D-I-TASSER Q9Y4P8

D-I-TASSER results for Q9Y4P8

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

Summary of the Protein

Uniprot ID: Q9Y4P8
Protein Name: WD repeat domain phosphoinositide-interacting protein 2
Gene Name: WIPI2

Input Sequence in FASTA format

>Q9Y4P8 (454 residues)
MNLASQSGEAGAGQLLFANFNQDNTEVKGASRAAGLGRRAVVWSLAVGSKSGYKFFSLSS
VDKLEQIYECTDTEDVCIVERLFSSSLVAIVSLKAPRKLKVCHFKKGTEICNYSYSNTIL
AVKLNRQRLIVCLEESLYIHNIRDMKVLHTIRETPPNPAGLCALSINNDNCYLAYPGSAT
IGEVQVFDTINLRAANMIPAHDSPLAALAFDASGTKLATASEKGTVIRVFSIPEGQKLFE
FRRGVKRCVSICSLAFSMDGMFLSASSNTETVHIFKLETVKEKPPEEPTTWTGYFGKVLM
ASTSYLPSQVTEMFNQGRAFATVRLPFCGHKNICSLATIQKIPRLLVGAADGYLYMYNLD
PQEGGECALMKQHRLDGSLETTNEILDSASHDCPLVTQTYGAAAGKGTYVPSSPTRLAYT
DDLGAVGGACLEDEASALRLDEDSEHPPMILRTD

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	Q9Y4P8-D1	1-70,200-454	325		MNLASQSGEAGAGQLLFANFNQDNTEVKGASRAAGLGRRAVVWSLAVGSKSGYKFFSLSSVDKLEQIYECAHDSPLAALAFDASGTKLATASEKGTVIRVFSIPEGQKLFEFRRGVKRCVSICSLAFSMDGMFLSASSNTETVHIFKLETVKEKPPEEPTTWTGYFGKVLMASTSYLPSQVTEMFNQGRAFATVRLPFCGHKNICSLATIQKIPRLLVGAADGYLYMYNLDPQEGGECALMKQHRLDGSLETTNEILDSASHDCPLVTQTYGAAAGKGTYVPSSPTRLAYTDDLGAVGGACLEDEASALRLDEDSEHPPMILRTD
2	Q9Y4P8-D2	71-199	129		TDTEDVCIVERLFSSSLVAIVSLKAPRKLKVCHFKKGTEICNYSYSNTILAVKLNRQRLIVCLEESLYIHNIRDMKVLHTIRETPPNPAGLCALSINNDNCYLAYPGSATIGEVQVFDTINLRAANMIP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.83

(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	4wjsA	0.64	2.44	0.106	0.687	model1_4wjsA.pdb.gz
2	3jctx	0.64	3.09	0.094	0.709	model1_3jctx.pdb.gz
3	6zcvA	0.63	4.35	0.071	0.777	model1_6zcvA.pdb.gz
4	2d0vA	0.63	4.45	0.059	0.791	model1_2d0vA.pdb.gz
5	1kv9A	0.63	4.40	0.065	0.780	model1_1kv9A.pdb.gz
6	4cvbA	0.63	4.44	0.059	0.786	model1_4cvbA.pdb.gz
7	1hj5A	0.63	4.13	0.066	0.766	model1_1hj5A.pdb.gz
8	6oc5A	0.63	4.42	0.077	0.782	model1_6oc5A.pdb.gz
9	1flgA	0.63	4.37	0.063	0.777	model1_1flgA.pdb.gz
10	4zn4A	0.63	2.95	0.135	0.703	model1_4zn4A.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:0035091	0.99	phosphatidylinositol binding
GO:0080025	0.98	phosphatidylinositol-3,5-bisphosphate binding
GO:0032266	0.98	phosphatidylinositol-3-phosphate 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:0051179	0.96	localization
GO:0044699	0.95	single-organism process
GO:0022607	0.95	cellular component assembly
GO:0071704	0.94	organic substance metabolic process
GO:0044763	0.94	single-organism cellular process
GO:0000045	0.94	autophagosome assembly
GO:0044260	0.93	cellular macromolecule metabolic process
GO:0044238	0.93	primary metabolic process
GO:0006914	0.93	autophagy
GO:0019538	0.92	protein metabolic process
GO:0051641	0.91	cellular localization
GO:0008104	0.91	protein localization
GO:0006464	0.91	cellular protein modification process
GO:0044804	0.90	nucleophagy
GO:0034497	0.90	protein localization to pre-autophagosomal structure
GO:0006497	0.90	protein lipidation
GO:0000422	0.90	mitophagy

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:0044444	0.96	cytoplasmic part
GO:0016020	0.94	membrane
GO:0098805	0.93	whole membrane
GO:0005829	0.93	cytosol
GO:0044425	0.92	membrane part
GO:0034045	0.92	pre-autophagosomal structure membrane
GO:0019898	0.91	extrinsic 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	0.067	1jofA	0.560	4.01	0.088	0.676	5.5.1.5	NA
2	0.067	2madH	0.530	4.49	0.057	0.667	1.4.99.3	NA
3	0.060	2bklB	0.505	4.47	0.044	0.630	3.4.21.26	NA
4	0.060	2d0vA	0.635	4.45	0.059	0.791	1.1.99.8	NA
5	0.060	2htrA	0.475	5.14	0.039	0.628	3.2.1.18	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	0.01	2ovr1	0.609	3.49	0.093	0.694	0.16	III	complex1.pdb.gz	34,38,60,100
2	0.01	2ovqB	0.609	3.48	0.093	0.694	0.10	III	complex2.pdb.gz	60,129,217
3	0.01	1h9xA	0.637	4.10	0.073	0.771	0.16	DHE	complex3.pdb.gz	131,176,208,378
4	0.01	1h4iA	0.634	4.36	0.072	0.786	0.14	PQQ	complex4.pdb.gz	134,175,177,185
5	0.01	1lrw0	0.632	4.37	0.074	0.786	0.11	III	complex5.pdb.gz	145,147,399,407,408
6	0.01	1e2rB	0.636	4.11	0.070	0.769	0.13	UUU	complex6.pdb.gz	165,166,210,378,418,420
7	0.01	1gq10	0.634	4.16	0.069	0.769	0.14	III	complex7.pdb.gz	235,236,237,238,239
8	0.01	1aofB	0.634	4.17	0.067	0.769	0.12	UUU	complex8.pdb.gz	119,204,205
9	0.01	1hzu0	0.626	4.25	0.065	0.769	0.15	III	complex9.pdb.gz	36,235,236,237,238
10	0.01	1kb0A	0.627	4.01	0.052	0.751	0.11	HEC	complex10.pdb.gz	173,187,195,196

	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.