D-I-TASSER Q9Y2W1

D-I-TASSER results for Q9Y2W1

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

Summary of the Protein

Uniprot ID: Q9Y2W1
Protein Name: Thyroid hormone receptor-associated protein 3
Gene Name: THRAP3

Input Sequence in FASTA format

>Q9Y2W1 (955 residues)
MSKTNKSKSGSRSSRSRSASRSRSRSFSKSRSRSRSLSRSRKRRLSSRSRSRSYSPAHNR
ERNHPRVYQNRDFRGHNRGYRRPYYFRGRNRGFYPWGQYNRGGYGNYRSNWQNYRQAYSP
RRGRSRSRSPKRRSPSPRSRSHSRNSDKSSSDRSRRSSSSRSSSNHSRVESSKRKSAKEK
KSSSKDSRPSQAAGDNQGDEAKEQTFSGGTSQDTKASESSKPWPDATYGTGSASRASAVS
ELSPRERSPALKSPLQSVVVRRRSPRPSPVPKPSPPLSSTSQMGSTLPSGAGYQSGTHQG
QFDHGSGSLSPSKKSPVGKSPPSTGSTYGSSQKEESAASGGAAYTKRYLEEQKTENGKDK
EQKQTNTDKEKIKEKGSFSDTGLGDGKMKSDSFAPKTDSEKPFRGSQSPKRYKLRDDFEK
KMADFHKEEMDDQDKDKAKGRKESEFDDEPKFMSKVIGANKNQEEEKSGKWEGLVYAPPG
KEKQRKTEELEEESFPERSKKEDRGKRSEGGHRGFVPEKNFRVTAYKAVQEKSSSPPPRK
TSESRDKLGAKGDFPTGKSSFSITREAQVNVRMDSFDEDLARPSGLLAQERKLCRDLVHS
NKKEQEFRSIFQHIQSAQSQRSPSELFAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKR
GTEQEAAKNKKSPEIHRRIDISPSTFRKHGLAHDEMKSPREPGYKAEGKYKDDPVDLRLD
IERRKKHKERDLKRGKSRESVDSRDSSHSRERSAEKTEKTHKGSKKQKKHRRARDRSRSS
SSSSQSSHSYKAEEYTEETEEREESTTGFDKSRLGTKDFVGPSERGGGRARGTFQFRARG
RGWGRGNYSGNNNNNSNNDFQKRNREEEWDPEYTPKSKKYYLHDDREGEGSDKWVSRGRG
RGAFPRGRGRFMFRKSSTSPKWAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE

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	Q9Y2W1-D1	1-65,168-269,791-832,856-955	309		MSKTNKSKSGSRSSRSRSASRSRSRSFSKSRSRSRSLSRSRKRRLSSRSRSRSYSPAHNRERNHPRVESSKRKSAKEKKSSSKDSRPSQAAGDNQGDEAKEQTFSGGTSQDTKASESSKPWPDATYGTGSASRASAVSELSPRERSPALKSPLQSVVVRRRSPRPSPKAEEYTEETEEREESTTGFDKSRLGTKDFVGPSERGGGRARGSNNDFQKRNREEEWDPEYTPKSKKYYLHDDREGEGSDKWVSRGRGRGAFPRGRGRFMFRKSSTSPKWAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE
2	Q9Y2W1-D2	66-111,678-720,833-855	112		RVYQNRDFRGHNRGYRRPYYFRGRNRGFYPWGQYNRGGYGNYRSNWRIDISPSTFRKHGLAHDEMKSPREPGYKAEGKYKDDPVDLRLDTFQFRARGRGWGRGNYSGNNNNN
3	Q9Y2W1-D3	112-167,721-790	126		QNYRQAYSPRRGRSRSRSPKRRSPSPRSRSHSRNSDKSSSDRSRRSSSSRSSSNHSIERRKKHKERDLKRGKSRESVDSRDSSHSRERSAEKTEKTHKGSKKQKKHRRARDRSRSSSSSSQSSHSY
4	Q9Y2W1-D4	270-320,580-677	149		VPKPSPPLSSTSQMGSTLPSGAGYQSGTHQGQFDHGSGSLSPSKKSPVGKSLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIHR
5	Q9Y2W1-D5	321-407	87		PPSTGSTYGSSQKEESAASGGAAYTKRYLEEQKTENGKDKEQKQTNTDKEKIKEKGSFSDTGLGDGKMKSDSFAPKTDSEKPFRGSQ
6	Q9Y2W1-D6	408-579	172		SPKRYKLRDDFEKKMADFHKEEMDDQDKDKAKGRKESEFDDEPKFMSKVIGANKNQEEEKSGKWEGLVYAPPGKEKQRKTEELEEESFPERSKKEDRGKRSEGGHRGFVPEKNFRVTAYKAVQEKSSSPPPRKTSESRDKLGAKGDFPTGKSSFSITREAQVNVRMDSFDED

