D-I-TASSER Q9Y5X4

D-I-TASSER results for Q9Y5X4

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

Summary of the Protein

Uniprot ID: Q9Y5X4
Protein Name: Photoreceptor-specific nuclear receptor
Gene Name: NR2E3

Input Sequence in FASTA format

>Q9Y5X4 (410 residues)
METRPTALMSSTVAAAAPAAGAASRKESPGRWGLGEDPTGVSPSLQCRVCGDSSSGKHYG
IYACNGCSGFFKRSVRRRLIYRCQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN
ERQPRSTAQVHLDSMESNTESRPESLVAPPAPAGRSPRGPTPMSAARALGHHFMASLITA
ETCAKLEPEDADENIDVTSNDPEFPSSPYSSSSPCGLDSIHETSARLLFMAVKWAKNLPV
FSSLPFRDQVILLEEAWSELFLLGAIQWSLPLDSCPLLAPPEASAAGGAQGRLTLASMET
RVLQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQSQVMLSQHSKAH
HPSQPVRFGKLLLLLPSLRFITAERIELLFFRKTIGNTPMEKLLCDMFKN

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	Q9Y5X4-D1	1-410	410		METRPTALMSSTVAAAAPAAGAASRKESPGRWGLGEDPTGVSPSLQCRVCGDSSSGKHYGIYACNGCSGFFKRSVRRRLIYRCQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQNERQPRSTAQVHLDSMESNTESRPESLVAPPAPAGRSPRGPTPMSAARALGHHFMASLITAETCAKLEPEDADENIDVTSNDPEFPSSPYSSSSPCGLDSIHETSARLLFMAVKWAKNLPVFSSLPFRDQVILLEEAWSELFLLGAIQWSLPLDSCPLLAPPEASAAGGAQGRLTLASMETRVLQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQSQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFITAERIELLFFRKTIGNTPMEKLLCDMFKN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6314

(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	4nqaB	0.85	1.84	0.245	0.890	model1_4nqaB.pdb.gz
2	1pq6B	0.57	1.08	0.200	0.585	model1_1pq6B.pdb.gz
3	3a40X	0.55	2.60	0.154	0.600	model1_3a40X.pdb.gz
4	1r1kD	0.54	1.68	0.198	0.566	model1_1r1kD.pdb.gz
5	1xvpD	0.54	2.46	0.188	0.585	model1_1xvpD.pdb.gz
6	2nxxE	0.54	1.60	0.195	0.561	model1_2nxxE.pdb.gz
7	3e00D	0.53	3.32	0.135	0.595	model1_3e00D.pdb.gz
8	3hvlB	0.53	2.72	0.190	0.578	model1_3hvlB.pdb.gz
9	6fzfA	0.53	2.69	0.189	0.573	model1_6fzfA.pdb.gz
10	6lx5A	0.53	2.63	0.175	0.568	model1_6lx5A.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:0004871	0.79	signal transducer activity
GO:0097159	0.74	organic cyclic compound binding
GO:0003700	0.74	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.64	heterocyclic compound binding
GO:0004872	0.62	receptor activity
GO:0038023	0.61	signaling receptor activity
GO:0003677	0.57	DNA binding
GO:0000981	0.54	RNA polymerase II transcription factor activity, sequence-specific DNA 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	0.92	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0019222	0.76	regulation of metabolic process
GO:0060255	0.75	regulation of macromolecule metabolic process
GO:0010468	0.72	regulation of gene expression
GO:0031323	0.69	regulation of cellular metabolic process
GO:0080090	0.68	regulation of primary metabolic process
GO:0019219	0.67	regulation of nucleobase-containing compound metabolic process
GO:0010556	0.65	regulation of macromolecule biosynthetic process
GO:0050896	0.64	response to stimulus
GO:0048518	0.64	positive regulation of biological process
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0009987	0.63	cellular process
GO:0010604	0.61	positive regulation of macromolecule metabolic process
GO:0048522	0.57	positive regulation of cellular process
GO:0010628	0.57	positive regulation of gene expression
GO:0031325	0.54	positive regulation of cellular metabolic process
GO:0045935	0.53	positive regulation of nucleobase-containing compound metabolic process
GO:0007165	0.51	signal transduction

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:0043229	0.87	intracellular organelle
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0005634	0.85	nucleus

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	1j36A	0.331	6.91	0.073	0.554	3.4.15.1	NA
2	0.060	2c6fA	0.346	7.13	0.048	0.585	3.4.15.1	NA
3	0.060	2dqmA	0.318	7.22	0.061	0.541	3.4.11.2	NA
4	0.060	1u3rA	0.508	2.15	0.237	0.544	2.3.1.48	113
5	0.060	3ikmD	0.338	7.38	0.033	0.588	2.7.7.7	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	0.13	2aclD	0.576	1.21	0.198	0.590	0.17	L05	complex1.pdb.gz	67,70,71,74,81
2	0.10	1pq9C	0.554	1.00	0.208	0.563	0.19	UUU	complex2.pdb.gz	65,68,69,72
3	0.05	3ipsA	0.534	1.05	0.211	0.544	0.25	III	complex3.pdb.gz	66,69,70,72,73
4	0.04	3o1dA	0.539	2.19	0.174	0.573	0.31	III	complex4.pdb.gz	59,67,68,72
5	0.04	3ipsA	0.534	1.05	0.211	0.544	0.14	O90	complex5.pdb.gz	66,67,70
6	0.04	3fc6D	0.577	1.04	0.199	0.588	0.14	LX2	complex6.pdb.gz	66,67,70,73,80,82,108,109
7	0.04	2aclF	0.577	1.15	0.198	0.590	0.16	L05	complex7.pdb.gz	51,53,54,55,95,96,97,103,113
8	0.04	1pq6B	0.574	1.08	0.200	0.585	0.15	965	complex8.pdb.gz	55,102,105,106,109
9	0.04	1pq6D	0.542	0.99	0.212	0.551	0.15	965	complex9.pdb.gz	56,58,104,108,109
10	0.04	3kfcA	0.557	1.07	0.206	0.568	0.14	61X	complex10.pdb.gz	52,53,95,113

	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.