D-I-TASSER A0A2R8YFL7

D-I-TASSER results for A0A2R8YFL7

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

Summary of the Protein

Uniprot ID: A0A2R8YFL7
Protein Name: Oocyte-secreted protein 4A
Gene Name: OOSP4A

Input Sequence in FASTA format

>A0A2R8YFL7 (184 residues)
MKISCVLGKLLMLFELIHGLQDLSITCSESWLQVKLRRTPLLNDLQPLQNELSLGIGCPV
NMVEVDFFGFLYLLTFCGIRVSEHGVGILIESLIVYEPTNFDFNLHIPVSCYVQRRFPII
LVMRGRENDSRRECRRSVGQHRSLSHELEDLEIRPRVSYVNSVPLLSYLIVSLPKCKNKA
VHSG

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	A0A2R8YFL7-D1	1-184	184		MKISCVLGKLLMLFELIHGLQDLSITCSESWLQVKLRRTPLLNDLQPLQNELSLGIGCPVNMVEVDFFGFLYLLTFCGIRVSEHGVGILIESLIVYEPTNFDFNLHIPVSCYVQRRFPIILVMRGRENDSRRECRRSVGQHRSLSHELEDLEIRPRVSYVNSVPLLSYLIVSLPKCKNKAVHSG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5816

(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	3nk3A	0.51	1.17	0.154	0.527	model1_3nk3A.pdb.gz
2	1pcxA	0.48	4.60	0.026	0.712	model1_1pcxA.pdb.gz
3	3prxB	0.48	4.86	0.059	0.766	model1_3prxB.pdb.gz
4	3efoB	0.47	4.90	0.043	0.728	model1_3efoB.pdb.gz
5	3eh2A	0.47	5.43	0.035	0.772	model1_3eh2A.pdb.gz
6	2icfB	0.46	4.82	0.052	0.734	model1_2icfB.pdb.gz
7	3eg9A	0.45	4.59	0.024	0.674	model1_3eg9A.pdb.gz
8	2pn5A3	0.43	4.92	0.056	0.652	model1_2pn5A3.pdb.gz
9	2qtvA	0.41	5.27	0.051	0.663	model1_2qtvA.pdb.gz
10	2ww8A	0.40	4.74	0.043	0.598	model1_2ww8A.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

./A0A2R8YFL7-D1/GOsearchresult_final_MF.svg

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0019899	0.77	enzyme binding
GO:0032190	0.67	acrosin 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]

./A0A2R8YFL7-D1/GOsearchresult_final_BP.svg

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.91	single-organism process
GO:0022414	0.91	reproductive process
GO:0044702	0.90	single organism reproductive process
GO:0065007	0.71	biological regulation
GO:0050789	0.71	regulation of biological process
GO:0044763	0.70	single-organism cellular process
GO:0035036	0.69	sperm-egg recognition
GO:2000241	0.68	regulation of reproductive process
GO:0043900	0.68	regulation of multi-organism process
GO:0048518	0.67	positive regulation of biological process
GO:0060046	0.66	regulation of acrosome reaction
GO:2000243	0.65	positive regulation of reproductive process
GO:0043902	0.65	positive regulation of multi-organism process
GO:0022412	0.64	cellular process involved in reproduction in multicellular organism
GO:0048856	0.60	anatomical structure development
GO:0044767	0.60	single-organism developmental process
GO:0003006	0.59	developmental process involved in reproduction
GO:0007339	0.57	binding of sperm to zona pellucida
GO:2000344	0.51	positive regulation of acrosome reaction
GO:0035803	0.50	egg coat formation

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]

./A0A2R8YFL7-D1/GOsearchresult_final_CC.svg

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.89	cell part
GO:0044421	0.83	extracellular region part
GO:0043227	0.81	membrane-bounded organelle
GO:0016020	0.76	membrane
GO:0031982	0.67	vesicle
GO:0044425	0.61	membrane part
GO:0044424	0.61	intracellular part
GO:0005576	0.61	extracellular region
GO:0044444	0.60	cytoplasmic part
GO:0031012	0.60	extracellular matrix
GO:0005615	0.58	extracellular space
GO:0044446	0.57	intracellular organelle part
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0031988	0.56	membrane-bounded vesicle
GO:0044433	0.53	cytoplasmic vesicle part
GO:0005794	0.50	Golgi apparatus
GO:0005783	0.50	endoplasmic reticulum

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	1a47A	0.424	4.86	0.029	0.668	2.4.1.19	NA
2	0.060	3k2iA	0.424	5.12	0.049	0.685	3.1.2.2	72
3	0.060	1d7fA	0.423	4.81	0.022	0.668	2.4.1.19	NA
4	0.060	1kqfA	0.359	5.64	0.049	0.641	1.2.1.2	NA
5	0.060	2q3zA	0.426	4.97	0.056	0.690	2.3.2.13	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	0.02	3nk3B	0.503	1.09	0.137	0.522	0.40	III	complex1.pdb.gz	80,93,106,108
2	0.01	3brfA	0.450	5.10	0.046	0.734	0.14	III	complex2.pdb.gz	78,79,80,82
3	0.01	3sqgE	0.429	4.92	0.061	0.696	0.32	TP7	complex3.pdb.gz	58,76,78
4	0.01	2qkiD	0.448	4.39	0.030	0.641	0.19	III	complex4.pdb.gz	54,55,56,78,80,106,109
5	0.01	3eg9B	0.474	4.81	0.043	0.723	0.17	III	complex5.pdb.gz	52,53,54,55,56
6	0.01	3efoB	0.474	4.90	0.043	0.728	0.22	III	complex6.pdb.gz	78,79,93,95,96,106
7	0.01	3sqgA	0.442	5.26	0.063	0.750	0.15	M43	complex7.pdb.gz	53,54,55
8	0.01	3zstA	0.447	5.00	0.064	0.728	0.28	ACX	complex8.pdb.gz	32,33,79,80
9	0.01	2qkiA	0.449	4.34	0.025	0.636	0.14	III	complex9.pdb.gz	78,79,80,81,116
10	0.01	2iv8A	0.439	4.64	0.068	0.658	0.24	III	complex10.pdb.gz	79,81,82,93

	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.