D-I-TASSER Q70EK8

D-I-TASSER results for Q70EK8

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

Summary of the Protein

Uniprot ID: Q70EK8
Protein Name: Inactive ubiquitin carboxyl-terminal hydrolase 53
Gene Name: USP53

Input Sequence in FASTA format

>Q70EK8 (1073 residues)
MAWVKFLRKPGGNLGKVYQPGSMLSLAPTKGLLNEPGQNSCFLNSAVQVLWQLDIFRRSL
RVLTGHVCQGDACIFCALKTIFAQFQHSREKALPSDNIRHALAESFKDEQRFQLGLMDDA
AECFENMLERIHFHIVPSRDADMCTSKSCITHQKFAMTLYEQCVCRSCGASSDPLPFTEF
VRYISTTALCNEVERMLERHERFKPEMFAELLQAANTTDDYRKCPSNCGQKIKIRRVLMN
CPEIVTIGLVWDSEHSDLTEAVVRNLATHLYLPGLFYRVTDENAKNSELNLVGMICYTSQ
HYCAFAFHTKSSKWVFFDDANVKEIGTRWKDVVSKCIRCHFQPLLLFYANPDGTAVSTED
ALRQVISWSHYKSVAENMGCEKPVIHKSDNLKENGFGDQAKQRENQKFPTDNISSSNRSH
SHTGVGKGPAKLSHIDQREKIKDISRECALKAIEQKNLLSSQRKDLEKGQRKDLGRHRDL
VDEDLSHFQSGSPPAPNGFKQHGNPHLYHSQGKGSYKHDRVVPQSRASAQIISSSKSQIL
APGEKITGKVKSDNGTGYDTDSSQDSRDRGNSCDSSSKSRNRGWKPMRETLNVDSIFSES
EKRQHSPRHKPNISNKPKSSKDPSFSNWPKENPKQKGLMTIYEDEMKQEIGSRSSLESNG
KGAEKNKGLVEGKVHGDNWQMQRTESGYESSDHISNGSTNLDSPVIDGNGTVMDISGVKE
TVCFSDQITTSNLNKERGDCTSLQSQHHLEGFRKELRNLEAGYKSHEFHPESHLQIKNHL
IKRSHVHEDNGKLFPSSSLQIPKDHNAREHIHQSDEQKLEKPNECKFSEWLNIENSERTG
LPFHVDNSASGKRVNSNEPSSLWSSHLRTVGLKPETAPLIQQQNIMDQCYFENSLSTECI
IRSASRSDGCQMPKLFCQNLPPPLPPKKYAITSVPQSEKSESTPDVKLTEVFKATSHLPK
HSLSTASEPSLEVSTHMNDERHKETFQVRECFGNTPNCPSSSSTNDFQANSGAIDAFCQP
ELDSISTCPNETVSLTTYFSVDSCMTDTYRLKYHQRPKLSFPESSGFCNNSLS

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	Q70EK8-D1	1-1073	1073		MAWVKFLRKPGGNLGKVYQPGSMLSLAPTKGLLNEPGQNSCFLNSAVQVLWQLDIFRRSLRVLTGHVCQGDACIFCALKTIFAQFQHSREKALPSDNIRHALAESFKDEQRFQLGLMDDAAECFENMLERIHFHIVPSRDADMCTSKSCITHQKFAMTLYEQCVCRSCGASSDPLPFTEFVRYISTTALCNEVERMLERHERFKPEMFAELLQAANTTDDYRKCPSNCGQKIKIRRVLMNCPEIVTIGLVWDSEHSDLTEAVVRNLATHLYLPGLFYRVTDENAKNSELNLVGMICYTSQHYCAFAFHTKSSKWVFFDDANVKEIGTRWKDVVSKCIRCHFQPLLLFYANPDGTAVSTEDALRQVISWSHYKSVAENMGCEKPVIHKSDNLKENGFGDQAKQRENQKFPTDNISSSNRSHSHTGVGKGPAKLSHIDQREKIKDISRECALKAIEQKNLLSSQRKDLEKGQRKDLGRHRDLVDEDLSHFQSGSPPAPNGFKQHGNPHLYHSQGKGSYKHDRVVPQSRASAQIISSSKSQILAPGEKITGKVKSDNGTGYDTDSSQDSRDRGNSCDSSSKSRNRGWKPMRETLNVDSIFSESEKRQHSPRHKPNISNKPKSSKDPSFSNWPKENPKQKGLMTIYEDEMKQEIGSRSSLESNGKGAEKNKGLVEGKVHGDNWQMQRTESGYESSDHISNGSTNLDSPVIDGNGTVMDISGVKETVCFSDQITTSNLNKERGDCTSLQSQHHLEGFRKELRNLEAGYKSHEFHPESHLQIKNHLIKRSHVHEDNGKLFPSSSLQIPKDHNAREHIHQSDEQKLEKPNECKFSEWLNIENSERTGLPFHVDNSASGKRVNSNEPSSLWSSHLRTVGLKPETAPLIQQQNIMDQCYFENSLSTECIIRSASRSDGCQMPKLFCQNLPPPLPPKKYAITSVPQSEKSESTPDVKLTEVFKATSHLPKHSLSTASEPSLEVSTHMNDERHKETFQVRECFGNTPNCPSSSSTNDFQANSGAIDAFCQPELDSISTCPNETVSLTTYFSVDSCMTDTYRLKYHQRPKLSFPESSGFCNNSLS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4092

