D-I-TASSER Q9BY71

D-I-TASSER results for Q9BY71

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

Summary of the Protein

Uniprot ID: Q9BY71
Protein Name: Leucine-rich repeat-containing protein 3
Gene Name: LRRC3

Input Sequence in FASTA format

>Q9BY71 (257 residues)
MGTVRPPRPSLLLVSTRESCLFLLFCLHLGAACPQPCRCPDHAGAVAVFCSLRGLQEVPE
DIPANTVLLKLDANKISHLPDGAFQHLHRLRELDLSHNAIEAIGSATFAGLAGGLRLLDL
SYNRIQRIPKDALGKLSAKIRLSHNPLHCECALQEALWELKLDPDSVDEIACHTSVQEEF
VGKPLVQALDAGASLCSVPHRTTDVAMLVTMFGWFAMVIAYVVYYVRHNQEDARRHLEYL
KSLPSAPASKDPIGPGP

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	Q9BY71-D1	1-257	257		MGTVRPPRPSLLLVSTRESCLFLLFCLHLGAACPQPCRCPDHAGAVAVFCSLRGLQEVPEDIPANTVLLKLDANKISHLPDGAFQHLHRLRELDLSHNAIEAIGSATFAGLAGGLRLLDLSYNRIQRIPKDALGKLSAKIRLSHNPLHCECALQEALWELKLDPDSVDEIACHTSVQEEFVGKPLVQALDAGASLCSVPHRTTDVAMLVTMFGWFAMVIAYVVYYVRHNQEDARRHLEYLKSLPSAPASKDPIGPGP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6117

(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	6hluA	0.64	4.43	0.104	0.872	model1_6hluA.pdb.gz
2	4r5dA	0.64	4.43	0.152	0.829	model1_4r5dA.pdb.gz
3	4z0cA	0.63	4.83	0.124	0.844	model1_4z0cA.pdb.gz
4	1p8tA	0.62	3.08	0.233	0.708	model1_1p8tA.pdb.gz
5	4k17A	0.62	4.34	0.090	0.844	model1_4k17A.pdb.gz
6	4u7lA	0.61	4.68	0.131	0.825	model1_4u7lA.pdb.gz
7	3a79A	0.61	4.61	0.071	0.841	model1_3a79A.pdb.gz
8	4p8sA	0.61	3.07	0.216	0.700	model1_4p8sA.pdb.gz
9	2v70A	0.61	3.20	0.177	0.704	model1_2v70A.pdb.gz
10	4rcaB	0.61	2.98	0.218	0.697	model1_4rcaB.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:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0098772	0.59	molecular function regulator
GO:0097367	0.59	carbohydrate derivative binding
GO:0004857	0.57	enzyme inhibitor activity
GO:0005102	0.50	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:0065007	0.88	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0050794	0.86	regulation of cellular process
GO:0009987	0.83	cellular process
GO:0044699	0.80	single-organism process
GO:0007165	0.78	signal transduction
GO:0044763	0.76	single-organism cellular process
GO:0032502	0.71	developmental process
GO:0044767	0.70	single-organism developmental process
GO:0048583	0.67	regulation of response to stimulus
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0048519	0.63	negative regulation of biological process
GO:0016043	0.62	cellular component organization
GO:0051246	0.61	regulation of protein metabolic process
GO:0009653	0.61	anatomical structure morphogenesis
GO:0048523	0.60	negative regulation of cellular process
GO:0023051	0.60	regulation of signaling
GO:0010646	0.60	regulation of cell communication
GO:0009966	0.59	regulation of signal transduction
GO:0050790	0.58	regulation of catalytic activity
GO:0032268	0.58	regulation of cellular protein metabolic process
GO:0019220	0.58	regulation of phosphate metabolic process
GO:0042325	0.57	regulation of phosphorylation
GO:0031399	0.57	regulation of protein modification process
GO:0009968	0.57	negative regulation of signal transduction
GO:1902531	0.56	regulation of intracellular signal transduction
GO:0045936	0.56	negative regulation of phosphate metabolic process
GO:0044092	0.56	negative regulation of molecular function
GO:0032269	0.56	negative regulation of cellular protein metabolic process
GO:1902532	0.55	negative regulation of intracellular signal transduction
GO:0043086	0.55	negative regulation of catalytic activity
GO:0042326	0.55	negative regulation of phosphorylation
GO:0031400	0.55	negative regulation of protein modification process
GO:0048518	0.53	positive regulation of biological process
GO:0008152	0.53	metabolic process
GO:0071704	0.51	organic substance metabolic process
GO:0051239	0.51	regulation of multicellular organismal process
GO:0044238	0.50	primary metabolic process
GO:0044237	0.50	cellular 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:0044464	0.98	cell part
GO:0044424	0.87	intracellular part
GO:0016020	0.83	membrane
GO:0044425	0.66	membrane part
GO:0016021	0.63	integral component of membrane
GO:0005737	0.62	cytoplasm
GO:0005886	0.57	plasma membrane
GO:0043226	0.54	organelle
GO:0043227	0.51	membrane-bounded organelle

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	1dceA	0.471	3.48	0.207	0.572	2.5.1.60	NA
2	0.060	1oocB	0.490	4.73	0.063	0.704	4.2.2.2	NA
3	0.060	3dsxA	0.410	5.42	0.054	0.654	2.5.1.60	NA
4	0.060	2ifgA	0.513	2.80	0.146	0.591	2.7.10.1	92,115
5	0.060	1dboA	0.524	5.32	0.029	0.805	4.2.2.19	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	0.03	2z7xB	0.566	5.03	0.097	0.841	0.65	UUU	complex1.pdb.gz	72,96,97,119,121,141
2	0.02	3cigA	0.614	4.88	0.107	0.860	0.65	UUU	complex2.pdb.gz	104,127,129,130
3	0.02	2z66B	0.551	4.55	0.118	0.735	0.43	UUU	complex3.pdb.gz	101,103,105,128
4	0.01	3a7bA	0.602	5.04	0.077	0.868	0.42	LTC	complex4.pdb.gz	134,142,145,146,147

	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.