D-I-TASSER Q04206

D-I-TASSER results for Q04206

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

Summary of the Protein

Uniprot ID: Q04206
Protein Name: Transcription factor p65
Gene Name: RELA

Input Sequence in FASTA format

>Q04206 (551 residues)
MDELFPLIFPAEPAQASGPYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPT
IKINGYTGPGTVRISLVTKDPPHRPHPHELVGKDCRDGFYEAELCPDRCIHSFQNLGIQC
VKKRDLEQAISQRIQTNNNPFQVPIEEQRGDYDLNAVRLCFQVTVRDPSGRPLRLPPVLS
HPIFDNRAPNTAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFS
QADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEE
KRKRTYETFKSIMKKSPFSGPTDPRPPPRRIAVPSRSSASVPKPAPQPYPFTSSLSTINY
DEFPTMVFPSGQISQASALAPAPPQVLPQAPAPAPAPAMVSALAQAPAPVPVLAPGPPQA
VAPPAPKPTQAGEGTLSEALLQLQFDDEDLGALLGNSTDPAVFTDLASVDNSEFQQLLNQ
GIPVAPHTTEPMLMEYPEAITRLVTGAQRPPDPAPAPLGAPGLPNGLLSGDEDFSSIADM
DFSALLSQISS

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	Q04206-D1	1-187	187		MDELFPLIFPAEPAQASGPYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVTKDPPHRPHPHELVGKDCRDGFYEAELCPDRCIHSFQNLGIQCVKKRDLEQAISQRIQTNNNPFQVPIEEQRGDYDLNAVRLCFQVTVRDPSGRPLRLPPVLSHPIFDNR
2	Q04206-D2	188-551	364		APNTAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRKRTYETFKSIMKKSPFSGPTDPRPPPRRIAVPSRSSASVPKPAPQPYPFTSSLSTINYDEFPTMVFPSGQISQASALAPAPPQVLPQAPAPAPAPAMVSALAQAPAPVPVLAPGPPQAVAPPAPKPTQAGEGTLSEALLQLQFDDEDLGALLGNSTDPAVFTDLASVDNSEFQQLLNQGIPVAPHTTEPMLMEYPEAITRLVTGAQRPPDPAPAPLGAPGLPNGLLSGDEDFSSIADMDFSALLSQISS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5

(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	2o61A	0.75	3.52	0.607	0.855	model1_2o61A.pdb.gz
2	3do7A	0.48	2.66	0.509	0.524	model1_3do7A.pdb.gz
3	2o61B	0.47	2.25	0.457	0.501	model1_2o61B.pdb.gz
4	1gjiA	0.45	2.54	0.651	0.494	model1_1gjiA.pdb.gz
5	1bvoA	0.30	1.25	0.479	0.307	model1_1bvoA.pdb.gz
6	1xtkA	0.18	7.54	0.058	0.299	model1_1xtkA.pdb.gz
7	4bn2A	0.17	6.16	0.013	0.245	model1_4bn2A.pdb.gz
8	1imhC2	0.17	1.54	0.247	0.176	model1_1imhC2.pdb.gz
9	4asmB	0.16	6.49	0.017	0.236	model1_4asmB.pdb.gz
10	2dllA	0.15	3.83	0.097	0.181	model1_2dllA.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:0003700	0.96	transcription factor activity, sequence-specific DNA binding
GO:0003677	0.96	DNA binding
GO:0000975	0.93	regulatory region DNA binding
GO:0000981	0.92	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0044212	0.90	transcription regulatory region DNA binding
GO:0000976	0.89	transcription regulatory region sequence-specific DNA binding
GO:0000977	0.88	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003682	0.87	chromatin 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:0048518	0.99	positive regulation of biological process
GO:0050794	0.98	regulation of cellular process
GO:0048522	0.97	positive regulation of cellular process
GO:0048523	0.95	negative regulation of cellular process
GO:0080090	0.94	regulation of primary metabolic process
GO:0060255	0.94	regulation of macromolecule metabolic process
GO:0031323	0.94	regulation of cellular metabolic process
GO:0031325	0.93	positive regulation of cellular metabolic process
GO:0010628	0.93	positive regulation of gene expression
GO:0006355	0.93	regulation of transcription, DNA-templated
GO:0045893	0.92	positive regulation of transcription, DNA-templated
GO:0006357	0.92	regulation of transcription from RNA polymerase II promoter
GO:0006950	0.89	response to stress
GO:0000122	0.89	negative regulation of transcription from RNA polymerase II promoter
GO:0045944	0.88	positive regulation of transcription from RNA polymerase II promoter
GO:0007165	0.88	signal transduction
GO:0042221	0.87	response to chemical
GO:0002376	0.87	immune system process
GO:0035556	0.86	intracellular signal transduction
GO:0034097	0.86	response to cytokine
GO:0006952	0.85	defense response
GO:0006954	0.84	inflammatory response
GO:0045087	0.82	innate immune response
GO:0038061	0.82	NIK/NF-kappaB signaling
GO:0007249	0.79	I-kappaB kinase/NF-kappaB signaling

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:0044424	1.00	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0005829	0.86	cytosol
GO:0032991	0.85	macromolecular complex
GO:0043234	0.84	protein complex
GO:0033256	0.80	I-kappaB/NF-kappaB complex

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	1ea0A	0.306	7.93	0.039	0.523	1.4.1.13	400
2	0.060	1z0hB	0.178	7.71	0.013	0.294	3.4.24.69	155
3	0.060	2vdcA	0.333	8.01	0.037	0.570	1.4.1.13	NA
4	0.060	2np0A	0.321	8.59	0.038	0.575	3.4.24.69	NA
5	0.060	1jkyA	0.313	7.47	0.047	0.506	3.4.24.83	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	0.53	1le5A	0.459	2.39	0.886	0.494	0.86	QNA	complex1.pdb.gz	35,36,39
2	0.43	3gutE	0.465	2.25	0.971	0.495	1.80	QNA	complex2.pdb.gz	32,33,35,41,42,43,44,45
3	0.38	1leiA	0.452	2.53	0.856	0.490	1.69	UUU	complex3.pdb.gz	33,35,42,43,44,45,56
4	0.34	3do7A	0.483	2.66	0.509	0.524	1.36	QNA	complex4.pdb.gz	33,35,41,45
5	0.22	3gutB	0.473	1.93	0.456	0.497	1.56	QNA	complex5.pdb.gz	33,35,43,44,187
6	0.12	1ramA	0.452	2.56	0.893	0.492	1.16	QNA	complex6.pdb.gz	33,35,43,44
7	0.07	1imhD	0.379	3.78	0.165	0.447	1.21	QNA	complex7.pdb.gz	35,39,42
8	0.06	3gutF	0.473	1.94	0.453	0.497	1.09	QNA	complex8.pdb.gz	33,35,43,44,187
9	0.06	3gutD	0.463	2.27	0.432	0.495	0.88	QNA	complex9.pdb.gz	36,38,39,43,120,123,187
10	0.04	1imhC	0.390	3.22	0.184	0.441	0.85	QNA	complex10.pdb.gz	33,40,42,43,44,152

	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.