D-I-TASSER Q9UIY3

D-I-TASSER results for Q9UIY3

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

Summary of the Protein

Uniprot ID: Q9UIY3
Protein Name: RWD domain-containing protein 2A
Gene Name: RWDD2A

Input Sequence in FASTA format

>Q9UIY3 (292 residues)
MSASVKESLQLQLLEMEMLFSMFPNQGEVKLEDVNALTNIKRYLEGTREALPPKIEFVIT
LQIEEPKVKIDLQVTMPHSYPYVALQLFGRSSELDRHQQLLLNKGLTSYIGTFDPGELCV
CAAIQWLQDNSASYFLNRKLVYEPSTQAKPVKNTFLRMWIYSHHIYQQDLRKKILDVGKR
LDVTGFCMTGKPGIICVEGFKEHCEEFWHTIRYPNWKHISCKHAESVETEGNGEDLRLFH
SFEELLLEAHGDYGLRNDYHMNLGQFLEFLKKHKSEHVFQILFGIESKSSDS

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	Q9UIY3-D1	1-148	148		MSASVKESLQLQLLEMEMLFSMFPNQGEVKLEDVNALTNIKRYLEGTREALPPKIEFVITLQIEEPKVKIDLQVTMPHSYPYVALQLFGRSSELDRHQQLLLNKGLTSYIGTFDPGELCVCAAIQWLQDNSASYFLNRKLVYEPSTQA
2	Q9UIY3-D2	149-292	144		KPVKNTFLRMWIYSHHIYQQDLRKKILDVGKRLDVTGFCMTGKPGIICVEGFKEHCEEFWHTIRYPNWKHISCKHAESVETEGNGEDLRLFHSFEELLLEAHGDYGLRNDYHMNLGQFLEFLKKHKSEHVFQILFGIESKSSDS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.77

(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	2dawA	0.47	2.00	0.918	0.493	model1_2dawA.pdb.gz
2	2daxA	0.45	2.48	0.259	0.490	model1_2daxA.pdb.gz
3	4qshA	0.43	6.29	0.042	0.726	model1_4qshA.pdb.gz
4	5vywA	0.42	6.41	0.049	0.726	model1_5vywA.pdb.gz
5	6hydA	0.42	6.38	0.046	0.695	model1_6hydA.pdb.gz
6	1qvrA	0.42	6.29	0.069	0.699	model1_1qvrA.pdb.gz
7	3bg5A	0.42	6.20	0.048	0.702	model1_3bg5A.pdb.gz
8	2qf7A	0.41	6.36	0.060	0.723	model1_2qf7A.pdb.gz
9	6nplA	0.41	6.07	0.050	0.678	model1_6nplA.pdb.gz
10	7emfN	0.41	5.49	0.040	0.623	model1_7emfN.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:0043169	0.73	cation binding
GO:0003824	0.73	catalytic activity
GO:0046872	0.60	metal ion binding
GO:0016740	0.59	transferase activity
GO:0019899	0.55	enzyme binding
GO:0061630	0.52	ubiquitin protein ligase activity

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:0050794	0.90	regulation of cellular process
GO:0009987	0.83	cellular process
GO:0080090	0.82	regulation of primary metabolic process
GO:0060255	0.82	regulation of macromolecule metabolic process
GO:0031323	0.82	regulation of cellular metabolic process
GO:0048518	0.78	positive regulation of biological process
GO:0044237	0.75	cellular metabolic process
GO:0071704	0.72	organic substance metabolic process
GO:0044238	0.72	primary metabolic process
GO:0032268	0.67	regulation of cellular protein metabolic process
GO:0031325	0.66	positive regulation of cellular metabolic process
GO:0010604	0.66	positive regulation of macromolecule metabolic process
GO:0032270	0.62	positive regulation of cellular protein metabolic process
GO:0044260	0.59	cellular macromolecule metabolic process
GO:0007165	0.55	signal transduction
GO:0006464	0.53	cellular protein modification process
GO:0044699	0.51	single-organism process
GO:0044763	0.50	single-organism cellular 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:0043226	0.93	organelle
GO:0043229	0.92	intracellular organelle
GO:0043227	0.90	membrane-bounded organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005737	0.88	cytoplasm
GO:0032991	0.86	macromolecular complex
GO:0005634	0.82	nucleus
GO:0044444	0.81	cytoplasmic part
GO:0043234	0.76	protein complex
GO:1902494	0.58	catalytic complex
GO:0000151	0.53	ubiquitin ligase complex
GO:0044446	0.51	intracellular organelle part
GO:0016020	0.51	membrane

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	2ayvA	0.338	3.57	0.096	0.404	6.3.2.19	130
2	0.060	1hn0A	0.357	6.31	0.064	0.610	4.2.2.20	NA
3	0.060	2wanA	0.335	5.99	0.022	0.541	3.2.1.41	216
4	0.060	1z0hB	0.220	7.01	0.023	0.404	3.4.24.69	NA
5	0.060	2vr5A	0.367	6.22	0.040	0.610	3.2.1.-	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	0.01	3tw6A	0.408	6.47	0.053	0.706	0.19	ADP	complex1.pdb.gz	170,194,255
2	0.01	3bg5C	0.412	6.30	0.041	0.709	0.15	BTI	complex2.pdb.gz	185,200,203,204
3	0.01	1qvrA	0.416	6.29	0.069	0.699	0.14	ANP	complex3.pdb.gz	189,190,191,192,193
4	0.01	3hb9C	0.417	6.12	0.048	0.702	0.20	BTI	complex4.pdb.gz	190,193,194,195,242
5	0.01	3bg5C	0.412	6.30	0.041	0.709	0.15	ATP	complex5.pdb.gz	185,187,190,195
6	0.01	3hblC	0.416	6.32	0.052	0.716	0.15	BTI	complex6.pdb.gz	185,200,203,204
7	0.01	3tw6C	0.414	6.50	0.024	0.726	0.29	PAE	complex7.pdb.gz	198,199,201,206,207,208
8	0.01	3tw6B	0.425	6.54	0.028	0.743	0.16	ADP	complex8.pdb.gz	186,193,194,207,208,219
9	0.01	3ho8C	0.433	6.18	0.063	0.723	0.13	COA	complex9.pdb.gz	184,187,189
10	0.01	3ho8D	0.428	6.37	0.058	0.736	0.26	COA	complex10.pdb.gz	202,203,204,205

	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.