D-I-TASSER Q643R3

D-I-TASSER results for Q643R3

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

Summary of the Protein

Uniprot ID: Q643R3
Protein Name: Lysophospholipid acyltransferase LPCAT4
Gene Name: LPCAT4

Input Sequence in FASTA format

>Q643R3 (524 residues)
MSQGSPGDWAPLDPTPGPPASPNPFVHELHLSRLQRVKFCLLGALLAPIRVLLAFIVLFL
LWPFAWLQVAGLSEEQLQEPITGWRKTVCHNGVLGLSRLLFFLLGFLRIRVRGQRASRLQ
APVLVAAPHSTFFDPIVLLPCDLPKVVSRAENLSVPVIGALLRFNQAILVSRHDPASRRR
VVEEVRRRATSGGKWPQVLFFPEGTCSNKKALLKFKPGAFIAGVPVQPVLIRYPNSLDTT
SWAWRGPGVLKVLWLTASQPCSIVDVEFLPVYHPSPEESRDPTLYANNVQRVMAQALGIP
ATECEFVGSLPVIVVGRLKVALEPQLWELGKVLRKAGLSAGYVDAGAEPGRSRMISQEEF
ARQLQLSDPQTVAGAFGYFQQDTKGLVDFRDVALALAALDGGRSLEELTRLAFELFAEEQ
AEGPNRLLYKDGFSTILHLLLGSPHPAATALHAELCQAGSSQGLSLCQFQNFSLHDPLYG
KLFSTYLRPPHTSRGTSQTPNASSPGNPTALANGTVQAPKQKGD

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 DeepPotential. 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	Q643R3-D1	1-305	305		MSQGSPGDWAPLDPTPGPPASPNPFVHELHLSRLQRVKFCLLGALLAPIRVLLAFIVLFLLWPFAWLQVAGLSEEQLQEPITGWRKTVCHNGVLGLSRLLFFLLGFLRIRVRGQRASRLQAPVLVAAPHSTFFDPIVLLPCDLPKVVSRAENLSVPVIGALLRFNQAILVSRHDPASRRRVVEEVRRRATSGGKWPQVLFFPEGTCSNKKALLKFKPGAFIAGVPVQPVLIRYPNSLDTTSWAWRGPGVLKVLWLTASQPCSIVDVEFLPVYHPSPEESRDPTLYANNVQRVMAQALGIPATECE
2	Q643R3-D2	306-524	219		FVGSLPVIVVGRLKVALEPQLWELGKVLRKAGLSAGYVDAGAEPGRSRMISQEEFARQLQLSDPQTVAGAFGYFQQDTKGLVDFRDVALALAALDGGRSLEELTRLAFELFAEEQAEGPNRLLYKDGFSTILHLLLGSPHPAATALHAELCQAGSSQGLSLCQFQNFSLHDPLYGKLFSTYLRPPHTSRGTSQTPNASSPGNPTALANGTVQAPKQKGD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.53

(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 DeepPotential, 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	5kymA	0.42	2.25	0.169	0.447	model1_5kymA.pdb.gz
2	1k30A	0.41	4.98	0.094	0.508	model1_1k30A.pdb.gz
3	6etzA	0.40	7.83	0.051	0.666	model1_6etzA.pdb.gz
4	3czjA	0.40	7.65	0.056	0.656	model1_3czjA.pdb.gz
5	2x2hA	0.40	7.39	0.080	0.645	model1_2x2hA.pdb.gz
6	5hb4B	0.40	7.17	0.055	0.634	model1_5hb4B.pdb.gz
7	3decA	0.39	7.87	0.049	0.660	model1_3decA.pdb.gz
8	1yq2A	0.39	7.93	0.052	0.666	model1_1yq2A.pdb.gz
9	3ob8A	0.39	7.78	0.042	0.647	model1_3ob8A.pdb.gz
10	6sd0A	0.38	7.89	0.058	0.655	model1_6sd0A.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:0003824	0.99	catalytic activity
GO:0016740	0.98	transferase activity
GO:0016747	0.97	transferase activity, transferring acyl groups other than amino-acyl groups
GO:0008374	0.81	O-acyltransferase activity
GO:0071617	0.63	lysophospholipid acyltransferase activity
GO:0042171	0.52	lysophosphatidic acid acyltransferase activity
GO:0016411	0.52	acylglycerol O-acyltransferase 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	0.98	single-organism process
GO:0008152	0.98	metabolic process
GO:0071704	0.97	organic substance metabolic process
GO:0009987	0.97	cellular process
GO:0044238	0.96	primary metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0044710	0.95	single-organism metabolic process
GO:0044763	0.94	single-organism cellular process
GO:0006629	0.94	lipid metabolic process
GO:0044255	0.93	cellular lipid metabolic process
GO:0006793	0.85	phosphorus metabolic process
GO:1901576	0.84	organic substance biosynthetic process
GO:0044249	0.83	cellular biosynthetic process
GO:0008610	0.83	lipid biosynthetic process
GO:0006796	0.83	phosphate-containing compound metabolic process
GO:0006644	0.81	phospholipid metabolic process
GO:0045017	0.72	glycerolipid biosynthetic process
GO:0008654	0.64	phospholipid biosynthetic process
GO:0006650	0.61	glycerophospholipid metabolic process
GO:0046474	0.51	glycerophospholipid 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	0.99	cell part
GO:0044424	0.95	intracellular part
GO:0044444	0.94	cytoplasmic part
GO:0016020	0.80	membrane
GO:0043229	0.76	intracellular organelle
GO:0043227	0.76	membrane-bounded organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0005783	0.72	endoplasmic reticulum
GO:0044446	0.70	intracellular organelle part
GO:0044425	0.59	membrane part
GO:0044432	0.54	endoplasmic reticulum part
GO:0005789	0.51	endoplasmic reticulum 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	0.060	1z1wA	0.352	7.45	0.048	0.567	3.4.11.-	NA
2	0.060	2g8eA	0.215	6.50	0.075	0.319	3.4.22.52	NA
3	0.060	1bxrA	0.330	8.30	0.044	0.595	6.3.5.5	NA
4	0.060	2fhbA	0.320	7.55	0.048	0.527	3.2.1.41	NA
5	0.060	1fo4A	0.364	7.65	0.029	0.607	1.17.1.4	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	1dgkN	0.374	7.31	0.026	0.588	0.27	ADP	complex1.pdb.gz	128,129,204,216,219
2	0.01	1dgkN	0.374	7.31	0.026	0.588	0.20	GLC	complex2.pdb.gz	198,201,218
3	0.01	1qhaA	0.378	7.26	0.042	0.590	0.20	GLC	complex3.pdb.gz	133,134,135,149,213
4	0.01	2nztA	0.374	7.44	0.036	0.599	0.16	GLC	complex4.pdb.gz	200,201,219
5	0.01	3mwyW	0.380	6.98	0.053	0.595	0.13	ATG	complex5.pdb.gz	113,114,118,219,220
6	0.01	1hkbB	0.375	7.25	0.032	0.588	0.25	G6P	complex6.pdb.gz	148,200,218
7	0.01	1bg3B	0.395	7.32	0.044	0.634	0.23	G6P	complex7.pdb.gz	130,202,204,205,230
8	0.01	1czaN	0.374	7.27	0.037	0.586	0.19	GLC	complex8.pdb.gz	204,205,206,213

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.