D-I-TASSER Q70EL4

D-I-TASSER results for Q70EL4

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

Summary of the Protein

Uniprot ID: Q70EL4
Protein Name: Ubiquitin carboxyl-terminal hydrolase 43
Gene Name: USP43

Input Sequence in FASTA format

>Q70EL4 (1123 residues)
MDLGPGDAAGGGPLAPRPRRRRSLRRLFSRFLLALGSRSRPGDSPPRPQPGHCDGDGEGG
FACAPGPVPAAPGSPGEERPPGPQPQLQLPAGDGARPPGAQGLKNHGNTCFMNAVVQCLS
NTDLLAEFLALGRYRAAPGRAEVTEQLAALVRALWTREYTPQLSAEFKNAVSKYGSQFQG
NSQHDALEFLLWLLDRVHEDLEGSSRGPVSEKLPPEATKTSENCLSPSAQLPLGQSFVQS
HFQAQYRSSLTCPHCLKQSNTFDPFLCVSLPIPLRQTRFLSVTLVFPSKSQRFLRVGLAV
PILSTVAALRKMVAEEGGVPADEVILVELYPSGFQRSFFDEEDLNTIAEGDNVYAFQVPP
SPSQGTLSAHPLGLSASPRLAAREGQRFSLSLHSESKVLILFCNLVGSGQQASRFGPPFL
IREDRAVSWAQLQQSILSKVRHLMKSEAPVQNLGSLFSIRVVGLSVACSYLSPKDSRPLC
HWAVDRVLHLRRPGGPPHVKLAVEWDSSVKERLFGSLQEERAQDADSVWQQQQAHQQHSC
TLDECFQFYTKEEQLAQDDAWKCPHCQVLQQGMVKLSLWTLPDILIIHLKRFCQVGERRN
KLSTLVKFPLSGLNMAPHVAQRSTSPEAGLGPWPSWKQPDCLPTSYPLDFLYDLYAVCNH
HGNLQGGHYTAYCRNSLDGQWYSYDDSTVEPLREDEVNTRGAYILFYQKRNSIPPWSASS
SMRGSTSSSLSDHWLLRLGSHAGSTRGSLLSWSSAPCPSLPQVPDSPIFTNSLCNQEKGG
LEPRRLVRGVKGRSISMKAPTTSRAKQGPFKTMPLRWSFGSKEKPPGASVELVEYLESRR
RPRSTSQSIVSLLTGTAGEDEKSASPRSNVALPANSEDGGRAIERGPAGVPCPSAQPNHC
LAPGNSDGPNTARKLKENAGQDIKLPRKFDLPLTVMPSVEHEKPARPEGQKAMNWKESFQ
MGSKSSPPSPYMGFSGNSKDSRRGTSELDRPLQGTLTLLRSVFRKKENRRNERAEVSPQV
PPVSLVSGGLSPAMDGQAPGSPPALRIPEGLARGLGSRLERDVWSAPSSLRLPRKASRAP
RGSALGMSQRTVPGEQASYGTFQRVKYHTLSLGRKKTLPESSF

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	Q70EL4-D1	1-58	58		MDLGPGDAAGGGPLAPRPRRRRSLRRLFSRFLLALGSRSRPGDSPPRPQPGHCDGDGE
2	Q70EL4-D2	59-101,274-324,797-819,850-874	142		GGFACAPGPVPAAPGSPGEERPPGPQPQLQLPAGDGARPPGAQLRQTRFLSVTLVFPSKSQRFLRVGLAVPILSTVAALRKMVAEEGGVPADEVMKAPTTSRAKQGPFKTMPLRWSFVSLLTGTAGEDEKSASPRSNVALPA
3	Q70EL4-D3	102-273,875-883	181		GLKNHGNTCFMNAVVQCLSNTDLLAEFLALGRYRAAPGRAEVTEQLAALVRALWTREYTPQLSAEFKNAVSKYGSQFQGNSQHDALEFLLWLLDRVHEDLEGSSRGPVSEKLPPEATKTSENCLSPSAQLPLGQSFVQSHFQAQYRSSLTCPHCLKQSNTFDPFLCVSLPIPNSEDGGRAI
4	Q70EL4-D4	325-390,820-849	96		ILVELYPSGFQRSFFDEEDLNTIAEGDNVYAFQVPPSPSQGTLSAHPLGLSASPRLAAREGQRFSLGSKEKPPGASVELVEYLESRRRPRSTSQSI
5	Q70EL4-D5	391-796,884-1123	646		SLHSESKVLILFCNLVGSGQQASRFGPPFLIREDRAVSWAQLQQSILSKVRHLMKSEAPVQNLGSLFSIRVVGLSVACSYLSPKDSRPLCHWAVDRVLHLRRPGGPPHVKLAVEWDSSVKERLFGSLQEERAQDADSVWQQQQAHQQHSCTLDECFQFYTKEEQLAQDDAWKCPHCQVLQQGMVKLSLWTLPDILIIHLKRFCQVGERRNKLSTLVKFPLSGLNMAPHVAQRSTSPEAGLGPWPSWKQPDCLPTSYPLDFLYDLYAVCNHHGNLQGGHYTAYCRNSLDGQWYSYDDSTVEPLREDEVNTRGAYILFYQKRNSIPPWSASSSMRGSTSSSLSDHWLLRLGSHAGSTRGSLLSWSSAPCPSLPQVPDSPIFTNSLCNQEKGGLEPRRLVRGVKGRSISERGPAGVPCPSAQPNHCLAPGNSDGPNTARKLKENAGQDIKLPRKFDLPLTVMPSVEHEKPARPEGQKAMNWKESFQMGSKSSPPSPYMGFSGNSKDSRRGTSELDRPLQGTLTLLRSVFRKKENRRNERAEVSPQVPPVSLVSGGLSPAMDGQAPGSPPALRIPEGLARGLGSRLERDVWSAPSSLRLPRKASRAPRGSALGMSQRTVPGEQASYGTFQRVKYHTLSLGRKKTLPESSF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.42

