D-I-TASSER P15692

D-I-TASSER results for P15692

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

Summary of the Protein

Uniprot ID: P15692
Protein Name: Vascular endothelial growth factor A
Gene Name: VEGFA

Input Sequence in FASTA format

>P15692 (232 residues)
MNFLLSWVHWSLALLLYLHHAKWSQAAPMAEGGGQNHHEVVKFMDVYQRSYCHPIETLVD
IFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEM
SFLQHNKCECRPKKDRARQEKKSVRGKGKGQKRKRKKSRYKSWSVYVGARCCLMPWSLPG
PHPCGPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR

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	P15692-D1	1-232	232		MNFLLSWVHWSLALLLYLHHAKWSQAAPMAEGGGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKDRARQEKKSVRGKGKGQKRKRKKSRYKSWSVYVGARCCLMPWSLPGPHPCGPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5648

(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	5a22A	0.43	5.90	0.048	0.724	model1_5a22A.pdb.gz
2	6ysgA	0.42	6.34	0.054	0.776	model1_6ysgA.pdb.gz
3	6yttB	0.42	5.67	0.054	0.690	model1_6yttB.pdb.gz
4	1llwA	0.42	6.14	0.025	0.746	model1_1llwA.pdb.gz
5	4w8yA	0.42	6.40	0.065	0.772	model1_4w8yA.pdb.gz
6	3i04A	0.41	5.45	0.052	0.668	model1_3i04A.pdb.gz
7	6gszA	0.41	5.69	0.043	0.698	model1_6gszA.pdb.gz
8	6s8bK	0.41	6.51	0.032	0.776	model1_6s8bK.pdb.gz
9	5bv9A	0.41	6.17	0.045	0.716	model1_5bv9A.pdb.gz
10	3w0lB	0.41	6.30	0.038	0.737	model1_3w0lB.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:0005102	0.96	receptor binding
GO:0070851	0.88	growth factor receptor binding
GO:0008083	0.86	growth factor activity
GO:0005172	0.84	vascular endothelial growth factor receptor binding
GO:0042056	0.74	chemoattractant activity
GO:0097367	0.71	carbohydrate derivative binding
GO:0043184	0.71	vascular endothelial growth factor receptor 2 binding
GO:0005125	0.70	cytokine activity
GO:0005161	0.69	platelet-derived growth factor receptor binding
GO:0004871	0.69	signal transducer activity
GO:0098772	0.68	molecular function regulator
GO:0008201	0.68	heparin binding
GO:0043183	0.67	vascular endothelial growth factor receptor 1 binding
GO:0048018	0.66	receptor agonist activity
GO:0001968	0.66	fibronectin 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:

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[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	0.93	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0044699	0.91	single-organism process
GO:0048518	0.88	positive regulation of biological process
GO:0048522	0.87	positive regulation of cellular process
GO:0044767	0.85	single-organism developmental process
GO:0080090	0.83	regulation of primary metabolic process
GO:0060255	0.83	regulation of macromolecule metabolic process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0008284	0.83	positive regulation of cell proliferation
GO:0031399	0.81	regulation of protein modification process
GO:0031325	0.81	positive regulation of cellular metabolic process
GO:0019220	0.81	regulation of phosphate metabolic process
GO:0010604	0.81	positive regulation of macromolecule metabolic process
GO:0001934	0.80	positive regulation of protein phosphorylation
GO:0048646	0.79	anatomical structure formation involved in morphogenesis
GO:0050678	0.76	regulation of epithelial cell proliferation
GO:0009987	0.76	cellular process
GO:0001938	0.75	positive regulation of endothelial cell proliferation
GO:0050731	0.74	positive regulation of peptidyl-tyrosine phosphorylation
GO:0051239	0.73	regulation of multicellular organismal process
GO:0051130	0.73	positive regulation of cellular component organization
GO:0045785	0.73	positive regulation of cell adhesion
GO:0051240	0.72	positive regulation of multicellular organismal process
GO:0032879	0.71	regulation of localization
GO:0050793	0.70	regulation of developmental process
GO:0030334	0.70	regulation of cell migration
GO:1901342	0.69	regulation of vasculature development
GO:0051094	0.69	positive regulation of developmental process
GO:0030335	0.69	positive regulation of cell migration
GO:0022603	0.69	regulation of anatomical structure morphogenesis
GO:1904018	0.68	positive regulation of vasculature development
GO:0045765	0.68	regulation of angiogenesis
GO:0045766	0.67	positive regulation of angiogenesis
GO:0044763	0.67	single-organism cellular process
GO:0010595	0.65	positive regulation of endothelial cell migration
GO:0007165	0.65	signal transduction
GO:0007166	0.63	cell surface receptor signaling pathway
GO:0001525	0.63	angiogenesis
GO:0048583	0.62	regulation of response to stimulus
GO:0007169	0.62	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0048010	0.60	vascular endothelial growth factor receptor signaling pathway
GO:0050896	0.58	response to stimulus
GO:0048584	0.58	positive regulation of response to stimulus
GO:0042221	0.56	response to chemical
GO:0065008	0.55	regulation of biological quality
GO:0009966	0.55	regulation of signal transduction
GO:0048519	0.54	negative regulation of biological process
GO:0040011	0.54	locomotion
GO:0006928	0.54	movement of cell or subcellular component
GO:0048523	0.53	negative regulation of cellular process
GO:0032101	0.53	regulation of response to external stimulus
GO:0016477	0.53	cell migration
GO:0051716	0.52	cellular response to stimulus
GO:0050921	0.52	positive regulation of chemotaxis
GO:0010033	0.52	response to organic substance
GO:0009967	0.52	positive regulation of signal transduction
GO:0006950	0.52	response to stress
GO:2000112	0.51	regulation of cellular macromolecule biosynthetic process
GO:0070887	0.51	cellular response to chemical stimulus
GO:0048869	0.51	cellular developmental process
GO:0019219	0.51	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.51	regulation of gene expression
GO:0001666	0.51	response to hypoxia
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:0038084	0.50	vascular endothelial growth factor signaling pathway
GO:0006935	0.50	chemotaxis

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	0.93	cell part
GO:0044421	0.91	extracellular region part
GO:0005615	0.90	extracellular space
GO:0044424	0.88	intracellular part
GO:0044444	0.80	cytoplasmic part
GO:0043226	0.80	organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0043229	0.76	intracellular organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0031988	0.75	membrane-bounded vesicle
GO:0009986	0.74	cell surface
GO:0005737	0.73	cytoplasm
GO:0031410	0.71	cytoplasmic vesicle
GO:0030141	0.70	secretory granule

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	1pj6A	0.369	5.49	0.055	0.603	1.5.3.10	NA
2	0.060	1jroB	0.368	5.95	0.027	0.638	1.1.1.204	NA
3	0.060	1q16A	0.340	6.10	0.032	0.595	1.7.99.4	94
4	0.060	1wz2A	0.363	6.10	0.024	0.634	6.1.1.4	NA
5	0.060	2r7oA	0.373	5.92	0.051	0.642	2.7.7.48	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	2z8yD	0.402	5.82	0.039	0.681	0.41	SF4	complex1.pdb.gz	58,83,85

	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.