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.38

(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	6ar6A	0.30	8.95	0.041	0.473	model1_6ar6A.pdb.gz
2	3og2A	0.29	8.84	0.029	0.457	model1_3og2A.pdb.gz
3	6edoA	0.29	8.86	0.044	0.453	model1_6edoA.pdb.gz
4	1tg7A	0.29	8.61	0.035	0.443	model1_1tg7A.pdb.gz
5	6r9tA	0.28	8.81	0.039	0.443	model1_6r9tA.pdb.gz
6	6mixA	0.28	8.98	0.052	0.441	model1_6mixA.pdb.gz
7	5x6oC	0.28	9.64	0.031	0.468	model1_5x6oC.pdb.gz
8	1llwA	0.28	9.14	0.043	0.452	model1_1llwA.pdb.gz
9	6z2wE	0.28	9.18	0.023	0.451	model1_6z2wE.pdb.gz
10	5ijlA	0.28	8.46	0.043	0.422	model1_5ijlA.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:0003677	1.00	DNA binding
GO:0003712	0.87	transcription cofactor activity
GO:0044212	0.86	transcription regulatory region DNA binding
GO:0051219	0.85	phosphoprotein binding
GO:0003713	0.85	transcription coactivator activity
GO:0001046	0.85	core promoter sequence-specific DNA binding
GO:0003723	0.82	RNA binding
GO:0044822	0.80	poly(A) RNA binding
GO:0004872	0.61	receptor activity
GO:0001104	0.61	RNA polymerase II transcription cofactor activity
GO:0035257	0.60	nuclear hormone receptor binding
GO:0008134	0.60	transcription factor binding
GO:0046966	0.59	thyroid hormone 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:0051254	1.00	positive regulation of RNA metabolic process
GO:0010628	1.00	positive regulation of gene expression
GO:0009987	1.00	cellular process
GO:0008152	0.93	metabolic process
GO:0044238	0.92	primary metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0043170	0.92	macromolecule metabolic process
GO:0016070	0.91	RNA metabolic process
GO:0016071	0.87	mRNA metabolic process
GO:0010608	0.86	posttranscriptional regulation of gene expression
GO:0048255	0.85	mRNA stabilization
GO:0048026	0.85	positive regulation of mRNA splicing, via spliceosome
GO:0042753	0.85	positive regulation of circadian rhythm
GO:0000956	0.85	nuclear-transcribed mRNA catabolic process
GO:0000381	0.85	regulation of alternative mRNA splicing, via spliceosome
GO:0031326	0.77	regulation of cellular biosynthetic process
GO:0006355	0.76	regulation of transcription, DNA-templated
GO:0045893	0.75	positive regulation of transcription, DNA-templated
GO:0032774	0.65	RNA biosynthetic process
GO:0007165	0.62	signal transduction
GO:0006367	0.60	transcription initiation from RNA polymerase II promoter
GO:0045944	0.59	positive regulation of transcription from RNA polymerase II promoter
GO:0030518	0.59	intracellular steroid hormone receptor signaling pathway
GO:0030521	0.58	androgen receptor signaling pathway

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:0044428	1.00	nuclear part
GO:0005634	1.00	nucleus
GO:0005654	0.98	nucleoplasm
GO:0044451	0.94	nucleoplasm part
GO:0016607	0.93	nuclear speck
GO:0032991	0.87	macromolecular complex
GO:0043234	0.83	protein complex
GO:0035145	0.79	exon-exon junction complex
GO:0016592	0.62	mediator complex
GO:0044421	0.56	extracellular region part
GO:0070062	0.55	extracellular exosome

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	3ecqB	0.255	8.50	0.042	0.389	3.2.1.97	NA
2	0.060	2jfdA	0.140	7.99	0.038	0.207	2.3.1.85	NA
3	0.060	1bxrA	0.238	8.78	0.029	0.372	6.3.5.5	NA
4	0.060	1wz2A	0.234	9.19	0.035	0.379	6.1.1.4	NA
5	0.060	1n1hA	0.227	9.37	0.021	0.372	2.7.7.48	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.