D-I-TASSER Q96DE0

D-I-TASSER results for Q96DE0

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

Summary of the Protein

Uniprot ID: Q96DE0
Protein Name: U8 snoRNA-decapping enzyme
Gene Name: NUDT16

Input Sequence in FASTA format

>Q96DE0 (195 residues)
MAGARRLELGEALALGSGWRHACHALLYAPDPGMLFGRIPLRYAILMQMRFDGRLGFPGG
FVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGPRVVAHFYAKRLTLEEL
LAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAREQLLEALQDLGL
LQSGSISGLKIPAHH

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	Q96DE0-D1	1-195	195		MAGARRLELGEALALGSGWRHACHALLYAPDPGMLFGRIPLRYAILMQMRFDGRLGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGPRVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAREQLLEALQDLGLLQSGSISGLKIPAHH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.931

(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	1u20A	0.93	1.54	0.575	0.985	model1_1u20A.pdb.gz
2	3couA	0.92	0.39	0.994	0.923	model1_3couA.pdb.gz
3	3kvhA	0.87	1.46	0.575	0.928	model1_3kvhA.pdb.gz
4	5t3pA	0.66	3.02	0.140	0.790	model1_5t3pA.pdb.gz
5	5lf9A	0.65	3.35	0.159	0.831	model1_5lf9A.pdb.gz
6	1qvjA	0.64	3.77	0.135	0.831	model1_1qvjA.pdb.gz
7	3dupA	0.64	3.23	0.124	0.810	model1_3dupA.pdb.gz
8	5lf8A	0.64	3.47	0.180	0.795	model1_5lf8A.pdb.gz
9	2fmlA	0.62	2.84	0.157	0.728	model1_2fmlA.pdb.gz
10	2pnyA	0.61	2.69	0.114	0.728	model1_2pnyA.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:0050072	1.00	m7G(5')pppN diphosphatase activity
GO:0042803	1.00	protein homodimerization activity
GO:0030515	1.00	snoRNA binding
GO:0044822	0.90	poly(A) RNA binding
GO:1901641	0.71	ITP binding
GO:1901640	0.71	XTP binding
GO:0098519	0.71	nucleotide phosphatase activity, acting on free nucleotides
GO:0050897	0.71	cobalt ion binding
GO:0035870	0.71	dITP diphosphatase activity
GO:0030145	0.71	manganese ion binding
GO:0008235	0.71	metalloexopeptidase activity
GO:0005525	0.71	GTP binding
GO:0003729	0.71	mRNA binding
GO:0000287	0.71	magnesium ion 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:2000781	1.00	positive regulation of double-strand break repair
GO:2000233	1.00	negative regulation of rRNA processing
GO:1901639	1.00	XDP catabolic process
GO:0090068	1.00	positive regulation of cell cycle process
GO:0046709	1.00	IDP catabolic process
GO:0035863	1.00	dITP catabolic process
GO:0016077	1.00	snoRNA catabolic process
GO:0008284	1.00	positive regulation of cell proliferation
GO:0006402	1.00	mRNA catabolic process
GO:0006382	1.00	adenosine to inosine editing

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:0005737	1.00	cytoplasm
GO:0005730	1.00	nucleolus
GO:0005634	1.00	nucleus

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	0.366	2yvmA	0.562	2.91	0.203	0.682	3.6.1.-	50,136
2	0.289	1mqwA	0.565	3.02	0.139	0.692	3.6.1.13	50,136
3	0.199	1f3yA	0.580	3.34	0.168	0.733	3.6.1.17	20,76,78,80,136
4	0.067	2w4eA	0.538	2.49	0.172	0.631	3.6.1.13	50
5	0.067	2i6kA	0.619	2.62	0.114	0.728	5.3.3.2	83

	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	0.77	2a8rB	0.929	1.31	0.587	0.969	1.87	POP	complex1.pdb.gz	24,50,59,60,61,80,136
2	0.76	2a8pB	0.937	1.32	0.581	0.980	1.84	MN	complex2.pdb.gz	24,48,59,80
3	0.75	2a8pB	0.937	1.32	0.581	0.980	1.69	MN	complex3.pdb.gz	59,76,80,132,136
4	0.64	2a8tB	0.930	1.32	0.587	0.969	1.78	UUU	complex4.pdb.gz	24,50,51,57,59,60,61,76,80,108,136,164,166,167,170
5	0.50	2xsqA	0.915	0.32	0.994	0.918	1.90	IMP	complex5.pdb.gz	24,50,57,61,106,164,170
6	0.34	1u200	0.934	1.54	0.575	0.985	1.63	III	complex6.pdb.gz	34,35,36,41,49,51,52,53,54,124,133,134,135,136,138,139,140,141,142,146,148,152,154,157,158,160,161,162
7	0.19	2qjtB	0.592	3.21	0.151	0.733	1.39	MN	complex7.pdb.gz	61,63,75,76
8	0.09	2dhoA	0.606	2.88	0.108	0.739	0.99	MN	complex8.pdb.gz	48,57,58,76,77,80,81
9	0.03	3i9x0	0.585	2.79	0.197	0.703	0.81	III	complex9.pdb.gz	18,19,20,21,62,64,65,68,69,98,99,107,109

	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.