D-I-TASSER Q4JDL3

D-I-TASSER results for Q4JDL3

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

Summary of the Protein

Uniprot ID: Q4JDL3
Protein Name: Tyrosine-protein phosphatase non-receptor type 20
Gene Name: PTPN20

Input Sequence in FASTA format

>Q4JDL3 (420 residues)
MSSPRDFRAEPVNDYEGNDSEAEDLNFRETLPSSSQENTPRSKVFENKVNSEKVKLSLRN
FPHNDYEDVFEEPSESGSDPSMWTARGPFRRDRWSSEDEEAAGPSQALSPLLSDTRKIVS
EGELDQLAQIRPLIFNFHEQTAIKDCLKILEEKTAAYDIMQEFMALELKNLPGEFNSGNQ
PSNREKNRYRDILPYDSTRVPLGKSKDYINASYIRIVNCGEEYFYIATQGPLLSTIDDFW
QMVLENNSNVIAMITREIEGGIIKCYHYWPISLKKPLELKHFRVFLENYQILQYFIIRMF
QVVEKSTGTSHSVKQLQFTKWPDHGTPASADSFIKYIRYARKSHLTGPMVVHCSAGIGRT
GVFLCVDVVFCAIVKNCSFNIMDIVAQMREQRSGMVQTKEQYHFCYDIVLEVLRKLLTLD

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	Q4JDL3-D1	1-420	420		MSSPRDFRAEPVNDYEGNDSEAEDLNFRETLPSSSQENTPRSKVFENKVNSEKVKLSLRNFPHNDYEDVFEEPSESGSDPSMWTARGPFRRDRWSSEDEEAAGPSQALSPLLSDTRKIVSEGELDQLAQIRPLIFNFHEQTAIKDCLKILEEKTAAYDIMQEFMALELKNLPGEFNSGNQPSNREKNRYRDILPYDSTRVPLGKSKDYINASYIRIVNCGEEYFYIATQGPLLSTIDDFWQMVLENNSNVIAMITREIEGGIIKCYHYWPISLKKPLELKHFRVFLENYQILQYFIIRMFQVVEKSTGTSHSVKQLQFTKWPDHGTPASADSFIKYIRYARKSHLTGPMVVHCSAGIGRTGVFLCVDVVFCAIVKNCSFNIMDIVAQMREQRSGMVQTKEQYHFCYDIVLEVLRKLLTLD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6784

(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	6md7A	0.80	3.14	0.288	0.883	model1_6md7A.pdb.gz
2	2b3oA	0.80	3.24	0.267	0.888	model1_2b3oA.pdb.gz
3	1wchA	0.67	1.14	0.397	0.681	model1_1wchA.pdb.gz
4	2i1yB	0.64	1.60	0.337	0.662	model1_2i1yB.pdb.gz
5	2pi7A	0.64	2.05	0.344	0.671	model1_2pi7A.pdb.gz
6	2hc1A	0.63	2.12	0.357	0.671	model1_2hc1A.pdb.gz
7	1yguB	0.63	2.03	0.325	0.667	model1_1yguB.pdb.gz
8	2nlkA	0.63	1.86	0.350	0.659	model1_2nlkA.pdb.gz
9	2f6fA	0.63	1.89	0.319	0.664	model1_2f6fA.pdb.gz
10	2pa5A	0.63	2.00	0.353	0.664	model1_2pa5A.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:0016791	0.98	phosphatase activity
GO:0004721	0.97	phosphoprotein phosphatase activity
GO:0004725	0.96	protein tyrosine phosphatase activity
GO:0004871	0.75	signal transducer activity
GO:0005001	0.73	transmembrane receptor protein tyrosine phosphatase activity
GO:0019899	0.50	enzyme 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:0009987	0.98	cellular process
GO:0006796	0.97	phosphate-containing compound metabolic process
GO:0006464	0.97	cellular protein modification process
GO:0006470	0.96	protein dephosphorylation
GO:0035335	0.93	peptidyl-tyrosine dephosphorylation
GO:0044699	0.91	single-organism process
GO:0065007	0.88	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0050794	0.86	regulation of cellular process
GO:0044763	0.77	single-organism cellular process
GO:0032502	0.75	developmental process
GO:0044767	0.71	single-organism developmental process
GO:0048856	0.65	anatomical structure development
GO:0048519	0.65	negative regulation of biological process
GO:0007165	0.65	signal transduction
GO:0048523	0.64	negative regulation of cellular process
GO:0048583	0.60	regulation of response to stimulus
GO:0023051	0.59	regulation of signaling
GO:0010646	0.59	regulation of cell communication
GO:0009966	0.58	regulation of signal transduction
GO:0006928	0.58	movement of cell or subcellular component
GO:0051239	0.56	regulation of multicellular organismal process
GO:0032879	0.56	regulation of localization
GO:0080090	0.55	regulation of primary metabolic process
GO:0050896	0.55	response to stimulus
GO:0031323	0.55	regulation of cellular metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0048518	0.53	positive regulation of biological process
GO:0023057	0.53	negative regulation of signaling
GO:0010648	0.53	negative regulation of cell communication
GO:0007411	0.53	axon guidance
GO:0009968	0.52	negative regulation of signal transduction
GO:0051241	0.51	negative regulation of multicellular organismal process
GO:0032501	0.51	multicellular organismal process
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0007166	0.51	cell surface receptor signaling pathway
GO:0050793	0.50	regulation of developmental process
GO:0042127	0.50	regulation of cell proliferation
GO:0031399	0.50	regulation of protein modification process
GO:0019220	0.50	regulation of phosphate metabolic 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:0044464	1.00	cell part
GO:0044424	0.93	intracellular part
GO:0043226	0.83	organelle
GO:0016020	0.82	membrane
GO:0044425	0.76	membrane part
GO:0044444	0.74	cytoplasmic part
GO:0043227	0.74	membrane-bounded organelle
GO:0043229	0.70	intracellular organelle
GO:0005886	0.64	plasma membrane
GO:0005737	0.62	cytoplasm
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0044459	0.56	plasma membrane part
GO:0031224	0.51	intrinsic component of 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	0.579	2nz6A	0.609	1.80	0.323	0.636	3.1.3.48	359
2	0.486	2hc1A	0.630	2.12	0.356	0.667	3.1.3.48	189,193,209,232,238,354
3	0.366	2a3kA	0.585	2.52	0.324	0.629	3.1.3.48	189,253,316,322,324,353,355,357,397
4	0.299	2qdpA	0.610	2.50	0.325	0.655	3.1.3.48	199,209,213,215,347,387
5	0.143	2ooqB	0.622	1.72	0.353	0.648	3.1.3.48	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	0.69	2h02A	0.620	1.66	0.375	0.645	1.73	2UN	complex1.pdb.gz	189,191,192,323,324,353,354,355,357,358,359,397
2	0.46	1nwlA	0.625	1.59	0.322	0.650	1.46	964	complex2.pdb.gz	188,189,190,355,357,358,359,397,401
3	0.45	1pynA	0.623	1.59	0.327	0.648	1.31	941	complex3.pdb.gz	164,189,190,191,353,354,355,358,359,389,393,394,397,401
4	0.43	1nnyA	0.622	1.61	0.327	0.648	1.18	515	complex4.pdb.gz	163,167,189,191,192,264,353,354,355,356,357,358,359,389,393,397,398
5	0.06	2b4s1	0.618	1.87	0.320	0.648	1.11	III	complex5.pdb.gz	154,155,256,264,291,292,293,294,322,323,324,326,327,328,329,335,400,403

	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.