D-I-TASSER Q9Y546

D-I-TASSER results for Q9Y546

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

Summary of the Protein

Uniprot ID: Q9Y546
Protein Name: Leucine-rich repeat-containing protein 42
Gene Name: LRRC42

Input Sequence in FASTA format

>Q9Y546 (428 residues)
MSYYLSSENHLDPGPIYMRENGQLHMVNLALDGVRSSLQKPRPFRLFPKGFSVELCMNRE
DDTARKEKTDHFIFTYTREGNLRYSAKSLFSLVLGFISDNVDHIDSLIGFPEQIAEKLFS
AAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFRELTCLDL
SCCKLGDEHELLEHLTNEALSSVTQLHLKDNCLSDAGVRKMTAPVRVMKRGLENLTLLDL
SCNPEITDAGIGYLFSFRKLNCLDISGTGLKDIKTVKHKLQTHIGLVHSKVPLKEFDHSN
CKTEGWADQIVLQWERVTAEAVKPRETSEPRAAAQRFYGKRSRAEAPLKCPLADTHMNSS
EKLQFYKEKAPDCHGPVLKHEAISSQESKKSKKRPFEESETEQNNSSQPSKQKYVCLAVE
DWDLLNSY

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	Q9Y546-D1	1-428	428		MSYYLSSENHLDPGPIYMRENGQLHMVNLALDGVRSSLQKPRPFRLFPKGFSVELCMNREDDTARKEKTDHFIFTYTREGNLRYSAKSLFSLVLGFISDNVDHIDSLIGFPEQIAEKLFSAAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFRELTCLDLSCCKLGDEHELLEHLTNEALSSVTQLHLKDNCLSDAGVRKMTAPVRVMKRGLENLTLLDLSCNPEITDAGIGYLFSFRKLNCLDISGTGLKDIKTVKHKLQTHIGLVHSKVPLKEFDHSNCKTEGWADQIVLQWERVTAEAVKPRETSEPRAAAQRFYGKRSRAEAPLKCPLADTHMNSSEKLQFYKEKAPDCHGPVLKHEAISSQESKKSKKRPFEESETEQNNSSQPSKQKYVCLAVEDWDLLNSY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6256