(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	6yejA	0.28	9.51	0.039	0.446	model1_6yejA.pdb.gz
2	2vz8B	0.28	9.66	0.045	0.446	model1_2vz8B.pdb.gz
3	7cpxA	0.27	9.44	0.033	0.420	model1_7cpxA.pdb.gz
4	5a22A	0.27	9.36	0.027	0.415	model1_5a22A.pdb.gz
5	4u48A	0.27	9.91	0.031	0.435	model1_4u48A.pdb.gz
6	5anbK	0.26	8.88	0.042	0.389	model1_5anbK.pdb.gz
7	6l7eA	0.26	9.06	0.039	0.395	model1_6l7eA.pdb.gz
8	7b54X	0.26	8.75	0.019	0.381	model1_7b54X.pdb.gz
9	6eqoA	0.26	9.38	0.031	0.407	model1_6eqoA.pdb.gz
10	3hmjG	0.26	10.04	0.029	0.430	model1_3hmjG.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	0.97	catalytic activity
GO:0070011	0.96	peptidase activity, acting on L-amino acid peptides
GO:0008234	0.95	cysteine-type peptidase activity
GO:0019783	0.92	ubiquitin-like protein-specific protease activity
GO:0004843	0.83	thiol-dependent ubiquitin-specific protease 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:0008152	0.91	metabolic process
GO:0044238	0.90	primary metabolic process
GO:0044237	0.90	cellular metabolic process
GO:0043170	0.90	macromolecule metabolic process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0019538	0.84	protein metabolic process
GO:0006508	0.82	proteolysis
GO:0006464	0.74	cellular protein modification process
GO:0070647	0.73	protein modification by small protein conjugation or removal
GO:0016579	0.70	protein deubiquitination
GO:0065007	0.64	biological regulation
GO:0050789	0.63	regulation of biological process
GO:0050794	0.62	regulation of cellular process

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:0043226	0.81	organelle
GO:0043229	0.80	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0005634	0.66	nucleus

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	3eqlM	0.230	9.81	0.047	0.372	2.7.7.6	NA
2	0.060	1n1hA	0.239	9.62	0.039	0.381	2.7.7.48	NA
3	0.060	1q16A	0.217	10.07	0.037	0.362	1.7.99.4	63
4	0.060	1vbgA	0.221	8.71	0.053	0.331	2.7.9.1	NA
5	0.060	2pffA	0.240	9.43	0.017	0.373	2.3.1.41 2.3.1.86	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	2yu93	0.034	3.84	0.018	0.037	0.26	III	complex1.pdb.gz	92,93,94,95,96,877
2	0.01	2nm1A	0.121	7.52	0.033	0.167	0.19	III	complex2.pdb.gz	99,101,102,604,605
3	0.01	2v469	0.042	4.35	0.063	0.048	0.27	III	complex3.pdb.gz	117,119,120,121,122
4	0.01	1f31A	0.247	9.57	0.035	0.395	0.27	UUU	complex4.pdb.gz	106,107,180,605
5	0.01	2np0A	0.246	9.48	0.029	0.387	0.19	III	complex5.pdb.gz	101,102,104,107,112
6	0.01	3rzdB	0.194	9.62	0.028	0.305	0.13	QNA	complex6.pdb.gz	662,663,669
7	0.01	1i1eA	0.247	9.68	0.032	0.395	0.33	DM2	complex7.pdb.gz	107,108,180,181
8	0.01	2yu95	0.065	5.45	0.037	0.078	0.20	III	complex8.pdb.gz	73,577,578,579,580,585,611
9	0.01	1l0l5	0.089	5.88	0.036	0.111	0.31	III	complex9.pdb.gz	99,100,107,112,113,114,116
10	0.01	1hnz4	0.037	3.98	0.038	0.042	0.30	III	complex10.pdb.gz	98,684,685

	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.