D-I-TASSER A8MYZ0

D-I-TASSER results for A8MYZ0

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

Summary of the Protein

Uniprot ID: A8MYZ0
Protein Name: Inactive ubiquitin carboxyl-terminal hydrolase MINDY-4B
Gene Name: MINDY4B

Input Sequence in FASTA format

>A8MYZ0 (460 residues)
MDMEVLGQEQSSEQLDLEEISRKISFLDKWREIFSYHRLGTNNSTPQNHEGNHTSADENE
DGTGLSQPKGQGHLPSSGLCSIPNPSIISSKLGGFPISLAMATKLRQILFGNTVHVFSYN
WKKAYFRFHDPSSELAFTLEVGKGGARSIQMAVQGSIIKYLLFTRKGKDCNLGNLCEISK
KEQEQALAAALAGILWAAGAAQKATICLVTEDIYVASTPDYSVDNFTERLQLFEFLEKEA
AEKFIYDHLLCFRGEGSHGVILFLYSLIFSRTFERLQMDLDVTTTQLLQPNAGGFLCRQA
VLNMILTGRASPNVFNGCEEGKSQETLHGVLTRSDVGYLQWGKDASEDDRLSQVGSMLKT
PKLPIWLCNINGNYSILFCTNRQLLSDWKMERLFDLYFYSGQPSQKKLVRLTIDTHSHHW
ERDQQEEKHGPRRRFSPVEMAIRTKWSEATINWNGTVPFF

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	A8MYZ0-D1	1-312	312		MDMEVLGQEQSSEQLDLEEISRKISFLDKWREIFSYHRLGTNNSTPQNHEGNHTSADENEDGTGLSQPKGQGHLPSSGLCSIPNPSIISSKLGGFPISLAMATKLRQILFGNTVHVFSYNWKKAYFRFHDPSSELAFTLEVGKGGARSIQMAVQGSIIKYLLFTRKGKDCNLGNLCEISKKEQEQALAAALAGILWAAGAAQKATICLVTEDIYVASTPDYSVDNFTERLQLFEFLEKEAAEKFIYDHLLCFRGEGSHGVILFLYSLIFSRTFERLQMDLDVTTTQLLQPNAGGFLCRQAVLNMILTGRASP
2	A8MYZ0-D2	313-460	148		NVFNGCEEGKSQETLHGVLTRSDVGYLQWGKDASEDDRLSQVGSMLKTPKLPIWLCNINGNYSILFCTNRQLLSDWKMERLFDLYFYSGQPSQKKLVRLTIDTHSHHWERDQQEEKHGPRRRFSPVEMAIRTKWSEATINWNGTVPFF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.74

(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	6eojA	0.39	7.52	0.039	0.665	model1_6eojA.pdb.gz
2	2x2hA	0.38	7.52	0.058	0.646	model1_2x2hA.pdb.gz
3	3ecqB	0.38	7.47	0.058	0.646	model1_3ecqB.pdb.gz
4	7abhE1	0.38	7.08	0.066	0.609	model1_7abhE1.pdb.gz
5	2b3yA	0.37	7.36	0.027	0.630	model1_2b3yA.pdb.gz
6	7bwmA2	0.37	7.12	0.048	0.600	model1_7bwmA2.pdb.gz
7	5jcss	0.37	7.18	0.047	0.615	model1_5jcss.pdb.gz
8	5hy7A	0.37	7.52	0.059	0.643	model1_5hy7A.pdb.gz
9	6rc9A1	0.37	7.27	0.061	0.613	model1_6rc9A1.pdb.gz
10	3ei2A	0.37	7.38	0.079	0.624	model1_3ei2A.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:0035379	0.40	carbon dioxide transmembrane transporter activity
GO:0015254	0.40	glycerol channel activity
GO:0015250	0.40	water channel activity
GO:0008519	0.40	ammonium transmembrane transporter activity
GO:0043169	0.31	cation 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:0044763	1.00	single-organism cellular process
GO:0016043	1.00	cellular component organization
GO:0006810	1.00	transport
GO:0072488	0.67	ammonium transmembrane transport
GO:0009992	0.67	cellular water homeostasis

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:0044464	1.00	cell part
GO:0016020	0.94	membrane
GO:0044424	0.84	intracellular part
GO:0016021	0.73	integral component of membrane
GO:0098590	0.56	plasma membrane region
GO:0005886	0.56	plasma membrane
GO:0044446	0.54	intracellular organelle part
GO:0031090	0.54	organelle membrane

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	1mswD	0.309	7.74	0.023	0.533	2.7.7.6	NA
2	0.060	1ynnD	0.274	7.75	0.028	0.493	2.7.7.6	NA
3	0.060	1yq2A	0.341	7.83	0.039	0.611	3.2.1.23	184
4	0.060	2e9bA	0.330	7.23	0.036	0.548	3.2.1.41	307
5	0.060	3eqlD	0.276	7.22	0.050	0.446	2.7.7.6	298,301

	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	2c3oB	0.329	7.58	0.046	0.561	0.23	SF4	complex1.pdb.gz	119,120,142,143,144,149
2	0.01	2x2iC	0.378	7.46	0.060	0.641	0.25	QPS	complex2.pdb.gz	111,122,144,145,146
3	0.01	2jgdA	0.369	7.64	0.044	0.637	0.16	AMP	complex3.pdb.gz	154,299,337,338
4	0.01	2x2iD	0.379	7.35	0.048	0.635	0.20	QPS	complex4.pdb.gz	105,109,110,121,260,261,262
5	0.01	2x2jA	0.336	7.18	0.024	0.556	0.14	NOJ	complex5.pdb.gz	138,140,259
6	0.01	2vf7C	0.297	7.37	0.036	0.498	0.26	ADP	complex6.pdb.gz	146,147,149,150,151,152
7	0.01	2c3oA	0.362	7.49	0.039	0.613	0.27	SF4	complex7.pdb.gz	149,152,154
8	0.01	2vf7B	0.291	7.39	0.040	0.483	0.21	ADP	complex8.pdb.gz	259,261,262,263,264,265,266
9	0.01	2vf7A	0.270	7.28	0.021	0.452	0.13	ADP	complex9.pdb.gz	259,261,262,266
10	0.01	2vf7B	0.291	7.39	0.040	0.483	0.21	ADP	complex10.pdb.gz	148,149,150,151,152

	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, 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.