D-I-TASSER Q5VUJ9

D-I-TASSER results for Q5VUJ9

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

Summary of the Protein

Uniprot ID: Q5VUJ9
Protein Name: Dynein regulatory complex protein 8
Gene Name: EFCAB2

Input Sequence in FASTA format

>Q5VUJ9 (269 residues)
MLGPGQVRLRPRVWRDKAGGRVADGASGLPPARGSWRETGTGRALGASSPPRPAQGSSSP
GIQSGPSSRPGSPRGAEQAGTPRPRLSLGISQATGSAARWRTRRTGKGLGYNSDEIRPRT
LLIEHLMEGGRRDHHTMTVLWGTQEIIVAEFHKKIKEAFEVFDHESNNTVDVREIGTIIR
SLGCCPTEGELHDLIAEVEEEEPTGYIRFEKFLPVMTEILLERKYRPIPEDVLLRAFEVL
DSAKRGFLTKDELIKYMTEEDGVSLRRPG

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	Q5VUJ9-D1	1-269	269		MLGPGQVRLRPRVWRDKAGGRVADGASGLPPARGSWRETGTGRALGASSPPRPAQGSSSPGIQSGPSSRPGSPRGAEQAGTPRPRLSLGISQATGSAARWRTRRTGKGLGYNSDEIRPRTLLIEHLMEGGRRDHHTMTVLWGTQEIIVAEFHKKIKEAFEVFDHESNNTVDVREIGTIIRSLGCCPTEGELHDLIAEVEEEEPTGYIRFEKFLPVMTEILLERKYRPIPEDVLLRAFEVLDSAKRGFLTKDELIKYMTEEDGVSLRRPG

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3153

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1aorA	0.46	5.90	0.054	0.769	model1_1aorA.pdb.gz
2	6ka4A	0.45	6.30	0.077	0.766	model1_6ka4A.pdb.gz
3	6mcpA	0.44	5.95	0.047	0.706	model1_6mcpA.pdb.gz
4	2fo0A	0.44	5.81	0.048	0.721	model1_2fo0A.pdb.gz
5	6bhcA	0.44	5.93	0.055	0.706	model1_6bhcA.pdb.gz
6	2ptkA	0.44	6.18	0.085	0.714	model1_2ptkA.pdb.gz
7	6x91A	0.43	6.30	0.073	0.758	model1_6x91A.pdb.gz
8	3azoA	0.43	6.38	0.056	0.766	model1_3azoA.pdb.gz
9	4fl2A	0.43	5.92	0.042	0.706	model1_4fl2A.pdb.gz
10	7c72A	0.43	6.33	0.043	0.762	model1_7c72A.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	0.59	catalytic activity
GO:0016772	0.54	transferase activity, transferring phosphorus-containing groups
GO:0004672	0.53	protein kinase activity
GO:0032403	0.51	protein complex 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	0.86	cellular process
GO:0065007	0.84	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.76	regulation of cellular process
GO:0071704	0.75	organic substance metabolic process
GO:0019538	0.74	protein metabolic process
GO:0007165	0.72	signal transduction
GO:0044237	0.68	cellular metabolic process
GO:0044267	0.67	cellular protein metabolic process
GO:0044699	0.63	single-organism process
GO:0006796	0.63	phosphate-containing compound metabolic process
GO:0006464	0.63	cellular protein modification process
GO:0006468	0.62	protein phosphorylation
GO:0046777	0.61	protein autophosphorylation
GO:0018193	0.61	peptidyl-amino acid modification
GO:0018105	0.57	peptidyl-serine phosphorylation
GO:0032502	0.56	developmental process
GO:0032501	0.56	multicellular organismal process
GO:0051239	0.55	regulation of multicellular organismal process
GO:0044767	0.55	single-organism developmental process
GO:0016043	0.55	cellular component organization
GO:0003008	0.55	system process
GO:0050896	0.54	response to stimulus
GO:0009755	0.54	hormone-mediated signaling pathway
GO:0065008	0.52	regulation of biological quality
GO:0065009	0.51	regulation of molecular function
GO:0048583	0.51	regulation of response to stimulus
GO:0048519	0.51	negative regulation of biological process
GO:0048518	0.51	positive regulation of biological process
GO:0042221	0.51	response to chemical
GO:0032879	0.51	regulation of localization
GO:0022607	0.51	cellular component assembly
GO:1902531	0.50	regulation of intracellular signal transduction
GO:0080090	0.50	regulation of primary metabolic process
GO:0051716	0.50	cellular response to stimulus
GO:0051171	0.50	regulation of nitrogen compound metabolic process
GO:0051049	0.50	regulation of transport
GO:0050790	0.50	regulation of catalytic activity
GO:0048584	0.50	positive regulation of response to stimulus
GO:0048523	0.50	negative regulation of cellular process
GO:0048522	0.50	positive regulation of cellular process
GO:0044093	0.50	positive regulation of molecular function
GO:0031323	0.50	regulation of cellular metabolic process
GO:0009628	0.50	response to abiotic stimulus
GO:0006950	0.50	response to stress

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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043226	0.92	organelle
GO:0016020	0.91	membrane
GO:0043227	0.89	membrane-bounded organelle
GO:0043229	0.86	intracellular organelle
GO:0005737	0.85	cytoplasm
GO:0044444	0.83	cytoplasmic part
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0005886	0.76	plasma membrane
GO:0044459	0.74	plasma membrane part
GO:0005634	0.74	nucleus
GO:0005829	0.67	cytosol
GO:0044422	0.60	organelle part
GO:0044446	0.58	intracellular organelle part
GO:0031982	0.57	vesicle

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

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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	1yi6A	0.390	5.75	0.062	0.625	2.7.10.2	NA
2	0.060	2zf5Y	0.418	6.08	0.044	0.699	2.7.1.30	123,148
3	0.060	2dq7X	0.371	5.72	0.065	0.595	2.7.10.2	132
4	0.060	1y57A	0.399	6.04	0.065	0.662	2.7.10.2	132
5	0.060	2hk5A	0.376	5.58	0.062	0.595	2.7.10.2	132

	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

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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	3mssB	0.392	5.79	0.050	0.628	0.47	MS7	complex1.pdb.gz	176,179,180
2	0.01	3pyyB	0.387	5.47	0.046	0.602	0.44	3YY	complex2.pdb.gz	106,117,182,183,185,186
3	0.01	3gvuA	0.402	5.62	0.059	0.632	0.45	STI	complex3.pdb.gz	176,186,189
4	0.01	2xynC	0.374	5.67	0.041	0.595	0.40	VX6	complex4.pdb.gz	121,122,127
5	0.01	3ms9A	0.396	5.62	0.045	0.621	0.41	MS9	complex5.pdb.gz	115,179,180,187,190
6	0.01	2g2fA	0.385	5.88	0.066	0.625	0.43	III	complex6.pdb.gz	106,115,116,121,179

	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.