D-I-TASSER Q6IQ20

D-I-TASSER results for Q6IQ20

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

Summary of the Protein

Uniprot ID: Q6IQ20
Protein Name: N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
Gene Name: NAPEPLD

Input Sequence in FASTA format

>Q6IQ20 (393 residues)
MDENESNQSLMTSSQYPKEAVRKRQNSARNSGASDSSRFSRKSFKLDYRLEEDVTKSKKG
KDGRFVNPWPTWKNPSIPNVLRWLIMEKDHSSVPSSKEELDKELPVLKPYFITNPEEAGV
REAGLRVTWLGHATVMVEMDELIFLTDPIFSSRASPSQYMGPKRFRRSPCTISELPPIDA
VLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLDWMQKCGCENVIELDWWEENCVPG
HDKVTFVFTPSQHWCKRTLMDDNKVLWGSWSVLGPWNRFFFAGDTGYCPAFEEIGKRFGP
FDLAAIPIGAYEPRWFMKYQHVDPEEAVRIHTDVQTKKSMAIHWGTFALANEHYLEPPVK
LNEALERYGLNAEDFFVLKHGESRYLNNDDENF

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	Q6IQ20-D1	1-393	393		MDENESNQSLMTSSQYPKEAVRKRQNSARNSGASDSSRFSRKSFKLDYRLEEDVTKSKKGKDGRFVNPWPTWKNPSIPNVLRWLIMEKDHSSVPSSKEELDKELPVLKPYFITNPEEAGVREAGLRVTWLGHATVMVEMDELIFLTDPIFSSRASPSQYMGPKRFRRSPCTISELPPIDAVLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLDWMQKCGCENVIELDWWEENCVPGHDKVTFVFTPSQHWCKRTLMDDNKVLWGSWSVLGPWNRFFFAGDTGYCPAFEEIGKRFGPFDLAAIPIGAYEPRWFMKYQHVDPEEAVRIHTDVQTKKSMAIHWGTFALANEHYLEPPVKLNEALERYGLNAEDFFVLKHGESRYLNNDDENF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7255

(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	4qn9A	0.78	1.44	0.928	0.807	model1_4qn9A.pdb.gz
2	3bv6B	0.62	3.09	0.150	0.702	model1_3bv6B.pdb.gz
3	3af5A	0.57	4.09	0.113	0.687	model1_3af5A.pdb.gz
4	2ycbA	0.57	4.34	0.118	0.692	model1_2ycbA.pdb.gz
5	2xr1A	0.56	4.20	0.143	0.687	model1_2xr1A.pdb.gz
6	5mtzA	0.56	4.18	0.090	0.687	model1_5mtzA.pdb.gz
7	6brmA	0.56	3.03	0.181	0.631	model1_6brmA.pdb.gz
8	5a0tA	0.55	3.75	0.151	0.651	model1_5a0tA.pdb.gz
9	6j4nA	0.55	3.04	0.184	0.623	model1_6j4nA.pdb.gz
10	4jo0A	0.54	3.68	0.140	0.636	model1_4jo0A.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:0004620	1.00	phospholipase activity
GO:0042578	0.78	phosphoric ester hydrolase activity
GO:0008081	0.77	phosphoric diester hydrolase activity
GO:0070290	0.76	N-acylphosphatidylethanolamine-specific phospholipase D 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:0044699	0.95	single-organism process
GO:0009987	0.95	cellular process
GO:0044763	0.94	single-organism cellular process
GO:0008152	0.94	metabolic process
GO:0071704	0.93	organic substance metabolic process
GO:0044710	0.93	single-organism metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0044238	0.77	primary metabolic process
GO:0006629	0.72	lipid metabolic process
GO:0044255	0.71	cellular lipid metabolic 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	0.95	cell part
GO:0044424	0.78	intracellular part
GO:0043227	0.78	membrane-bounded organelle
GO:0016020	0.56	membrane
GO:0044421	0.52	extracellular region part
GO:0070062	0.51	extracellular exosome
GO:0005737	0.50	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	0.067	1y44A	0.502	2.91	0.156	0.567	3.1.26.11	199
2	0.066	2cbnA	0.506	2.92	0.142	0.573	3.1.26.11	NA
3	0.060	1p9eA	0.411	4.86	0.115	0.542	3.1.8.1	NA
4	0.060	2i7tA	0.516	3.36	0.153	0.598	3.1.27.-	NA
5	0.060	2drsA	0.384	6.50	0.054	0.618	3.2.1.156	188,310

	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	0.04	3iemC	0.488	3.15	0.155	0.560	0.30	SSU	complex1.pdb.gz	147,148,149,191
2	0.03	3iemD	0.487	3.14	0.155	0.560	0.14	SSU	complex2.pdb.gz	186,187,189,211,212,284,347,349
3	0.02	3md7A	0.482	3.78	0.116	0.583	0.35	5GP	complex3.pdb.gz	186,187,188,189,192,284
4	0.02	2cbn0	0.506	2.92	0.142	0.573	0.36	III	complex4.pdb.gz	149,150,191,192,195,198,217,218
5	0.02	3iemB	0.490	3.08	0.155	0.560	0.26	SSU	complex5.pdb.gz	135,193,194,195,196,197,223
6	0.02	1zkp0	0.488	3.30	0.147	0.567	0.31	III	complex6.pdb.gz	150,187,188,189,345
7	0.01	3iemA	0.488	3.15	0.145	0.560	0.17	SSU	complex7.pdb.gz	168,190,191,284,309,310
8	0.01	3t3nA	0.531	3.65	0.127	0.634	0.12	QNA	complex8.pdb.gz	247,248,308,327

	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.