D-I-TASSER Q9UJQ1

D-I-TASSER results for Q9UJQ1

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

Summary of the Protein

Uniprot ID: Q9UJQ1
Protein Name: Lysosome-associated membrane glycoprotein 5
Gene Name: LAMP5

Input Sequence in FASTA format

>Q9UJQ1 (280 residues)
MDLQGRGVPSIDRLRVLLMLFHTMAQIMAEQEVENLSGLSTNPEKDIFVVRENGTTCLMA
EFAAKFIVPYDVWASNYVDLITEQADIALTRGAEVKGRCGHSQSELQVFWVDRAYALKML
FVKESHNMSKGPEATWRLSKVQFVYDSSEKTHFKDAVSAGKHTANSHHLSALVTPAGKSY
ECQAQQTISLASSDPQKTVTMILSAVHIQPFDIISDFVFSEEHKCPVDEREQLEETLPLI
LGLILGLVIMVTLAIYHVHHKMTANQVQIPRDRSQYKHMG

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	Q9UJQ1-D1	1-280	280		MDLQGRGVPSIDRLRVLLMLFHTMAQIMAEQEVENLSGLSTNPEKDIFVVRENGTTCLMAEFAAKFIVPYDVWASNYVDLITEQADIALTRGAEVKGRCGHSQSELQVFWVDRAYALKMLFVKESHNMSKGPEATWRLSKVQFVYDSSEKTHFKDAVSAGKHTANSHHLSALVTPAGKSYECQAQQTISLASSDPQKTVTMILSAVHIQPFDIISDFVFSEEHKCPVDEREQLEETLPLILGLILGLVIMVTLAIYHVHHKMTANQVQIPRDRSQYKHMG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6062

(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	6xbws	0.57	2.65	0.124	0.646	model1_6xbws.pdb.gz
2	5gv0A	0.55	1.59	0.235	0.579	model1_5gv0A.pdb.gz
3	5gv3A	0.53	1.93	0.225	0.571	model1_5gv3A.pdb.gz
4	4akmA	0.51	1.88	0.195	0.546	model1_4akmA.pdb.gz
5	3holA	0.45	5.57	0.049	0.696	model1_3holA.pdb.gz
6	3pqsA	0.44	5.26	0.033	0.657	model1_3pqsA.pdb.gz
7	3pquA	0.43	5.54	0.038	0.675	model1_3pquA.pdb.gz
8	3v8uA1	0.39	5.13	0.082	0.571	model1_3v8uA1.pdb.gz
9	4qq1A2	0.39	4.97	0.069	0.564	model1_4qq1A2.pdb.gz
10	3uaqA	0.37	5.19	0.072	0.543	model1_3uaqA.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:0019899	0.93	enzyme 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:0065008	0.84	regulation of biological quality
GO:0009987	0.84	cellular process
GO:0050789	0.81	regulation of biological process
GO:0050794	0.80	regulation of cellular process
GO:0048518	0.73	positive regulation of biological process
GO:0044699	0.67	single-organism process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:0010604	0.63	positive regulation of macromolecule metabolic process
GO:0051179	0.62	localization
GO:0006914	0.57	autophagy
GO:0050896	0.56	response to stimulus
GO:0051641	0.55	cellular localization
GO:0048519	0.54	negative regulation of biological process
GO:0010468	0.54	regulation of gene expression
GO:0051234	0.53	establishment of localization
GO:0044763	0.53	single-organism cellular process
GO:0043086	0.53	negative regulation of catalytic activity
GO:0032269	0.53	negative regulation of cellular protein metabolic process
GO:0010033	0.53	response to organic substance
GO:0050792	0.52	regulation of viral process
GO:0010951	0.52	negative regulation of endopeptidase activity
GO:0002376	0.52	immune system process
GO:2000117	0.51	negative regulation of cysteine-type endopeptidase activity
GO:1903051	0.51	negative regulation of proteolysis involved in cellular protein catabolic process
GO:0061136	0.51	regulation of proteasomal protein catabolic process
GO:0044419	0.51	interspecies interaction between organisms
GO:0043281	0.51	regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043066	0.51	negative regulation of apoptotic process
GO:0034097	0.51	response to cytokine
GO:0050821	0.50	protein stabilization

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:0010008	1.00	endosome membrane
GO:0005886	0.97	plasma membrane
GO:0044459	0.95	plasma membrane part
GO:0097458	0.92	neuron part
GO:0098590	0.90	plasma membrane region
GO:0030659	0.89	cytoplasmic vesicle membrane
GO:0055038	0.87	recycling endosome membrane
GO:0033116	0.87	endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0032590	0.87	dendrite membrane
GO:0032584	0.87	growth cone membrane
GO:0031901	0.87	early endosome 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	1s1mB	0.297	5.93	0.054	0.489	6.3.4.2	NA
2	0.060	1qf6A	0.375	6.19	0.082	0.636	6.1.1.3	NA
3	0.060	1peuA	0.361	6.17	0.044	0.611	1.17.4.1	61
4	0.060	1ggmB	0.385	6.21	0.055	0.646	6.1.1.14	58,230
5	0.060	2zxqA	0.366	6.48	0.019	0.639	3.2.1.97	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	1ggmA	0.391	6.09	0.060	0.646	0.13	GAP	complex1.pdb.gz	98,177,178,213
2	0.01	1ggmB	0.385	6.21	0.055	0.646	0.12	GAP	complex2.pdb.gz	210,211,212
3	0.01	3lihA	0.384	6.22	0.053	0.650	0.13	RAF	complex3.pdb.gz	49,105,122
4	0.01	1b76B	0.383	5.98	0.060	0.625	0.20	ATP	complex4.pdb.gz	53,58,177,220
5	0.01	3p9qB	0.386	6.16	0.038	0.632	0.13	UUU	complex5.pdb.gz	98,171,176
6	0.01	1qffA	0.393	5.77	0.048	0.625	0.14	UUU	complex6.pdb.gz	95,99,103,105,118,120,122,140
7	0.01	2grxA	0.359	6.01	0.036	0.582	0.19	UUU	complex7.pdb.gz	118,120,122
8	0.01	3fidB	0.421	5.28	0.079	0.646	0.36	CXE	complex8.pdb.gz	52,97,105,107,118
9	0.01	2grx0	0.359	6.01	0.036	0.582	0.14	III	complex9.pdb.gz	106,123,174
10	0.01	1uynX	0.392	5.82	0.036	0.614	0.35	CXE	complex10.pdb.gz	48,50,52

	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.