D-I-TASSER Q9BTU6

D-I-TASSER results for Q9BTU6

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Summary of the Protein

Uniprot ID: Q9BTU6
Protein Name: Phosphatidylinositol 4-kinase type 2-alpha
Gene Name: PI4K2A

Input Sequence in FASTA format

>Q9BTU6 (479 residues)
MDETSPLVSPERAQPPDYTFPSGSGAHFPQVPGGAVRVAAAAGSGPSPPGSPGHDRERQP
LLDRARGAAAQGQTQTVAAQAQALAAQAAAAAHAAQAHRERNEFPEDPEFEAVVRQAELA
IERCIFPERIYQGSSGSYFVKDPQGRIIAVFKPKNEEPYGHLNPKWTKWLQKLCCPCCFG
RDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEK
VPKVGQRFNRIGLPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLLQFERLVVL
DYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWR
AYPFYWAWLPQAKVPFSQEIKDLILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQI
AVMRGQILNLTQALKDNKSPLHLVQMPPVIVETARSHQRSSSESYTQSFQSRKPFFSWW

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	Q9BTU6-D1	1-479	479		MDETSPLVSPERAQPPDYTFPSGSGAHFPQVPGGAVRVAAAAGSGPSPPGSPGHDRERQPLLDRARGAAAQGQTQTVAAQAQALAAQAAAAAHAAQAHRERNEFPEDPEFEAVVRQAELAIERCIFPERIYQGSSGSYFVKDPQGRIIAVFKPKNEEPYGHLNPKWTKWLQKLCCPCCFGRDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEKVPKVGQRFNRIGLPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLLQFERLVVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWRAYPFYWAWLPQAKVPFSQEIKDLILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQILNLTQALKDNKSPLHLVQMPPVIVETARSHQRSSSESYTQSFQSRKPFFSWW

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6704

(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	4hndA	0.72	0.83	0.969	0.733	model1_4hndA.pdb.gz
2	4plaA	0.65	2.06	0.951	0.672	model1_4plaA.pdb.gz
3	7k10A	0.50	4.95	0.087	0.639	model1_7k10A.pdb.gz
4	6bcuA	0.48	4.99	0.070	0.620	model1_6bcuA.pdb.gz
5	4jspB	0.48	5.02	0.080	0.620	model1_4jspB.pdb.gz
6	5h64A	0.48	4.85	0.086	0.616	model1_5h64A.pdb.gz
7	5fvmA	0.47	5.10	0.078	0.626	model1_5fvmA.pdb.gz
8	6z2wE	0.47	5.60	0.081	0.660	model1_6z2wE.pdb.gz
9	2y3aA	0.47	5.83	0.088	0.643	model1_2y3aA.pdb.gz
10	6emkA	0.47	5.56	0.079	0.645	model1_6emkA.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	0.98	kinase activity
GO:0004430	0.96	1-phosphatidylinositol 4-kinase activity
GO:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0035639	0.72	purine ribonucleoside triphosphate binding
GO:0032555	0.72	purine ribonucleotide binding
GO:0032550	0.72	purine ribonucleoside binding
GO:0005524	0.71	ATP binding
GO:0035651	0.69	AP-3 adaptor complex 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:0044699	0.96	single-organism process
GO:0009987	0.94	cellular process
GO:0008152	0.93	metabolic process
GO:0071704	0.92	organic substance metabolic process
GO:0044238	0.92	primary metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0044763	0.86	single-organism cellular process
GO:0044710	0.86	single-organism metabolic process
GO:0046488	0.85	phosphatidylinositol metabolic process
GO:1901576	0.82	organic substance biosynthetic process
GO:0044249	0.82	cellular biosynthetic process
GO:0006661	0.68	phosphatidylinositol biosynthetic process
GO:0046854	0.67	phosphatidylinositol phosphorylation

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:0044424	1.00	intracellular part
GO:0016020	0.93	membrane
GO:0044444	0.90	cytoplasmic part
GO:0043226	0.86	organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0044425	0.62	membrane part
GO:0043234	0.62	protein complex
GO:0097458	0.61	neuron part
GO:0044459	0.61	plasma membrane part
GO:0031410	0.61	cytoplasmic vesicle
GO:0016021	0.61	integral component of membrane
GO:0005768	0.61	endosome
GO:0005739	0.61	mitochondrion
GO:0045121	0.60	membrane raft
GO:0044231	0.60	host cell presynaptic membrane
GO:0043025	0.60	neuronal cell body
GO:0042734	0.60	presynaptic membrane
GO:0035838	0.60	growing cell tip
GO:0031083	0.60	BLOC-1 complex
GO:0030425	0.60	dendrite
GO:0005887	0.60	integral component of plasma membrane
GO:0044446	0.56	intracellular organelle part
GO:0098588	0.53	bounding membrane of organelle
GO:0005774	0.52	vacuolar membrane
GO:0005634	0.51	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	0.060	3ihyC	0.456	5.45	0.088	0.614	2.7.1.137	213,308,312,315,345
2	0.060	2e1qA	0.335	7.82	0.048	0.585	1.17.3.2 1.17.1.4	NA
3	0.060	1gw6A	0.341	7.40	0.062	0.570	3.3.2.6	NA
4	0.060	3b9jI	0.169	5.92	0.063	0.244	1.17.1.4 1.17.3.2	136,221
5	0.060	3ebgA	0.356	7.59	0.038	0.608	3.4.11.-	157

	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	0.38	1cjaA	0.408	4.09	0.143	0.488	0.56	AMP	complex1.pdb.gz	132,133,134,137,150,152
2	0.35	3l13A	0.456	5.26	0.093	0.603	0.58	JZW	complex2.pdb.gz	131,132,150,190,192,196,209,261,262,263,264,315,345,346
3	0.04	3l08A	0.457	5.33	0.098	0.610	0.61	ZIG	complex3.pdb.gz	130,136,138,151,190,210,260,261,262,263,312,313,315,345,346
4	0.03	3s2aA	0.461	5.71	0.094	0.633	0.56	2NQ	complex4.pdb.gz	131,136,138,150,152,261,262,269,313,315,345,346
5	0.01	2x6kB	0.453	5.36	0.076	0.608	0.56	X6K	complex5.pdb.gz	133,152,209,261,262,263
6	0.01	1e7uA	0.459	5.52	0.078	0.620	0.53	KWT	complex6.pdb.gz	131,133,135,137,139,150,152,260,261,262,263,312,345,346

	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.