D-I-TASSER Q9HC52

D-I-TASSER results for Q9HC52

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

Summary of the Protein

Uniprot ID: Q9HC52
Protein Name: Chromobox protein homolog 8
Gene Name: CBX8

Input Sequence in FASTA format

>Q9HC52 (389 residues)
MELSAVGERVFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFEER
EREMELYGPKKRGPKPKTFLLKAQAKAKAKTYEFRSDSARGIRIPYPGRSPQDLASTSRA
REGLRNMGLSPPASSTSTSSTCRAEAPRDRDRDRDRDRERDRERERERERERERERERER
GTSRVDDKPSSPGDSSKKRGPKPRKELPDPSQRPLGEPSAGLGEYLKGRKLDDTPSGAGK
FPAGHSVIQLARRQDSDLVQCGVTSPSSAEATGKLAVDTFPARVIKHRAAFLEAKGQGAL
DPNGTRVRHGSGPPSSGGGLYRDMGAQGGRPSLIARIPVARILGDPEEESWSPSLTNLEK
VVVTDVTSNFLTVTIKESNTDQGFFKEKR

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	Q9HC52-D1	1-389	389		MELSAVGERVFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFEEREREMELYGPKKRGPKPKTFLLKAQAKAKAKTYEFRSDSARGIRIPYPGRSPQDLASTSRAREGLRNMGLSPPASSTSTSSTCRAEAPRDRDRDRDRDRERDRERERERERERERERERERGTSRVDDKPSSPGDSSKKRGPKPRKELPDPSQRPLGEPSAGLGEYLKGRKLDDTPSGAGKFPAGHSVIQLARRQDSDLVQCGVTSPSSAEATGKLAVDTFPARVIKHRAAFLEAKGQGALDPNGTRVRHGSGPPSSGGGLYRDMGAQGGRPSLIARIPVARILGDPEEESWSPSLTNLEKVVVTDVTSNFLTVTIKESNTDQGFFKEKR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4156

(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	5d06A	0.43	6.82	0.030	0.720	model1_5d06A.pdb.gz
2	4bxsV	0.43	7.26	0.077	0.751	model1_4bxsV.pdb.gz
3	7kveB	0.42	7.41	0.065	0.748	model1_7kveB.pdb.gz
4	6riwA	0.42	7.01	0.065	0.710	model1_6riwA.pdb.gz
5	4ktpA	0.42	6.92	0.042	0.702	model1_4ktpA.pdb.gz
6	4j5tA	0.42	6.85	0.057	0.692	model1_4j5tA.pdb.gz
7	5nz7A	0.41	7.24	0.024	0.728	model1_5nz7A.pdb.gz
8	3wiqA	0.41	7.01	0.035	0.702	model1_3wiqA.pdb.gz
9	6hq6A	0.41	7.05	0.031	0.699	model1_6hq6A.pdb.gz
10	2jg0A	0.41	6.85	0.042	0.679	model1_2jg0A.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:0042393	0.48	histone binding
GO:1901363	0.46	heterocyclic compound binding
GO:0097159	0.46	organic cyclic compound binding
GO:0035064	0.46	methylated histone binding
GO:0003676	0.42	nucleic acid binding
GO:0003824	0.37	catalytic activity
GO:0044877	0.30	macromolecular complex 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:0050794	0.87	regulation of cellular process
GO:0009987	0.83	cellular process
GO:0019222	0.82	regulation of metabolic process
GO:0080090	0.81	regulation of primary metabolic process
GO:0060255	0.81	regulation of macromolecule metabolic process
GO:0031323	0.81	regulation of cellular metabolic process
GO:0019219	0.78	regulation of nucleobase-containing compound metabolic process
GO:0010556	0.78	regulation of macromolecule biosynthetic process
GO:2001141	0.68	regulation of RNA biosynthetic process
GO:0048523	0.68	negative regulation of cellular process
GO:0010468	0.68	regulation of gene expression
GO:0006355	0.67	regulation of transcription, DNA-templated
GO:0009892	0.65	negative regulation of metabolic process
GO:0031327	0.64	negative regulation of cellular biosynthetic process
GO:0010629	0.64	negative regulation of gene expression
GO:0045892	0.63	negative regulation of transcription, DNA-templated
GO:0071704	0.58	organic substance metabolic process
GO:0044238	0.58	primary metabolic process
GO:0044237	0.57	cellular metabolic process
GO:0043170	0.57	macromolecule metabolic process
GO:0044260	0.56	cellular macromolecule metabolic process
GO:0044699	0.51	single-organism process
GO:0006357	0.50	regulation of transcription from RNA polymerase II promoter

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:0043229	0.94	intracellular organelle
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0005634	0.89	nucleus
GO:0044446	0.83	intracellular organelle part
GO:0032991	0.80	macromolecular complex
GO:0044428	0.76	nuclear part
GO:0043234	0.66	protein complex
GO:1990234	0.53	transferase complex
GO:0000785	0.52	chromatin
GO:0000151	0.50	ubiquitin ligase 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	1dl2A	0.405	6.90	0.040	0.679	3.2.1.113	NA
2	0.060	1lrwA	0.363	6.64	0.071	0.589	1.1.99.8	301
3	0.060	2vn4A	0.383	6.86	0.043	0.640	3.2.1.3	NA
4	0.060	1fmiA	0.374	7.17	0.052	0.655	3.2.1.113	NA
5	0.060	1g72A	0.372	7.10	0.048	0.632	1.1.99.8	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	0.01	1a9xA	0.364	7.46	0.049	0.653	0.12	ADP	complex1.pdb.gz	35,58,59
2	0.01	1a9x1	0.364	7.46	0.049	0.653	0.28	III	complex2.pdb.gz	21,24,26
3	0.01	1a9x3	0.383	7.34	0.046	0.671	0.13	III	complex3.pdb.gz	50,51,52
4	0.01	1a9xG	0.382	7.32	0.057	0.666	0.23	ADP	complex4.pdb.gz	39,40,95
5	0.01	1m6vC	0.382	7.37	0.051	0.673	0.20	ADP	complex5.pdb.gz	15,16,17,29,32,89,90
6	0.01	2ww0H	0.397	7.08	0.060	0.689	0.15	SWA	complex6.pdb.gz	21,28,51
7	0.01	1ce8G	0.383	7.34	0.059	0.666	0.20	IMP	complex7.pdb.gz	34,44,45,49
8	0.01	1ce8A	0.383	7.27	0.059	0.661	0.21	IMP	complex8.pdb.gz	7,31,32,93,94,95
9	0.01	2jjbB	0.407	6.88	0.048	0.671	0.12	UUU	complex9.pdb.gz	23,26,28,64,65,371
10	0.01	1t36A	0.380	7.24	0.062	0.658	0.24	U	complex10.pdb.gz	20,59,60,86

	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.