D-I-TASSER O75807

D-I-TASSER results for O75807

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

Summary of the Protein

Uniprot ID: O75807
Protein Name: Protein phosphatase 1 regulatory subunit 15A
Gene Name: PPP1R15A

Input Sequence in FASTA format

>O75807 (674 residues)
MAPGQAPHQATPWRDAHPFFLLSPVMGLLSRAWSRLRGLGPLEPWLVEAVKGAALVEAGL
EGEARTPLAIPHTPWGRRPEEEAEDSGGPGEDRETLGLKTSSSLPEAWGLLDDDDGMYGE
REATSVPRGQGSQFADGQRAPLSPSLLIRTLQGSDKNPGEEKAEEEGVAEEEGVNKFSYP
PSHRECCPAVEEEDDEEAVKKEAHRTSTSALSPGSKPSTWVSCPGEEENQATEDKRTERS
KGARKTSVSPRSSGSDPRSWEYRSGEASEEKEEKAHKETGKGEAAPGPQSSAPAQRPQLK
SWWCQPSDEEEGEVKALGAAEKDGEAECPPCIPPPSAFLKAWVYWPGEDTEEEEDEEEDE
DSDSGSDEEEGEAEASSSTPATGVFLKSWVYQPGEDTEEEEDEDSDTGSAEDEREAETSA
STPPASAFLKAWVYRPGEDTEEEEDEDVDSEDKEDDSEAALGEAESDPHPSHPDQRAHFR
GWGYRPGKETEEEEAAEDWGEAEPCPFRVAIYVPGEKPPPPWAPPRLPLRLQRRLKRPET
PTHDPDPETPLKARKVRFSEKVTVHFLAVWAGPAQAARQGPWEQLARDRSRFARRITQAQ
EELSPCLTPAARARAWARLRNPPLAPIPALTQTLPSSSVPSSPVQTTPLSQAVATPSRSS
AAAAAALDLSGRRG

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	O75807-D1	1-674	674		MAPGQAPHQATPWRDAHPFFLLSPVMGLLSRAWSRLRGLGPLEPWLVEAVKGAALVEAGLEGEARTPLAIPHTPWGRRPEEEAEDSGGPGEDRETLGLKTSSSLPEAWGLLDDDDGMYGEREATSVPRGQGSQFADGQRAPLSPSLLIRTLQGSDKNPGEEKAEEEGVAEEEGVNKFSYPPSHRECCPAVEEEDDEEAVKKEAHRTSTSALSPGSKPSTWVSCPGEEENQATEDKRTERSKGARKTSVSPRSSGSDPRSWEYRSGEASEEKEEKAHKETGKGEAAPGPQSSAPAQRPQLKSWWCQPSDEEEGEVKALGAAEKDGEAECPPCIPPPSAFLKAWVYWPGEDTEEEEDEEEDEDSDSGSDEEEGEAEASSSTPATGVFLKSWVYQPGEDTEEEEDEDSDTGSAEDEREAETSASTPPASAFLKAWVYRPGEDTEEEEDEDVDSEDKEDDSEAALGEAESDPHPSHPDQRAHFRGWGYRPGKETEEEEAAEDWGEAEPCPFRVAIYVPGEKPPPPWAPPRLPLRLQRRLKRPETPTHDPDPETPLKARKVRFSEKVTVHFLAVWAGPAQAARQGPWEQLARDRSRFARRITQAQEELSPCLTPAARARAWARLRNPPLAPIPALTQTLPSSSVPSSPVQTTPLSQAVATPSRSSAAAAAALDLSGRRG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5067