(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	4r5dA	0.69	4.38	0.144	0.848	model1_4r5dA.pdb.gz
2	2a0zA	0.68	4.73	0.110	0.848	model1_2a0zA.pdb.gz
3	3rg1A	0.67	4.95	0.124	0.867	model1_3rg1A.pdb.gz
4	3w3gA	0.67	4.87	0.132	0.862	model1_3w3gA.pdb.gz
5	4j0mA	0.67	5.07	0.093	0.874	model1_4j0mA.pdb.gz
6	7jluA	0.67	4.98	0.105	0.872	model1_7jluA.pdb.gz
7	4lxrA	0.66	4.83	0.098	0.846	model1_4lxrA.pdb.gz
8	3wpbA	0.66	5.27	0.121	0.883	model1_3wpbA.pdb.gz
9	4z63A	0.66	4.95	0.093	0.860	model1_4z63A.pdb.gz
10	5gmfA	0.66	5.21	0.102	0.883	model1_5gmfA.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	0.65	heterocyclic compound binding
GO:0097159	0.65	organic cyclic compound binding
GO:0097367	0.62	carbohydrate derivative binding
GO:0003824	0.62	catalytic activity
GO:0036094	0.58	small molecule binding
GO:0035639	0.57	purine ribonucleoside triphosphate binding
GO:0032555	0.57	purine ribonucleotide binding
GO:0032550	0.57	purine ribonucleoside binding
GO:0032559	0.56	adenyl ribonucleotide binding
GO:0030234	0.56	enzyme regulator activity
GO:0016740	0.56	transferase activity
GO:0004857	0.55	enzyme inhibitor activity
GO:0019887	0.54	protein kinase regulator activity
GO:0019210	0.54	kinase inhibitor activity
GO:0005102	0.51	receptor binding
GO:0016773	0.50	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.50	kinase 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:0009987	0.85	cellular process
GO:0065007	0.80	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0050794	0.78	regulation of cellular process
GO:0044699	0.78	single-organism process
GO:0044763	0.72	single-organism cellular process
GO:0007165	0.67	signal transduction
GO:0032502	0.65	developmental process
GO:0048583	0.64	regulation of response to stimulus
GO:0044767	0.64	single-organism developmental process
GO:0016043	0.62	cellular component organization
GO:0031323	0.61	regulation of cellular metabolic process
GO:0080090	0.60	regulation of primary metabolic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0048523	0.59	negative regulation of cellular process
GO:0048869	0.58	cellular developmental process
GO:0048518	0.58	positive regulation of biological process
GO:0007166	0.58	cell surface receptor signaling pathway
GO:0009653	0.57	anatomical structure morphogenesis
GO:0050790	0.56	regulation of catalytic activity
GO:0032268	0.56	regulation of cellular protein metabolic process
GO:0030030	0.56	cell projection organization
GO:0009966	0.56	regulation of signal transduction
GO:0048858	0.55	cell projection morphogenesis
GO:0031324	0.55	negative regulation of cellular metabolic process
GO:0051338	0.54	regulation of transferase activity
GO:0048585	0.54	negative regulation of response to stimulus
GO:0031399	0.54	regulation of protein modification process
GO:0019220	0.54	regulation of phosphate metabolic process
GO:0007409	0.54	axonogenesis
GO:1902532	0.53	negative regulation of intracellular signal transduction
GO:0045859	0.53	regulation of protein kinase activity
GO:0043086	0.53	negative regulation of catalytic activity
GO:0001933	0.53	negative regulation of protein phosphorylation
GO:1904893	0.52	negative regulation of STAT cascade
GO:0051239	0.52	regulation of multicellular organismal process
GO:0050896	0.52	response to stimulus
GO:0048522	0.52	positive regulation of cellular process
GO:0046425	0.52	regulation of JAK-STAT cascade
GO:0033673	0.52	negative regulation of kinase activity
GO:2000026	0.50	regulation of multicellular organismal development
GO:0051128	0.50	regulation of cellular component organization
GO:0045595	0.50	regulation of cell differentiation

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	0.99	cell part
GO:0016020	0.93	membrane
GO:0044424	0.91	intracellular part
GO:0016021	0.88	integral component of membrane
GO:0005886	0.78	plasma membrane
GO:0043226	0.69	organelle
GO:0044444	0.65	cytoplasmic part
GO:0043229	0.64	intracellular organelle
GO:0043227	0.64	membrane-bounded organelle
GO:0044459	0.63	plasma membrane part
GO:0005737	0.59	cytoplasm
GO:0044446	0.58	intracellular organelle part
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0031226	0.55	intrinsic component of plasma membrane
GO:0005887	0.51	integral component of plasma 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	3h09B	0.465	5.96	0.046	0.694	3.4.21.72	279
2	0.060	1od2A	0.365	7.17	0.044	0.612	6.3.4.14 6.4.1.2	NA
3	0.060	1hn0A	0.424	7.23	0.050	0.713	4.2.2.20	NA
4	0.060	3jurD	0.387	5.93	0.020	0.570	3.2.1.15	187
5	0.060	1uyrA	0.389	6.59	0.029	0.608	6.4.1.2 6.3.4.14	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	0.08	2z81A	0.649	5.21	0.103	0.867	0.65	PCJ	complex1.pdb.gz	170,178,180,206,208,232,240,245,246,247,250,251,252
2	0.07	3a79A	0.641	5.23	0.081	0.865	0.79	PXS	complex2.pdb.gz	161,162,165,166,169,180,208,211,213,219,232,240,243,245,246,247,250,251,252
3	0.02	1xec0	0.580	3.84	0.114	0.687	0.65	III	complex3.pdb.gz	87,107,109,152,154,179,181,237,239
4	0.02	3a79B	0.605	5.08	0.091	0.792	0.77	UUU	complex4.pdb.gz	186,211,213,244

	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.