D-I-TASSER A6NJW4

D-I-TASSER results for A6NJW4

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

Summary of the Protein

Uniprot ID: A6NJW4
Protein Name: Leucine-rich repeat-containing protein 3C
Gene Name: LRRC3C

Input Sequence in FASTA format

>A6NJW4 (275 residues)
MRMTSSSFVSYCTPGLCQFMAMLPTAGHLLPLLLVIGTGGTVPSPQVPPRGCYVAKEAGE
RTFRCSQAGLSAVPSGIPNDTRKLYLDANQLASVPAGAFQHLPVLEELDLSHNALAHLSG
AAFQGLEGTLRHLDLSANQLASVPVEAFVGLQIQVNLSANPWHCDCALQEVLRQVRLVPG
TGTGIVCGSGARPDLVGQEFLLLAGEEELCGSGWGGARRSTDVALLVTMGGWLTLMVAYL
VHYVWQNRDETRRSLKRAPVLPVRSEDSSILSTVV

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	A6NJW4-D1	1-275	275		MRMTSSSFVSYCTPGLCQFMAMLPTAGHLLPLLLVIGTGGTVPSPQVPPRGCYVAKEAGERTFRCSQAGLSAVPSGIPNDTRKLYLDANQLASVPAGAFQHLPVLEELDLSHNALAHLSGAAFQGLEGTLRHLDLSANQLASVPVEAFVGLQIQVNLSANPWHCDCALQEVLRQVRLVPGTGTGIVCGSGARPDLVGQEFLLLAGEEELCGSGWGGARRSTDVALLVTMGGWLTLMVAYLVHYVWQNRDETRRSLKRAPVLPVRSEDSSILSTVV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6493

