D-I-TASSER Q9BRF8

D-I-TASSER results for Q9BRF8

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

Summary of the Protein

Uniprot ID: Q9BRF8
Protein Name: Serine/threonine-protein phosphatase CPPED1
Gene Name: CPPED1

Input Sequence in FASTA format

>Q9BRF8 (314 residues)
MSAAEAGGVFHRARGRTLAAFPAEKESEWKGPFYFILGADPQFGLIKAWSTGDCDNGGDE
WEQEIRLTEQAVQAINKLNPKPKFFVLCGDLIHAMPGKPWRTEQTEDLKRVLRAVDRAIP
LVLVSGNHDIGNTPTAETVEEFCRTWGDDYFSFWVGGVLFLVLNSQFYENPSKCPSLKQA
QDQWLDEQLSIARQRHCQHAIVFQHIPLFLESIDEDDDYYFNLSKSTRKKLADKFIHAGV
KVVFSGHYHRNAGGTYQNLDMVVSSAIGCQLGRDPHGLRVVVVTAEKIVHRYYSLDELSE
KGIEDDLMDLIKKK

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	Q9BRF8-D1	1-314	314		MSAAEAGGVFHRARGRTLAAFPAEKESEWKGPFYFILGADPQFGLIKAWSTGDCDNGGDEWEQEIRLTEQAVQAINKLNPKPKFFVLCGDLIHAMPGKPWRTEQTEDLKRVLRAVDRAIPLVLVSGNHDIGNTPTAETVEEFCRTWGDDYFSFWVGGVLFLVLNSQFYENPSKCPSLKQAQDQWLDEQLSIARQRHCQHAIVFQHIPLFLESIDEDDDYYFNLSKSTRKKLADKFIHAGVKVVFSGHYHRNAGGTYQNLDMVVSSAIGCQLGRDPHGLRVVVVTAEKIVHRYYSLDELSEKGIEDDLMDLIKKK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8104

(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	5ebbA	0.78	3.07	0.170	0.888	model1_5ebbA.pdb.gz
2	5karA	0.77	3.16	0.172	0.879	model1_5karA.pdb.gz
3	5fi9A2	0.76	3.26	0.139	0.876	model1_5fi9A2.pdb.gz
4	3ib8A	0.73	2.68	0.173	0.809	model1_3ib8A.pdb.gz
5	2xmoA	0.73	3.10	0.162	0.819	model1_2xmoA.pdb.gz
6	3d03A	0.71	2.18	0.186	0.774	model1_3d03A.pdb.gz
7	2yeqA	0.69	3.39	0.150	0.815	model1_2yeqA.pdb.gz
8	1warA	0.68	2.97	0.161	0.780	model1_1warA.pdb.gz
9	3auzA	0.65	3.21	0.120	0.758	model1_3auzA.pdb.gz
10	4ltyC	0.64	3.82	0.092	0.787	model1_4ltyC.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	0.99	catalytic activity
GO:0016787	0.98	hydrolase activity
GO:0042578	0.97	phosphoric ester hydrolase activity
GO:0008081	0.90	phosphoric diester hydrolase activity
GO:0004115	0.86	3',5'-cyclic-AMP phosphodiesterase activity
GO:0046872	0.81	metal ion binding
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0046914	0.78	transition metal ion binding
GO:0000166	0.76	nucleotide binding
GO:0008199	0.73	ferric iron binding
GO:0016791	0.70	phosphatase activity
GO:0030145	0.67	manganese ion binding
GO:0003993	0.66	acid phosphatase 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:0044237	0.93	cellular metabolic process
GO:0006796	0.87	phosphate-containing compound metabolic process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.85	primary metabolic process
GO:0044699	0.82	single-organism process
GO:0065007	0.80	biological regulation
GO:0044763	0.79	single-organism cellular process
GO:0050789	0.78	regulation of biological process
GO:0050794	0.76	regulation of cellular process
GO:0044710	0.73	single-organism metabolic process
GO:0016311	0.72	dephosphorylation
GO:0034641	0.67	cellular nitrogen compound metabolic process
GO:0019637	0.65	organophosphate metabolic process
GO:0048519	0.63	negative regulation of biological process
GO:0048523	0.62	negative regulation of cellular process
GO:0044260	0.60	cellular macromolecule metabolic process
GO:0006139	0.60	nucleobase-containing compound metabolic process
GO:1901575	0.59	organic substance catabolic process
GO:1901564	0.59	organonitrogen compound metabolic process
GO:0050896	0.59	response to stimulus
GO:0044248	0.59	cellular catabolic process
GO:1901135	0.58	carbohydrate derivative metabolic process
GO:0044712	0.58	single-organism catabolic process
GO:0016043	0.58	cellular component organization
GO:1901565	0.56	organonitrogen compound catabolic process
GO:0046434	0.56	organophosphate catabolic process
GO:0044281	0.56	small molecule metabolic process
GO:0006950	0.55	response to stress
GO:0042545	0.54	cell wall modification
GO:0055086	0.53	nucleobase-containing small molecule metabolic process
GO:0048518	0.53	positive regulation of biological process
GO:0048522	0.52	positive regulation of cellular process
GO:1901292	0.51	nucleoside phosphate catabolic process
GO:0065008	0.51	regulation of biological quality
GO:0009605	0.50	response to external 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:0044464	1.00	cell part
GO:0044424	0.95	intracellular part
GO:0043227	0.93	membrane-bounded organelle
GO:0044421	0.91	extracellular region part
GO:0070062	0.90	extracellular exosome
GO:0005886	0.90	plasma membrane
GO:0005737	0.89	cytoplasm

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	0.094	1warA	0.683	2.97	0.161	0.780	3.1.3.2	NA
2	0.060	2qt3A	0.490	5.39	0.056	0.726	3.5.99.4	NA
3	0.060	1itqA	0.486	5.16	0.057	0.710	3.4.13.19	NA
4	0.060	1wcgA	0.498	5.56	0.067	0.761	3.2.1.147	NA
5	0.060	1e1eB	0.514	5.90	0.070	0.799	3.2.1.21	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	0.63	3d03E	0.710	2.18	0.186	0.774	1.71	CO	complex1.pdb.gz	40,90,127,128,205,247
2	0.29	3ib8A	0.730	2.68	0.173	0.809	0.97	AMP	complex2.pdb.gz	42,90,127,128,219,222,247,248,249
3	0.25	2qfrA	0.673	2.94	0.159	0.767	0.98	SO4	complex3.pdb.gz	127,128,219,247,249
4	0.25	3kbpA	0.673	2.93	0.159	0.767	0.96	WO4	complex4.pdb.gz	90,93,127,128,220,247,249
5	0.21	2wdeA	0.598	3.99	0.146	0.723	1.01	THJ	complex5.pdb.gz	42,90,126,127,247,249
6	0.09	1hp1A	0.535	4.79	0.078	0.758	0.94	CO3	complex6.pdb.gz	90,127,128,246,248
7	0.03	3dscA	0.617	3.19	0.133	0.723	0.92	QNA	complex7.pdb.gz	44,49,50,51,52,93

	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.