D-I-TASSER Q9UQV4

D-I-TASSER results for Q9UQV4

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Summary of the Protein

Uniprot ID: Q9UQV4
Protein Name: Lysosome-associated membrane glycoprotein 3
Gene Name: LAMP3

Input Sequence in FASTA format

>Q9UQV4 (416 residues)
MPRQLSAAAALFASLAVILHDGSQMRAKAFPETRDYSQPTAAATVQDIKKPVQQPAKQAP
HQTLAARFMDGHITFQTAATVKIPTTTPATTKNTATTSPITYTLVTTQATPNNSHTAPPV
TEVTVGPSLAPYSLPPTITPPAHTTGTSSSTVSHTTGNTTQPSNQTTLPATLSIALHKST
TGQKPVQPTHAPGTTAAAHNTTRTAAPASTVPGPTLAPQPSSVKTGIYQVLNGSRLCIKA
EMGIQLIVQDKESVFSPRRYFNIDPNATQASGNCGTRKSNLLLNFQGGFVNLTFTKDEES
YYISEVGAYLTVSDPETIYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQL
QAFDFEDDHFGNVDECSSDYTIVLPVIGAIVVGLCLMGMGVYKIRLRCQSSGYQRI

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	Q9UQV4-D1	1-416	416		MPRQLSAAAALFASLAVILHDGSQMRAKAFPETRDYSQPTAAATVQDIKKPVQQPAKQAPHQTLAARFMDGHITFQTAATVKIPTTTPATTKNTATTSPITYTLVTTQATPNNSHTAPPVTEVTVGPSLAPYSLPPTITPPAHTTGTSSSTVSHTTGNTTQPSNQTTLPATLSIALHKSTTGQKPVQPTHAPGTTAAAHNTTRTAAPASTVPGPTLAPQPSSVKTGIYQVLNGSRLCIKAEMGIQLIVQDKESVFSPRRYFNIDPNATQASGNCGTRKSNLLLNFQGGFVNLTFTKDEESYYISEVGAYLTVSDPETIYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQLQAFDFEDDHFGNVDECSSDYTIVLPVIGAIVVGLCLMGMGVYKIRLRCQSSGYQRI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5887

(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	4zktB	0.41	6.69	0.055	0.639	model1_4zktB.pdb.gz
2	3v0aB	0.40	6.87	0.036	0.644	model1_3v0aB.pdb.gz
3	3btaA	0.39	6.83	0.054	0.635	model1_3btaA.pdb.gz
4	3k71G	0.37	7.01	0.054	0.613	model1_3k71G.pdb.gz
5	2hg4D	0.37	7.07	0.037	0.627	model1_2hg4D.pdb.gz
6	3eifA	0.37	6.88	0.054	0.615	model1_3eifA.pdb.gz
7	2vz8B	0.37	6.90	0.048	0.599	model1_2vz8B.pdb.gz
8	2qo3B	0.36	7.05	0.053	0.615	model1_2qo3B.pdb.gz
9	3hmjA	0.36	7.40	0.032	0.625	model1_3hmjA.pdb.gz
10	7jpkF	0.36	7.40	0.039	0.606	model1_7jpkF.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	0.58	catalytic activity
GO:0005102	0.50	receptor 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:0065007	0.96	biological regulation
GO:0050789	0.73	regulation of biological process
GO:0050794	0.70	regulation of cellular process
GO:0048518	0.67	positive regulation of biological process
GO:0050896	0.65	response to stimulus
GO:0010033	0.60	response to organic substance
GO:0080090	0.55	regulation of primary metabolic process
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0048519	0.54	negative regulation of biological process
GO:0032268	0.54	regulation of cellular protein metabolic process
GO:0010604	0.54	positive regulation of macromolecule metabolic process
GO:0048523	0.53	negative regulation of cellular process
GO:0065009	0.52	regulation of molecular function
GO:0042981	0.52	regulation of apoptotic process
GO:0034097	0.52	response to cytokine
GO:0010628	0.52	positive regulation of gene expression
GO:1903900	0.51	regulation of viral life cycle
GO:1901799	0.51	negative regulation of proteasomal protein catabolic process
GO:0043154	0.51	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0035455	0.51	response to interferon-alpha
GO:0010506	0.51	regulation of autophagy

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:0016020	1.00	membrane
GO:0044464	0.95	cell part
GO:0044424	0.92	intracellular part
GO:0044444	0.91	cytoplasmic part
GO:0044446	0.89	intracellular organelle part
GO:0031090	0.89	organelle membrane
GO:0098805	0.88	whole membrane
GO:0098588	0.88	bounding membrane of organelle
GO:0005774	0.76	vacuolar membrane
GO:0005765	0.74	lysosomal membrane
GO:0043227	0.71	membrane-bounded organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0005886	0.69	plasma membrane
GO:0005773	0.68	vacuole
GO:0005768	0.64	endosome
GO:0030659	0.62	cytoplasmic vesicle membrane
GO:0031982	0.61	vesicle
GO:0030667	0.59	secretory granule membrane
GO:0097233	0.52	alveolar lamellar body 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	1eulA	0.280	7.42	0.052	0.483	3.6.3.8	NA
2	0.060	1kfxL	0.248	7.13	0.038	0.413	3.4.22.53	NA
3	0.060	2q1fA	0.252	7.58	0.018	0.438	4.2.2.21	NA
4	0.060	2gtqA	0.232	6.73	0.010	0.375	3.4.11.2	NA
5	0.060	3l4gB	0.311	7.41	0.040	0.531	6.1.1.20	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.