(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	2pffB	0.93	2.43	0.062	0.964	model1_2pffB.pdb.gz
2	3hmjG	0.90	2.75	0.068	0.945	model1_3hmjG.pdb.gz
3	2uvcG	0.89	3.18	0.055	0.955	model1_2uvcG.pdb.gz
4	6u5vB	0.89	3.03	0.057	0.951	model1_6u5vB.pdb.gz
5	7dxjA	0.36	9.54	0.033	0.574	model1_7dxjA.pdb.gz
6	5x6oC	0.34	9.44	0.033	0.544	model1_5x6oC.pdb.gz
7	6z2wE	0.33	9.47	0.029	0.536	model1_6z2wE.pdb.gz
8	6edoA	0.32	9.59	0.038	0.528	model1_6edoA.pdb.gz
9	5a22A	0.32	9.56	0.030	0.503	model1_5a22A.pdb.gz
10	5xjcQ	0.31	8.94	0.039	0.480	model1_5xjcQ.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	0.80	catalytic activity
GO:0016787	0.74	hydrolase activity
GO:0101005	0.69	ubiquitinyl hydrolase 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	0.98	cellular process
GO:0065007	0.93	biological regulation
GO:0044699	0.88	single-organism process
GO:0044763	0.83	single-organism cellular process
GO:0032501	0.78	multicellular organismal process
GO:0008219	0.74	cell death
GO:0012501	0.73	programmed cell death
GO:0008152	0.72	metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.68	cellular metabolic process
GO:0043170	0.68	macromolecule metabolic process
GO:0044260	0.65	cellular macromolecule metabolic process
GO:0019538	0.64	protein metabolic process
GO:0006508	0.60	proteolysis
GO:0050789	0.59	regulation of biological process
GO:0044267	0.59	cellular protein metabolic process
GO:0043412	0.59	macromolecule modification
GO:0050794	0.58	regulation of cellular process
GO:0006464	0.58	cellular protein modification process
GO:0016579	0.56	protein deubiquitination
GO:0050896	0.54	response to stimulus

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:0030054	0.67	cell junction
GO:0005911	0.66	cell-cell junction
GO:0032991	0.51	macromolecular 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	3ffzA	0.259	8.95	0.049	0.395	3.4.24.69	NA
2	0.060	2np0A	0.255	9.71	0.044	0.418	3.4.24.69	NA
3	0.060	2r7oA	0.230	9.32	0.039	0.358	2.7.7.48	125,131
4	0.060	1q2lA	0.236	9.12	0.053	0.367	3.4.24.55	NA
5	0.060	2qf7B	0.239	8.96	0.047	0.364	6.4.1.1	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	0.04	2uv8G	0.896	2.76	0.069	0.945	0.11	FMN	complex1.pdb.gz	31,32,115,119
2	0.03	2vkzG	0.897	2.75	0.068	0.945	0.10	FMN	complex2.pdb.gz	115,118,119
3	0.01	3cmvB	0.249	9.65	0.034	0.406	0.13	ANP	complex3.pdb.gz	31,32,33,34
4	0.01	2vz9A	0.333	9.02	0.038	0.512	0.10	NAP	complex4.pdb.gz	13,32,37
5	0.01	3bg5C	0.241	9.06	0.037	0.372	0.13	ATP	complex5.pdb.gz	23,39,40,42,43,116,118
6	0.01	3cmvA	0.250	9.91	0.031	0.417	0.19	ANP	complex6.pdb.gz	37,38,39,40,99
7	0.01	3ho8C	0.236	8.89	0.045	0.359	0.14	BTI	complex7.pdb.gz	32,35,40
8	0.01	2vz9B	0.299	7.78	0.031	0.419	0.10	NAP	complex8.pdb.gz	35,36,114
9	0.01	1xmsA	0.110	6.40	0.057	0.142	0.13	ANP	complex9.pdb.gz	31,32,33,34

	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.