMVEDAVEAIGFGKFQWKLSVLTGLAWMADAMEMMILSILAPQLHCEWRLPSWQVALLTSVVFVGMMSSSTLWGNISDQYGRKTGLKISVLWTLYYGILSAFAPVYSWILVLRGLVGFGIGGVPQSVTLYAEFLPMKARAKCILLIEVFWAIGTVFEVVLAVFVMPSLGWRWLLILSAVPLLLFAVLCFWLPESARYDVLSGNQEKAIATLKRIATENGAPMPLGKLIIS
3	Q8N4V2-D3	298-548	251		RQEDRGKMRDLFTPHFRWTTLLLWFIWFSNAFSYYGLVLLTTELFQAGDVCGISSRKKAVEAKCSLACEYLSEEDYMDLLWTTLSEFPGVLVTLWIIDRLGRKKTMALCFVIFSFCSLLLFICVGRNVLTLLLFIARAFISGGFQAAYVYTPEVYPTATRALGLGTCSGMARVGALITPFIAQVMLESSVYLTLAVYSGCCLLAALASCFLPIETKGRGLQESSHREWGQEMVGRGMHGAGVTRSNSGSQE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.56

(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	6h7dA	0.75	2.46	0.172	0.805	model1_6h7dA.pdb.gz
2	7crzA	0.73	2.49	0.137	0.786	model1_7crzA.pdb.gz
3	4gbyA	0.71	2.60	0.180	0.772	model1_4gbyA.pdb.gz
4	4ybqA	0.71	2.83	0.155	0.775	model1_4ybqA.pdb.gz
5	6rw3A	0.71	2.37	0.181	0.755	model1_6rw3A.pdb.gz
6	6thaA	0.69	2.61	0.146	0.752	model1_6thaA.pdb.gz
7	4ldsA	0.67	3.07	0.164	0.745	model1_4ldsA.pdb.gz
8	4j05A	0.66	2.65	0.219	0.708	model1_4j05A.pdb.gz
9	3wdoA	0.62	3.71	0.112	0.725	model1_3wdoA.pdb.gz
10	4zowA1	0.33	2.23	0.141	0.348	model1_4zowA1.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:0005215	1.00	transporter activity
GO:0022857	0.99	transmembrane transporter activity
GO:0022891	0.98	substrate-specific transmembrane transporter activity
GO:0015075	0.62	ion transmembrane transporter activity
GO:0022804	0.54	active transmembrane transporter 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:0006810	0.99	transport
GO:0071702	0.96	organic substance transport
GO:0044699	0.96	single-organism process
GO:0044765	0.93	single-organism transport
GO:0055085	0.86	transmembrane transport
GO:0008643	0.67	carbohydrate transport
GO:0015758	0.66	glucose transport
GO:0046323	0.64	glucose import
GO:0035428	0.63	hexose transmembrane transport
GO:0006811	0.51	ion transport
GO:0065007	0.50	biological regulation

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:0016021	0.98	integral component of membrane
GO:0044464	0.91	cell part
GO:0044459	0.69	plasma membrane part
GO:0005887	0.67	integral component of plasma membrane
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	3pjrA	0.349	7.86	0.055	0.586	3.6.4.12	NA
2	0.060	1ofdA	0.322	7.98	0.048	0.542	1.4.7.1	NA
3	0.060	2r7oA	0.349	6.70	0.043	0.511	2.7.7.48	127,329,337
4	0.060	2vdcA	0.321	7.77	0.034	0.531	1.4.1.13	NA
5	0.060	2is4B	0.334	7.71	0.060	0.555	3.6.1.-	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	0.01	1fo4A	0.326	7.32	0.043	0.513	0.51	FES	complex1.pdb.gz	129,130,132,181,183,186
2	0.01	2ckjD	0.278	8.32	0.035	0.485	0.59	FES	complex2.pdb.gz	141,142,143,145,147,152
3	0.01	2ckjA	0.309	8.08	0.044	0.531	0.62	FES	complex3.pdb.gz	131,132,182,183,184,185
4	0.01	3eubS	0.125	5.22	0.060	0.164	0.61	FES	complex4.pdb.gz	132,133,134,138,139,185,188
5	0.01	1fiqA	0.129	5.43	0.072	0.172	0.52	FAD	complex5.pdb.gz	131,132,188
6	0.01	2rddA	0.328	8.06	0.071	0.560	0.51	AIC	complex6.pdb.gz	142,463,464,465,466
7	0.01	2e1qC	0.312	7.80	0.060	0.527	0.57	BCT	complex7.pdb.gz	100,101,129,183,184,187
8	0.01	1fiqA	0.129	5.43	0.072	0.172	0.63	FES	complex8.pdb.gz	139,140,141,187,189
9	0.01	2is1B	0.332	8.08	0.046	0.575	0.75	QNA	complex9.pdb.gz	141,146,148,150,151
10	0.01	2is1A	0.339	7.68	0.047	0.566	0.54	QNA	complex10.pdb.gz	140,152,154,155

	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.