D-I-TASSER A4QPH2

D-I-TASSER results for A4QPH2

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

Summary of the Protein

Uniprot ID: A4QPH2
Protein Name: Putative phosphatidylinositol 4-kinase alpha-like protein P2
Gene Name: PI4KAP2

Input Sequence in FASTA format

>A4QPH2 (592 residues)
MTVEQKFGLFSAEIKEADPLAASEASQPKPCPPEVTPHYIWIDFLVQRFEIAKYCSSDQV
EIFSSLLQRSMSLNIGRAKGSMNRHVAAIGPRFKLLTLGLSLLHADVVPNATIRNVLREK
IYSTAFDYFSCPPKFPTQGEKRLREDISIMIKFWTAMFSDKKYLTASQLVPPADIGDLLE
QLVEENTGSLSGPAKDFYQRGFDFFNKITNVSAVIKPYPKGDERKKACLSALSEVTVQPG
CSLPSNPEAIVLDVDYKSGTPMQSAAKAPYLAKFKVKRCGVSELEKEGLRCRSDSEDECS
TQEADGQKISWQAAIFKLGDDCRQKSYWGARMPTDRILRLPASQDMLALQIIDLFKNIFQ
LVGLDLFVFPYRVVATAPGCGVIECIPDCTSRDQLGRQTDFGMYDYFTRQYGDESTLAFQ
QARYNFIRSMAAYSLLLFLLQIKDRHNGNIMLDKKGHIIHIDFGFMFESSPGGNLGWEPD
IKLTDEMVMIMGGKMEATPFKWFMEMCVQATWLCGEPGPYMDVVVSLVTIMLDTGLPCFR
GQTIKLLKHRFSPNMTEREAANFIMKVIQSCFLSNRSRTYNMIQYYQNDIPY

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	A4QPH2-D1	1-190	190		MTVEQKFGLFSAEIKEADPLAASEASQPKPCPPEVTPHYIWIDFLVQRFEIAKYCSSDQVEIFSSLLQRSMSLNIGRAKGSMNRHVAAIGPRFKLLTLGLSLLHADVVPNATIRNVLREKIYSTAFDYFSCPPKFPTQGEKRLREDISIMIKFWTAMFSDKKYLTASQLVPPADIGDLLEQLVEENTGSL
2	A4QPH2-D2	191-385	195		SGPAKDFYQRGFDFFNKITNVSAVIKPYPKGDERKKACLSALSEVTVQPGCSLPSNPEAIVLDVDYKSGTPMQSAAKAPYLAKFKVKRCGVSELEKEGLRCRSDSEDECSTQEADGQKISWQAAIFKLGDDCRQKSYWGARMPTDRILRLPASQDMLALQIIDLFKNIFQLVGLDLFVFPYRVVATAPGCGVIEC
3	A4QPH2-D3	386-496	111		IPDCTSRDQLGRQTDFGMYDYFTRQYGDESTLAFQQARYNFIRSMAAYSLLLFLLQIKDRHNGNIMLDKKGHIIHIDFGFMFESSPGGNLGWEPDIKLTDEMVMIMGGKME
4	A4QPH2-D4	497-592	96		ATPFKWFMEMCVQATWLCGEPGPYMDVVVSLVTIMLDTGLPCFRGQTIKLLKHRFSPNMTEREAANFIMKVIQSCFLSNRSRTYNMIQYYQNDIPY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.79

(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	4d0lA	0.60	3.95	0.242	0.689	model1_4d0lA.pdb.gz
2	2y3aA	0.60	4.63	0.168	0.710	model1_2y3aA.pdb.gz
3	2x6fA	0.60	4.24	0.164	0.693	model1_2x6fA.pdb.gz
4	5dfzC	0.59	4.60	0.154	0.703	model1_5dfzC.pdb.gz
5	6nctA	0.59	4.59	0.182	0.698	model1_6nctA.pdb.gz
6	3ihyC	0.58	4.57	0.164	0.691	model1_3ihyC.pdb.gz
7	2a5uA	0.58	5.15	0.176	0.706	model1_2a5uA.pdb.gz
8	2x38A	0.58	4.95	0.161	0.696	model1_2x38A.pdb.gz
9	4jspB	0.58	4.82	0.121	0.691	model1_4jspB.pdb.gz
10	5yz0A	0.58	4.88	0.123	0.703	model1_5yz0A.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:0016301	0.99	kinase activity
GO:0016773	0.93	phosphotransferase activity, alcohol group as acceptor
GO:0052742	0.90	phosphatidylinositol kinase activity
GO:0004430	0.51	1-phosphatidylinositol 4-kinase 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	0.95	cellular process
GO:0071704	0.87	organic substance metabolic process
GO:0044238	0.87	primary metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0044699	0.84	single-organism process
GO:0044763	0.80	single-organism cellular process
GO:0065007	0.78	biological regulation
GO:0050789	0.78	regulation of biological process
GO:0050794	0.77	regulation of cellular process
GO:0006796	0.72	phosphate-containing compound metabolic process
GO:0006644	0.69	phospholipid metabolic process
GO:0046488	0.68	phosphatidylinositol metabolic process
GO:0016310	0.68	phosphorylation
GO:0043067	0.67	regulation of programmed cell death
GO:0050896	0.65	response to stimulus
GO:0046854	0.64	phosphatidylinositol phosphorylation
GO:0006950	0.60	response to stress
GO:0051716	0.59	cellular response to stimulus
GO:0033554	0.58	cellular response to stress
GO:0043170	0.56	macromolecule metabolic process
GO:0016043	0.56	cellular component organization
GO:0048518	0.53	positive regulation of biological process
GO:1901576	0.51	organic substance biosynthetic process
GO:0048583	0.51	regulation of response to stimulus
GO:0048522	0.51	positive regulation of cellular process
GO:0044711	0.51	single-organism biosynthetic process
GO:0044249	0.51	cellular biosynthetic process
GO:0006661	0.50	phosphatidylinositol biosynthetic 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	0.87	intracellular part
GO:0016020	0.72	membrane
GO:0043226	0.68	organelle
GO:0043229	0.67	intracellular organelle
GO:0005886	0.67	plasma membrane
GO:0043227	0.62	membrane-bounded organelle
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0005634	0.60	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	0.067	2x6fA	0.596	4.24	0.164	0.693	2.7.1.137 2.7.1.153 2.7.1.154	319,378
2	0.067	3ihyC	0.582	4.57	0.164	0.691	2.7.1.137	264,315,317,320,371,373,444,446,461
3	0.060	1n1hA	0.353	7.50	0.065	0.554	2.7.7.48	NA
4	0.060	2g49A	0.288	7.91	0.030	0.470	3.4.24.56	NA
5	0.060	3dsxA	0.253	6.58	0.052	0.375	2.5.1.60	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	0.20	3l08A	0.582	4.95	0.174	0.699	0.89	ZIG	complex1.pdb.gz	262,315,317,371,383,384,385,386,448,449,451,461,462
2	0.17	2x6kA	0.600	4.30	0.168	0.698	0.62	X6K	complex2.pdb.gz	315,317,345,461,462
3	0.17	2a5uA	0.580	5.15	0.176	0.706	0.61	QYT	complex3.pdb.gz	269,315,317,320,383,384,385,386,449
4	0.17	2x6jB	0.596	4.35	0.167	0.698	0.63	093	complex4.pdb.gz	264,269,317,371
5	0.16	2wxpA	0.580	4.87	0.159	0.694	0.66	GD9	complex5.pdb.gz	221,261,262,263,270,316,318,371,383,384,386,391,451,461,462

	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.