(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	3zyiA	0.67	4.24	0.164	0.844	model1_3zyiA.pdb.gz
2	2id5B	0.65	4.36	0.175	0.836	model1_2id5B.pdb.gz
3	1p8tA	0.63	3.52	0.243	0.749	model1_1p8tA.pdb.gz
4	3zyjA	0.62	4.09	0.143	0.771	model1_3zyjA.pdb.gz
5	4u7lA	0.62	3.76	0.205	0.764	model1_4u7lA.pdb.gz
6	5xwuB	0.62	4.40	0.170	0.804	model1_5xwuB.pdb.gz
7	5a5cA	0.62	3.69	0.245	0.742	model1_5a5cA.pdb.gz
8	4rcaB	0.62	3.59	0.198	0.735	model1_4rcaB.pdb.gz
9	5xnpA	0.62	4.54	0.147	0.811	model1_5xnpA.pdb.gz
10	2o6qA	0.62	3.60	0.215	0.738	model1_2o6qA.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:0098772	0.70	molecular function regulator
GO:0097367	0.68	carbohydrate derivative binding
GO:0030234	0.68	enzyme regulator activity
GO:0005102	0.58	receptor binding
GO:0019887	0.56	protein kinase regulator activity
GO:0004857	0.56	enzyme inhibitor activity
GO:0004860	0.55	protein kinase inhibitor activity
GO:1901681	0.54	sulfur compound binding
GO:0005539	0.54	glycosaminoglycan 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	0.90	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0009987	0.86	cellular process
GO:0044699	0.84	single-organism process
GO:0044763	0.81	single-organism cellular process
GO:0032502	0.78	developmental process
GO:0044767	0.77	single-organism developmental process
GO:0048583	0.72	regulation of response to stimulus
GO:0016043	0.70	cellular component organization
GO:0048519	0.69	negative regulation of biological process
GO:0009653	0.69	anatomical structure morphogenesis
GO:0048523	0.68	negative regulation of cellular process
GO:0009966	0.68	regulation of signal transduction
GO:0050790	0.66	regulation of catalytic activity
GO:1902531	0.65	regulation of intracellular signal transduction
GO:0043086	0.65	negative regulation of catalytic activity
GO:0009968	0.65	negative regulation of signal transduction
GO:0007165	0.63	signal transduction
GO:0048518	0.61	positive regulation of biological process
GO:0051239	0.60	regulation of multicellular organismal process
GO:2000026	0.58	regulation of multicellular organismal development
GO:0051128	0.58	regulation of cellular component organization
GO:0051960	0.57	regulation of nervous system development
GO:0050896	0.57	response to stimulus
GO:0048522	0.57	positive regulation of cellular process
GO:0045595	0.57	regulation of cell differentiation
GO:0048589	0.56	developmental growth
GO:0022604	0.56	regulation of cell morphogenesis
GO:0010975	0.56	regulation of neuron projection development
GO:1902284	0.55	neuron projection extension involved in neuron projection guidance
GO:0050770	0.55	regulation of axonogenesis
GO:0048856	0.55	anatomical structure development
GO:0048675	0.55	axon extension
GO:0048584	0.55	positive regulation of response to stimulus
GO:0031323	0.55	regulation of cellular metabolic process
GO:0080134	0.54	regulation of response to stress
GO:0080090	0.54	regulation of primary metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0002682	0.54	regulation of immune system process
GO:0032501	0.53	multicellular organismal process
GO:0031347	0.53	regulation of defense response
GO:0009605	0.53	response to external stimulus
GO:0007411	0.53	axon guidance
GO:0065008	0.52	regulation of biological quality
GO:0044707	0.52	single-multicellular organism process
GO:0042221	0.52	response to chemical
GO:0051716	0.51	cellular response to stimulus
GO:0051336	0.51	regulation of hydrolase activity
GO:0051241	0.51	negative regulation of multicellular organismal process
GO:0051240	0.51	positive regulation of multicellular organismal process
GO:0051130	0.51	positive regulation of cellular component organization
GO:0051094	0.51	positive regulation of developmental process
GO:0051093	0.51	negative regulation of developmental process
GO:0044087	0.51	regulation of cellular component biogenesis
GO:0040008	0.51	regulation of growth
GO:0032879	0.51	regulation of localization
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0022414	0.51	reproductive process
GO:0019220	0.51	regulation of phosphate metabolic process
GO:0010033	0.51	response to organic substance
GO:0003008	0.51	system process
GO:1901700	0.50	response to oxygen-containing compound
GO:0070887	0.50	cellular response to chemical stimulus
GO:0051962	0.50	positive regulation of nervous system development
GO:0051270	0.50	regulation of cellular component movement
GO:0051129	0.50	negative regulation of cellular component organization
GO:0050768	0.50	negative regulation of neurogenesis
GO:0048646	0.50	anatomical structure formation involved in morphogenesis
GO:0045926	0.50	negative regulation of growth
GO:0045597	0.50	positive regulation of cell differentiation
GO:0044702	0.50	single organism reproductive process
GO:0043087	0.50	regulation of GTPase activity
GO:0042981	0.50	regulation of apoptotic process
GO:0040012	0.50	regulation of locomotion
GO:0033993	0.50	response to lipid
GO:0032101	0.50	regulation of response to external stimulus
GO:0016477	0.50	cell migration
GO:0012501	0.50	programmed cell death
GO:0009888	0.50	tissue development
GO:0001932	0.50	regulation of protein phosphorylation
GO:0001558	0.50	regulation of cell growth

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:0016020	0.92	membrane
GO:0044424	0.87	intracellular part
GO:0044425	0.73	membrane part
GO:0031224	0.71	intrinsic component of membrane
GO:0016021	0.70	integral component of membrane
GO:0005737	0.64	cytoplasm
GO:0005886	0.59	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	1gl9B	0.450	6.14	0.036	0.760	5.99.1.3	NA
2	0.060	1gq8A	0.441	5.65	0.040	0.702	3.1.1.11	NA
3	0.060	1vblA	0.440	5.36	0.065	0.673	4.2.2.2	NA
4	0.060	2qubA	0.435	5.82	0.050	0.709	3.1.1.3	NA
5	0.060	1dceA	0.442	4.05	0.206	0.560	2.5.1.60	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	0.07	2z7xB	0.580	3.65	0.182	0.698	0.79	UUU	complex1.pdb.gz	66,67,85,87,109,111
2	0.03	2z81A	0.567	3.96	0.219	0.695	0.57	PCJ	complex2.pdb.gz	86,89,90,91,92,93,94,95,98
3	0.03	3a7cA	0.567	3.98	0.214	0.695	0.58	PDK	complex3.pdb.gz	77,91,92,93,95,114,116,139
4	0.03	2z66B	0.585	3.65	0.193	0.716	0.51	UUU	complex4.pdb.gz	77,97,101
5	0.02	2z62A	0.551	4.14	0.152	0.716	0.61	UUU	complex5.pdb.gz	50,53,74,75

	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.