D-I-TASSER P21579

D-I-TASSER results for P21579

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

Summary of the Protein

Uniprot ID: P21579
Protein Name: Synaptotagmin-1
Gene Name: SYT1

Input Sequence in FASTA format

>P21579 (422 residues)
MVSESHHEALAAPPVTTVATVLPSNATEPASPGEGKEDAFSKLKEKFMNELHKIPLPPWA
LIAIAIVAVLLVLTCCFCICKKCLFKKKNKKKGKEKGGKNAINMKDVKDLGKTMKDQALK
DDDAETGLTDGEEKEEPKEEEKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDP
YVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDI
IGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNL
KKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVV
TVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAV
KK

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	P21579-D1	1-422	422		MVSESHHEALAAPPVTTVATVLPSNATEPASPGEGKEDAFSKLKEKFMNELHKIPLPPWALIAIAIVAVLLVLTCCFCICKKCLFKKKNKKKGKEKGGKNAINMKDVKDLGKTMKDQALKDDDAETGLTDGEEKEEPKEEEKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3794

(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	1dqvA	0.59	2.37	0.507	0.644	model1_1dqvA.pdb.gz
2	6pbcA	0.40	6.84	0.048	0.635	model1_6pbcA.pdb.gz
3	3ir7A	0.39	7.50	0.028	0.673	model1_3ir7A.pdb.gz
4	6ankA	0.38	3.49	0.371	0.431	model1_6ankA.pdb.gz
5	4igbA	0.38	6.15	0.039	0.566	model1_4igbA.pdb.gz
6	1h0hA	0.34	7.43	0.059	0.592	model1_1h0hA.pdb.gz
7	2ivfA	0.34	7.10	0.046	0.564	model1_2ivfA.pdb.gz
8	2cm6A	0.33	1.86	0.369	0.344	model1_2cm6A.pdb.gz
9	1djiB	0.31	5.11	0.120	0.396	model1_1djiB.pdb.gz
10	1eu1A	0.31	7.49	0.054	0.538	model1_1eu1A.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:0046872	0.87	metal ion binding
GO:0005543	0.86	phospholipid binding
GO:0005509	0.86	calcium ion binding
GO:0005544	0.84	calcium-dependent phospholipid binding
GO:0000149	0.78	SNARE binding
GO:0019905	0.77	syntaxin binding
GO:0030276	0.76	clathrin binding

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:0065007	0.97	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0009987	0.96	cellular process
GO:0050794	0.95	regulation of cellular process
GO:0044699	0.95	single-organism process
GO:0044763	0.93	single-organism cellular process
GO:0006810	0.89	transport
GO:0044765	0.88	single-organism transport
GO:0032940	0.86	secretion by cell
GO:0016192	0.86	vesicle-mediated transport
GO:0099531	0.85	presynaptic process involved in chemical synaptic transmission
GO:0051649	0.85	establishment of localization in cell
GO:0023061	0.85	signal release
GO:0016043	0.85	cellular component organization
GO:0006887	0.85	exocytosis
GO:0051049	0.84	regulation of transport
GO:0016079	0.84	synaptic vesicle exocytosis
GO:1903530	0.83	regulation of secretion by cell
GO:0060627	0.83	regulation of vesicle-mediated transport
GO:1903305	0.82	regulation of regulated secretory pathway
GO:0061024	0.81	membrane organization
GO:0017158	0.81	regulation of calcium ion-dependent exocytosis
GO:0006996	0.81	organelle organization
GO:1902589	0.80	single-organism organelle organization
GO:0048791	0.80	calcium ion-regulated exocytosis of neurotransmitter
GO:0044802	0.80	single-organism membrane organization
GO:0006906	0.79	vesicle fusion

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:0044464	1.00	cell part
GO:0016020	0.85	membrane
GO:0044424	0.81	intracellular part
GO:0005886	0.80	plasma membrane
GO:0044444	0.70	cytoplasmic part

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	2iukB	0.362	7.10	0.044	0.609	1.13.11.12	NA
2	0.060	1t3qB	0.357	6.73	0.023	0.571	1.3.99.17	NA
3	0.060	1ciuA	0.360	6.74	0.054	0.564	2.4.1.19	144,372
4	0.060	1d7fA	0.372	6.43	0.041	0.566	2.4.1.19	195
5	0.060	3b9jI	0.136	5.74	0.041	0.197	1.17.1.4 1.17.3.2	172,203,229

	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	1eo7A	0.368	6.43	0.051	0.571	0.26	GLC	complex1.pdb.gz	177,178,203
2	0.01	2dijA	0.369	6.28	0.034	0.559	0.16	GLC	complex2.pdb.gz	166,167,204
3	0.01	2cxgA	0.366	6.46	0.029	0.559	0.30	GLC	complex3.pdb.gz	141,142,143,144,168,176
4	0.01	1dedA	0.376	6.26	0.045	0.564	0.11	QPS	complex4.pdb.gz	168,177,178,239
5	0.01	1cdgA	0.372	6.40	0.037	0.569	0.23	MAL	complex5.pdb.gz	170,172,204
6	0.01	3ir6A	0.389	7.52	0.025	0.673	0.14	GDP	complex6.pdb.gz	144,169,170,171,178,243
7	0.01	1v3mA	0.373	6.45	0.048	0.569	0.34	GAL	complex7.pdb.gz	142,143,144,145,202,204
8	0.01	3cgtA	0.367	6.36	0.037	0.554	0.11	BCD	complex8.pdb.gz	143,172,173,174

	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.