D-I-TASSER Q8IY47

D-I-TASSER results for Q8IY47

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

Summary of the Protein

Uniprot ID: Q8IY47
Protein Name: Kelch repeat and BTB domain-containing protein 2
Gene Name: KBTBD2

Input Sequence in FASTA format

>Q8IY47 (623 residues)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKSMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV

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 AttentionPotential. 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	Q8IY47-D1	1-128	128		MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMFMSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRCREYLIKKI
2	Q8IY47-D2	129-261	133		NAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDILSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPNDKSVVVQGLYKSMPKFFKPRL
3	Q8IY47-D3	262-363,524-623	202		GMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCSPPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTWFPKCVRAVVISNSLCVFMRETHLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPTYLFSTDGTEEFELDGEMVALPPV
4	Q8IY47-D4	364-420	57		TPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
5	Q8IY47-D5	421-523	103		WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIATNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.58

(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 AttentionPotential, 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	6sytA	0.41	7.28	0.048	0.628	model1_6sytA.pdb.gz
2	6ez8A	0.41	7.69	0.038	0.652	model1_6ez8A.pdb.gz
3	5fvmA	0.40	7.55	0.063	0.628	model1_5fvmA.pdb.gz
4	5yz0A	0.40	7.07	0.035	0.597	model1_5yz0A.pdb.gz
5	2qj0A	0.40	7.49	0.052	0.615	model1_2qj0A.pdb.gz
6	5u1sA	0.39	7.69	0.044	0.624	model1_5u1sA.pdb.gz
7	5x6oC	0.39	7.35	0.053	0.597	model1_5x6oC.pdb.gz
8	4b8bA	0.39	6.65	0.059	0.565	model1_4b8bA.pdb.gz
9	5h64A	0.39	7.49	0.063	0.608	model1_5h64A.pdb.gz
10	5i8iA	0.39	7.80	0.046	0.632	model1_5i8iA.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:0003824	0.96	catalytic activity
GO:0004842	0.94	ubiquitin-protein transferase activity

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:0009987	0.96	cellular process
GO:0008152	0.77	metabolic process
GO:0071704	0.76	organic substance metabolic process
GO:0044237	0.75	cellular metabolic process
GO:0044238	0.74	primary metabolic process
GO:0043170	0.74	macromolecule metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0019538	0.68	protein metabolic process
GO:0044267	0.67	cellular protein metabolic process
GO:0006464	0.66	cellular protein modification process
GO:0016567	0.65	protein ubiquitination
GO:0065007	0.52	biological regulation
GO:0042787	0.52	protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:0044699	0.51	single-organism process
GO:0051179	0.50	localization

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:0043234	0.95	protein complex
GO:0031463	0.94	Cul3-RING 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	1z0hB	0.198	7.85	0.038	0.326	3.4.24.69	470,473
2	0.060	1ofdA	0.317	7.63	0.032	0.506	1.4.7.1	88
3	0.060	1lrwA	0.339	6.30	0.063	0.462	1.1.99.8	574
4	0.060	1f1sA	0.357	8.41	0.048	0.616	4.2.2.1	NA
5	0.060	1i8qA	0.355	8.42	0.052	0.613	4.2.2.1	486

	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	1usxB	0.342	4.64	0.038	0.419	0.16	DAN	complex1.pdb.gz	308,309,474
2	0.01	1i7x0	0.357	6.97	0.055	0.531	0.19	III	complex2.pdb.gz	322,415,416
3	0.01	3tw6D	0.352	7.60	0.055	0.560	0.27	ADP	complex3.pdb.gz	322,436,461
4	0.01	2qf7A	0.326	8.22	0.041	0.539	0.24	SAP	complex4.pdb.gz	322,361,363
5	0.01	2qf7A	0.326	8.22	0.041	0.539	0.17	COA	complex5.pdb.gz	384,385,386,387,388
6	0.01	3tw6B	0.356	7.31	0.050	0.549	0.22	ADP	complex6.pdb.gz	271,323,433,459
7	0.01	1e8uA	0.340	4.65	0.045	0.417	0.19	SLB	complex7.pdb.gz	463,474,552
8	0.01	2d0vI	0.343	6.07	0.095	0.467	0.18	PQQ	complex8.pdb.gz	327,387,388,459
9	0.01	1lrwA	0.339	6.30	0.063	0.462	0.14	PQQ	complex9.pdb.gz	421,423,475,476
10	0.01	2d0vA	0.342	6.03	0.095	0.466	0.15	PQQ	complex10.pdb.gz	310,323,324,475

	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.