D-I-TASSER Q8IYJ3

D-I-TASSER results for Q8IYJ3

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

Summary of the Protein

Uniprot ID: Q8IYJ3
Protein Name: Synaptotagmin-like protein 1
Gene Name: SYTL1

Input Sequence in FASTA format

>Q8IYJ3 (562 residues)
MPQRGHPSQEGLWALPSLPMAHGPKPETEGLLDLSFLTEEEQEAIAGVLQRDARLRQLEE
GRVSKLRASVADPGQLKILTGDWFQEARSQRHHNAHFGSDLVRASMRRKKSTRGDQAPGH
DREAEAAVKEKEEGPEPRLTIDEAPQERLRETEGPDFPSPSVPLKASDPEEASQAQEDPG
QGDQQVCAEEADPELEPASGGEQEPRPQQAQTKAASQILENGEEAPGPDPSLDRMLSSSS
SVSSLNSSTLSGSQMSLSGDAEAVQVRGSVHFALHYEPGAAELRVHVIQCQGLAAARRRR
SDPYVKSYLLPDKQSKRKTAVKKRNLNPVFNETLRYSVPQAELQGRVLSLSVWHRESLGR
NIFLGEVEVPLDTWDWGSEPTWLPLQPRVPPSPDDLPSRGLLALSLKYVPAGSEGAGLPP
SGELHFWVKEARDLLPLRAGSLDTYVQCFVLPDDSQASRQRTRVVRRSLSPVFNHTMVYD
GFGPADLRQACAELSLWDHGALANRQLGGTRLSLGTGSSYGLQVPWMDSTPEEKQLWQAL
LEQPCEWVDGLLPLRTNLAPRT

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	Q8IYJ3-D1	1-562	562		MPQRGHPSQEGLWALPSLPMAHGPKPETEGLLDLSFLTEEEQEAIAGVLQRDARLRQLEEGRVSKLRASVADPGQLKILTGDWFQEARSQRHHNAHFGSDLVRASMRRKKSTRGDQAPGHDREAEAAVKEKEEGPEPRLTIDEAPQERLRETEGPDFPSPSVPLKASDPEEASQAQEDPGQGDQQVCAEEADPELEPASGGEQEPRPQQAQTKAASQILENGEEAPGPDPSLDRMLSSSSSVSSLNSSTLSGSQMSLSGDAEAVQVRGSVHFALHYEPGAAELRVHVIQCQGLAAARRRRSDPYVKSYLLPDKQSKRKTAVKKRNLNPVFNETLRYSVPQAELQGRVLSLSVWHRESLGRNIFLGEVEVPLDTWDWGSEPTWLPLQPRVPPSPDDLPSRGLLALSLKYVPAGSEGAGLPPSGELHFWVKEARDLLPLRAGSLDTYVQCFVLPDDSQASRQRTRVVRRSLSPVFNHTMVYDGFGPADLRQACAELSLWDHGALANRQLGGTRLSLGTGSSYGLQVPWMDSTPEEKQLWQALLEQPCEWVDGLLPLRTNLAPRT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4447

(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	2r83A	0.46	2.04	0.276	0.484	model1_2r83A.pdb.gz
2	6r9tA	0.37	7.62	0.037	0.600	model1_6r9tA.pdb.gz
3	5a22A	0.37	8.00	0.034	0.619	model1_5a22A.pdb.gz
4	3cmuA	0.36	8.02	0.052	0.614	model1_3cmuA.pdb.gz
5	3dx4A	0.36	7.26	0.059	0.562	model1_3dx4A.pdb.gz
6	1cjyA	0.27	7.82	0.027	0.445	model1_1cjyA.pdb.gz
7	1djiB	0.25	7.32	0.054	0.390	model1_1djiB.pdb.gz
8	1dqvA2	0.24	2.76	0.188	0.256	model1_1dqvA2.pdb.gz
9	2d8kA	0.22	2.27	0.348	0.235	model1_2d8kA.pdb.gz
10	1v27A	0.22	2.18	0.304	0.233	model1_1v27A.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:0008289	0.88	lipid binding
GO:0046872	0.87	metal ion binding
GO:0005543	0.87	phospholipid binding
GO:0005544	0.86	calcium-dependent phospholipid binding
GO:0005509	0.86	calcium ion binding
GO:0000149	0.84	SNARE binding
GO:0030276	0.83	clathrin binding
GO:0019905	0.83	syntaxin 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	0.99	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0009987	0.97	cellular process
GO:0050794	0.96	regulation of cellular process
GO:0044763	0.95	single-organism cellular process
GO:0006810	0.93	transport
GO:1902578	0.90	single-organism localization
GO:0016043	0.90	cellular component organization
GO:0044765	0.89	single-organism transport
GO:0016192	0.89	vesicle-mediated transport
GO:0051649	0.88	establishment of localization in cell
GO:0051641	0.88	cellular localization
GO:0045055	0.88	regulated exocytosis
GO:0051049	0.87	regulation of transport
GO:0016079	0.87	synaptic vesicle exocytosis
GO:0006996	0.87	organelle organization
GO:1902589	0.86	single-organism organelle organization
GO:0017157	0.86	regulation of exocytosis
GO:0044802	0.85	single-organism membrane organization
GO:0017158	0.85	regulation of calcium ion-dependent exocytosis
GO:0048791	0.84	calcium ion-regulated exocytosis of neurotransmitter
GO:0006906	0.83	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	0.88	membrane
GO:0044424	0.87	intracellular part
GO:0005886	0.82	plasma membrane
GO:0044444	0.78	cytoplasmic part
GO:0043226	0.60	organelle
GO:0043229	0.59	intracellular organelle
GO:0043227	0.58	membrane-bounded organelle
GO:0043231	0.56	intracellular membrane-bounded organelle

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	3eifA	0.308	7.35	0.047	0.480	3.4.21.110	NA
2	0.060	1vlbA	0.311	7.35	0.042	0.491	1.2.99.7	NA
3	0.060	1ofdA	0.303	8.33	0.034	0.527	1.4.7.1	NA
4	0.060	1vbgA	0.304	7.91	0.035	0.511	2.7.9.1	NA
5	0.060	1ojnA	0.324	7.78	0.024	0.530	4.2.2.1	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	0.06	1ce8G	0.329	8.28	0.051	0.569	0.19	IMP	complex1.pdb.gz	268,269,291,301,302
2	0.04	1ce8C	0.307	7.93	0.050	0.518	0.35	ADP	complex2.pdb.gz	295,351,365,366
3	0.02	3cmvB	0.322	7.78	0.031	0.530	0.33	ANP	complex3.pdb.gz	268,269,292,303
4	0.01	3cmvF	0.325	7.86	0.037	0.536	0.10	ANP	complex4.pdb.gz	268,269,270,303
5	0.01	1a9x1	0.327	8.08	0.042	0.553	0.18	III	complex5.pdb.gz	267,268,293
6	0.01	1a9xA	0.327	8.08	0.042	0.553	0.34	PO4	complex6.pdb.gz	327,352,364,366,368
7	0.01	1jdbB	0.314	7.39	0.062	0.495	0.24	GLN	complex7.pdb.gz	268,269,270
8	0.01	1a9x3	0.306	7.64	0.037	0.504	0.21	III	complex8.pdb.gz	302,303,304,305
9	0.01	1a9xA	0.327	8.08	0.042	0.553	0.36	ADP	complex9.pdb.gz	292,293,305,350
10	0.01	1c30A	0.317	7.34	0.057	0.495	0.17	ORN	complex10.pdb.gz	291,293,303

	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.