D-I-TASSER P04180

D-I-TASSER results for P04180

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

Summary of the Protein

Uniprot ID: P04180
Protein Name: Phosphatidylcholine-sterol acyltransferase
Gene Name: LCAT

Input Sequence in FASTA format

>P04180 (440 residues)
MGPPGSPWQWVTLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQL
EAKLDKPDVVNWMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGV
QIRVPGFGKTYSVEYLDSSKLAGYLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEY
YRKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLLRQPQAWKDRFIDGFISLGAPWGGS
IKPMLVLASGDNQGIPIMSSIKLKEEQRITTTSPWMFPSRMAWPEDHVFISTPSFNYTGR
DFQRFFADLHFEEGWYMWLQSRDLLAGLPAPGVEVYCLYGVGLPTPRTYIYDHGFPYTDP
VGVLYEDGDDTVATRSTELCGLWQGRQPQPVHLLPLHGIQHLNMVFSNLTLEHINAILLG
AYRQGPPASPTASPEPPPPE

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	P04180-D1	1-231	231		MGPPGSPWQWVTLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNWMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGYLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYRKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLLRQPQAWKDRFIDGFI
2	P04180-D2	232-440	209		SLGAPWGGSIKPMLVLASGDNQGIPIMSSIKLKEEQRITTTSPWMFPSRMAWPEDHVFISTPSFNYTGRDFQRFFADLHFEEGWYMWLQSRDLLAGLPAPGVEVYCLYGVGLPTPRTYIYDHGFPYTDPVGVLYEDGDDTVATRSTELCGLWQGRQPQPVHLLPLHGIQHLNMVFSNLTLEHINAILLGAYRQGPPASPTASPEPPPPE

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4x90A	0.84	0.98	0.497	0.850	model1_4x90A.pdb.gz
2	6mvdA	0.82	1.68	0.973	0.848	model1_6mvdA.pdb.gz
3	4r1dA	0.66	3.57	0.132	0.766	model1_4r1dA.pdb.gz
4	1thgA	0.48	5.59	0.097	0.643	model1_1thgA.pdb.gz
5	4fg5A	0.47	6.12	0.072	0.666	model1_4fg5A.pdb.gz
6	5ah1A	0.47	5.14	0.101	0.609	model1_5ah1A.pdb.gz
7	2z5gA	0.46	4.27	0.119	0.568	model1_2z5gA.pdb.gz
8	2fj0A	0.46	5.76	0.071	0.625	model1_2fj0A.pdb.gz
9	5ah0A	0.46	4.22	0.138	0.561	model1_5ah0A.pdb.gz
10	1mx9D	0.46	5.92	0.074	0.634	model1_1mx9D.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	1.00	catalytic activity
GO:0016747	0.99	transferase activity, transferring acyl groups other than amino-acyl groups
GO:0008374	0.94	O-acyltransferase activity
GO:0004607	0.75	phosphatidylcholine-sterol 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:0006629	1.00	lipid metabolic process
GO:0044255	0.99	cellular lipid metabolic process
GO:0006807	0.94	nitrogen compound metabolic process
GO:0046470	0.91	phosphatidylcholine metabolic process
GO:0044281	0.80	small molecule metabolic process
GO:1901360	0.75	organic cyclic compound metabolic process
GO:1901615	0.74	organic hydroxy compound metabolic process
GO:0008202	0.74	steroid metabolic process
GO:0034434	0.73	sterol esterification
GO:0016125	0.73	sterol metabolic process
GO:0006066	0.73	alcohol metabolic process
GO:0034435	0.72	cholesterol esterification
GO:0008203	0.72	cholesterol 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:0043226	0.95	organelle
GO:0043227	0.91	membrane-bounded organelle
GO:0044464	0.89	cell part
GO:0044424	0.84	intracellular part
GO:0044421	0.76	extracellular region part
GO:0044444	0.75	cytoplasmic part
GO:0005615	0.75	extracellular space
GO:0043229	0.66	intracellular organelle
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0070062	0.53	extracellular exosome
GO:0005773	0.51	vacuole

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

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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	1qgeE	0.120	4.92	0.033	0.159	3.1.1.3	NA
2	0.060	1thgA	0.476	5.59	0.097	0.643	3.1.1.3	NA
3	0.060	1nx9A	0.452	4.78	0.065	0.577	3.1.1.43	167
4	0.060	1maaD	0.469	5.31	0.094	0.618	3.1.1.7	NA
5	0.060	2veoB	0.468	5.02	0.077	0.614	3.1.1.3	56

	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

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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	0.02	2w22A	0.456	4.29	0.125	0.554	0.54	EGC	complex1.pdb.gz	55,170,205,206,239,241,267,371,401
2	0.01	1mx5B	0.473	5.36	0.080	0.629	0.45	SIA	complex2.pdb.gz	202,203,204,205,206,236,237
3	0.01	1gpkA	0.452	6.08	0.057	0.636	0.61	HUP	complex3.pdb.gz	26,53,54,55,56,57,146,204,401
4	0.01	1ax9A	0.469	5.56	0.066	0.632	0.46	EDR	complex4.pdb.gz	54,55,57,204,205,404
5	0.01	1mx1C	0.474	5.51	0.084	0.636	0.46	THA	complex5.pdb.gz	54,56,57,206,207
6	0.01	1mx5A	0.473	5.38	0.084	0.629	0.43	HTQ	complex6.pdb.gz	27,54,55,205,401

	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.