(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	6g7eB	0.40	7.81	0.047	0.626	model1_6g7eB.pdb.gz
2	7b52A	0.39	7.79	0.045	0.599	model1_7b52A.pdb.gz
3	6reyc	0.38	8.33	0.037	0.636	model1_6reyc.pdb.gz
4	6yejA	0.37	7.81	0.032	0.589	model1_6yejA.pdb.gz
5	6cinA	0.37	8.07	0.037	0.596	model1_6cinA.pdb.gz
6	1kekA	0.37	7.89	0.041	0.591	model1_1kekA.pdb.gz
7	3c3lA	0.37	8.12	0.043	0.594	model1_3c3lA.pdb.gz
8	7cunG	0.36	8.14	0.039	0.576	model1_7cunG.pdb.gz
9	6g2dC	0.36	8.07	0.033	0.574	model1_6g2dC.pdb.gz
10	6z2wE	0.36	8.10	0.041	0.573	model1_6z2wE.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:0008157	0.96	protein phosphatase 1 binding
GO:0098772	0.74	molecular function regulator
GO:0019208	0.73	phosphatase regulator activity
GO:0019901	0.72	protein kinase binding
GO:0019888	0.72	protein phosphatase regulator activity
GO:0008047	0.50	enzyme activator 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:0045936	1.00	negative regulation of phosphate metabolic process
GO:0031400	1.00	negative regulation of protein modification process
GO:0010468	1.00	regulation of gene expression
GO:0009987	1.00	cellular process
GO:0034976	0.98	response to endoplasmic reticulum stress
GO:0007165	0.98	signal transduction
GO:0044699	0.97	single-organism process
GO:0045937	0.96	positive regulation of phosphate metabolic process
GO:0044763	0.96	single-organism cellular process
GO:0031401	0.96	positive regulation of protein modification process
GO:0071704	0.81	organic substance metabolic process
GO:0044237	0.81	cellular metabolic process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0044238	0.80	primary metabolic process
GO:2000112	0.79	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.79	regulation of nitrogen compound metabolic process
GO:0048583	0.79	regulation of response to stimulus
GO:0019538	0.79	protein metabolic process
GO:1903573	0.78	negative regulation of response to endoplasmic reticulum stress
GO:0006470	0.78	protein dephosphorylation
GO:0006446	0.78	regulation of translational initiation
GO:0065009	0.75	regulation of molecular function
GO:0051179	0.75	localization
GO:0051173	0.75	positive regulation of nitrogen compound metabolic process
GO:0031328	0.75	positive regulation of cellular biosynthetic process
GO:0010628	0.75	positive regulation of gene expression
GO:0010557	0.75	positive regulation of macromolecule biosynthetic process
GO:1903917	0.74	positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation
GO:1902310	0.74	positive regulation of peptidyl-serine dephosphorylation
GO:0070972	0.74	protein localization to endoplasmic reticulum
GO:0036496	0.74	regulation of translational initiation by eIF2 alpha dephosphorylation
GO:0032516	0.74	positive regulation of phosphoprotein phosphatase activity
GO:0032515	0.74	negative regulation of phosphoprotein phosphatase activity
GO:0009966	0.54	regulation of signal transduction
GO:0009968	0.53	negative regulation of signal transduction
GO:1903898	0.52	negative regulation of PERK-mediated unfolded protein response
GO:0001932	0.52	regulation of protein phosphorylation
GO:0045786	0.51	negative regulation of cell cycle
GO:0035556	0.51	intracellular signal transduction
GO:0022402	0.51	cell cycle process
GO:0008219	0.51	cell death
GO:0001933	0.51	negative regulation of protein phosphorylation
GO:0070059	0.50	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0032058	0.50	positive regulation of translational initiation in response to stress
GO:0007050	0.50	cell cycle arrest
GO:0006974	0.50	cellular response to DNA damage stimulus
GO:0006915	0.50	apoptotic 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:0044444	1.00	cytoplasmic part
GO:0005737	0.94	cytoplasm
GO:0043229	0.80	intracellular organelle
GO:0043234	0.79	protein complex
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0016020	0.77	membrane
GO:0000164	0.76	protein phosphatase type 1 complex
GO:0005829	0.75	cytosol
GO:0005783	0.75	endoplasmic reticulum
GO:0005794	0.72	Golgi apparatus
GO:0005739	0.72	mitochondrion
GO:0044446	0.60	intracellular organelle part
GO:0044425	0.54	membrane part

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	1jqnA	0.320	8.23	0.044	0.521	4.1.1.31	NA
2	0.060	2r7oA	0.298	8.17	0.054	0.479	2.7.7.48	NA
3	0.060	2pffD	0.319	8.05	0.030	0.516	2.3.1.86	NA
4	0.060	2vdcA	0.346	8.61	0.038	0.591	1.4.1.13	NA
5	0.060	2ebsB	0.310	8.50	0.043	0.518	3.2.1.150	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.