D-I-TASSER Q9BRQ3

D-I-TASSER results for Q9BRQ3

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

Summary of the Protein

Uniprot ID: Q9BRQ3
Protein Name: Uridine diphosphate glucose pyrophosphatase NUDT22
Gene Name: NUDT22

Input Sequence in FASTA format

>Q9BRQ3 (303 residues)
MDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPK
FRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADP
LGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVH
ELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLS
GGPEAHESTGIFFVETQNVQRLLETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALL
PPL

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	Q9BRQ3-D1	1-303	303		MDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVQRLLETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7851

(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	5lf9A	0.92	0.56	0.986	0.931	model1_5lf9A.pdb.gz
2	3dupA	0.57	3.84	0.123	0.706	model1_3dupA.pdb.gz
3	2pnyA	0.54	3.90	0.081	0.663	model1_2pnyA.pdb.gz
4	2i6kA	0.53	3.62	0.104	0.650	model1_2i6kA.pdb.gz
5	5lf8A	0.51	3.66	0.173	0.607	model1_5lf8A.pdb.gz
6	1nfsB	0.47	2.73	0.124	0.538	model1_1nfsB.pdb.gz
7	5t3pA	0.47	3.39	0.150	0.561	model1_5t3pA.pdb.gz
8	1mqwA	0.47	3.85	0.098	0.578	model1_1mqwA.pdb.gz
9	1viqA	0.47	3.71	0.090	0.568	model1_1viqA.pdb.gz
10	3e57B	0.46	2.62	0.096	0.528	model1_3e57B.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:0003824	0.64	catalytic activity
GO:0016787	0.58	hydrolase activity
GO:0043169	0.52	cation 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:0009987	0.98	cellular process
GO:0008152	0.84	metabolic process
GO:0044699	0.78	single-organism process
GO:0071704	0.76	organic substance metabolic process
GO:0044237	0.76	cellular metabolic process
GO:0044238	0.73	primary metabolic process
GO:1901360	0.72	organic cyclic compound metabolic process
GO:0044710	0.72	single-organism metabolic process
GO:0046483	0.71	heterocycle metabolic process
GO:0034641	0.71	cellular nitrogen compound metabolic process
GO:0006725	0.71	cellular aromatic compound metabolic process
GO:0044281	0.70	small molecule metabolic process
GO:0006139	0.68	nucleobase-containing compound metabolic process
GO:0044763	0.66	single-organism cellular process
GO:0055086	0.59	nucleobase-containing small molecule metabolic process
GO:1901575	0.57	organic substance catabolic process
GO:0044248	0.57	cellular catabolic process
GO:1901361	0.56	organic cyclic compound catabolic process
GO:0046700	0.56	heterocycle catabolic process
GO:0044270	0.56	cellular nitrogen compound catabolic process
GO:0019439	0.56	aromatic compound catabolic process
GO:0050896	0.55	response to stimulus
GO:0019637	0.55	organophosphate metabolic process
GO:0006796	0.55	phosphate-containing compound metabolic process
GO:0051716	0.54	cellular response to stimulus
GO:1901564	0.53	organonitrogen compound metabolic process
GO:0044712	0.52	single-organism catabolic process
GO:0034655	0.52	nucleobase-containing compound catabolic process
GO:1901565	0.51	organonitrogen compound catabolic process
GO:1901135	0.50	carbohydrate derivative metabolic process
GO:0006163	0.50	purine nucleotide metabolic 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:0044424	1.00	intracellular part
GO:0044422	0.91	organelle part
GO:0005654	0.90	nucleoplasm
GO:0044444	0.61	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	0.089	1viqA	0.466	3.71	0.090	0.568	3.6.1.13	189
2	0.067	1hx3B	0.472	2.72	0.124	0.541	5.3.3.2	NA
3	0.067	2yvmA	0.457	3.96	0.144	0.568	3.6.1.-	139
4	0.060	1n63B	0.363	6.23	0.028	0.601	1.2.99.2	NA
5	0.060	1vlbA	0.372	6.31	0.062	0.624	1.2.99.7	156

	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	0.28	2a8qB	0.446	3.27	0.123	0.531	1.29	MN	complex1.pdb.gz	124,154,155,193
2	0.27	1ppwA	0.465	2.98	0.114	0.545	0.85	EIP	complex2.pdb.gz	122,123,124,139,143,154,155,156,189,193,211,218,220,274
3	0.26	2a8sA	0.448	3.26	0.122	0.535	0.83	GTP	complex3.pdb.gz	125,138,152,154,155,189,192,193,221,247,277,278,280
4	0.10	2a8rB	0.446	3.36	0.128	0.538	1.08	POP	complex4.pdb.gz	125,139,154,155,156,193,247
5	0.09	2a8pB	0.448	3.45	0.125	0.545	0.99	MN	complex5.pdb.gz	154,189,193,247
6	0.05	2vnqA	0.474	2.78	0.113	0.548	0.85	IMD	complex6.pdb.gz	122,154,155,156,211,219,274
7	0.04	1qvjA	0.459	4.52	0.095	0.597	0.87	RP5	complex7.pdb.gz	122,124,139,155,212,214,272,275
8	0.02	1mqeA	0.449	3.46	0.083	0.538	0.82	UUU	complex8.pdb.gz	123,155,156,189,193,219,275

	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.