D-I-TASSER Q99489

D-I-TASSER results for Q99489

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

Summary of the Protein

Uniprot ID: Q99489
Protein Name: D-aspartate oxidase
Gene Name: DDO

Input Sequence in FASTA format

>Q99489 (341 residues)
MDTARIAVVGAGVVGLSTAVCISKLVPRCSVTIISDKFTPDTTSDVAAGMLIPHTYPDTP
IHTQKQWFRETFNHLFAIANSAEAGDAGVHLVSGWQIFQSTPTEEVPFWADVVLGFRKMT
EAELKKFPQYVFGQAFTTLKCECPAYLPWLEKRIKGSGGWTLTRRIEDLWELHPSFDIVV
NCSGLGSRQLAGDSKIFPVRGQVLQVQAPWVEHFIRDGSGLTYIYPGTSHVTLGGTRQKG
DWNLSPDAENSREILSRCCALEPSLHGACNIREKVGLRPYRPGVRLQTELLARDGQRLPV
VHHYGHGSGGISVHWGTALEAARLVSECVHALRTPIPKSNL

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	Q99489-D1	1-341	341		MDTARIAVVGAGVVGLSTAVCISKLVPRCSVTIISDKFTPDTTSDVAAGMLIPHTYPDTPIHTQKQWFRETFNHLFAIANSAEAGDAGVHLVSGWQIFQSTPTEEVPFWADVVLGFRKMTEAELKKFPQYVFGQAFTTLKCECPAYLPWLEKRIKGSGGWTLTRRIEDLWELHPSFDIVVNCSGLGSRQLAGDSKIFPVRGQVLQVQAPWVEHFIRDGSGLTYIYPGTSHVTLGGTRQKGDWNLSPDAENSREILSRCCALEPSLHGACNIREKVGLRPYRPGVRLQTELLARDGQRLPVVHHYGHGSGGISVHWGTALEAARLVSECVHALRTPIPKSNL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8741

(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	6rkfA	0.98	0.57	0.994	0.982	model1_6rkfA.pdb.gz
2	1ddoA	0.93	1.42	0.399	0.962	model1_1ddoA.pdb.gz
3	1c0lA	0.88	2.15	0.289	0.944	model1_1c0lA.pdb.gz
4	7ct4A	0.87	1.78	0.335	0.918	model1_7ct4A.pdb.gz
5	4yshA	0.83	2.83	0.194	0.927	model1_4yshA.pdb.gz
6	1x31B	0.83	2.70	0.106	0.927	model1_1x31B.pdb.gz
7	3if9A	0.83	2.89	0.171	0.921	model1_3if9A.pdb.gz
8	1y56B	0.83	2.62	0.131	0.918	model1_1y56B.pdb.gz
9	4x9mA	0.82	2.82	0.143	0.927	model1_4x9mA.pdb.gz
10	6j38A	0.82	2.90	0.198	0.930	model1_6j38A.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:0003884	1.00	D-amino-acid oxidase activity
GO:0048037	0.64	cofactor binding
GO:0008445	0.61	D-aspartate oxidase activity
GO:0005102	0.55	receptor 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:0044710	1.00	single-organism metabolic process
GO:0009987	0.80	cellular process
GO:0071704	0.76	organic substance metabolic process
GO:0044237	0.74	cellular metabolic process
GO:0044238	0.72	primary metabolic process
GO:0044281	0.71	small molecule metabolic process
GO:0044763	0.70	single-organism cellular process
GO:0006807	0.69	nitrogen compound metabolic process
GO:1901564	0.65	organonitrogen compound metabolic process
GO:0019752	0.64	carboxylic acid metabolic process
GO:1901605	0.62	alpha-amino acid metabolic process
GO:0006520	0.62	cellular amino acid metabolic process
GO:1901575	0.58	organic substance catabolic process
GO:0044712	0.57	single-organism catabolic process
GO:0044248	0.57	cellular catabolic process
GO:1901565	0.56	organonitrogen compound catabolic process
GO:0046395	0.56	carboxylic acid catabolic process
GO:0009063	0.55	cellular amino acid catabolic process

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:0005777	1.00	peroxisome
GO:0044446	0.70	intracellular organelle part
GO:0044439	0.57	peroxisomal part
GO:0070013	0.51	intracellular organelle lumen

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	0.452	1c0kA	0.878	2.16	0.286	0.944	1.4.3.3	10,12,42,44,47,185,201,277,279,281,283
2	0.363	1ng4B	0.828	2.78	0.165	0.921	1.4.3.19	10,12,47,183,201,279,311
3	0.174	1zovA	0.807	3.03	0.101	0.924	1.5.3.1	NA
4	0.154	1y56B	0.826	2.62	0.131	0.918	1.5.99.8	309
5	0.141	1vrqB	0.828	2.70	0.106	0.927	1.5.3.1	147

	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	0.69	3cukB	0.903	1.12	0.415	0.927	1.53	FAD	complex1.pdb.gz	10,11,12,13,14,35,36,37,42,43,44,47,49,50,164,166,182,183,184,186,203,276,278,307,308,309,310,311,312
2	0.35	3g3eB	0.932	1.53	0.395	0.965	1.40	G3E	complex2.pdb.gz	50,216,220,223,225,278,308
3	0.34	1ddoE	0.929	1.43	0.399	0.962	1.29	ITR	complex3.pdb.gz	52,53,220,223,278,308
4	0.24	2e82B	0.929	1.56	0.395	0.965	1.19	IM3	complex4.pdb.gz	52,216,218,223,308
5	0.23	3cukA	0.904	1.10	0.415	0.927	1.03	4P5	complex5.pdb.gz	50,52,223,225,278,309
6	0.23	2e49C	0.929	1.40	0.395	0.962	0.99	MH6	complex6.pdb.gz	223,278,308
7	0.08	1an90	0.929	1.57	0.398	0.965	0.94	III	complex7.pdb.gz	81,82,83,85,86,90,112,113,114,115,209,210,212,227,228

	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.