D-I-TASSER P54802

D-I-TASSER results for P54802

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

Summary of the Protein

Uniprot ID: P54802
Protein Name: Alpha-N-acetylglucosaminidase
Gene Name: NAGLU

Input Sequence in FASTA format

>P54802 (743 residues)
MEAVAVAAAVGVLLLAGAGGAAGDEAREAAAVRALVARLLGPGPAADFSVSVERALAAKP
GLDTYSLGGGGAARVRVRGSTGVAAAAGLHRYLRDFCGCHVAWSGSQLRLPRPLPAVPGE
LTEATPNRYRYYQNVCTQSYSFVWWDWARWEREIDWMALNGINLALAWSGQEAIWQRVYL
ALGLTQAEINEFFTGPAFLAWGRMGNLHTWDGPLPPSWHIKQLYLQHRVLDQMRSFGMTP
VLPAFAGHVPEAVTRVFPQVNVTKMGSWGHFNCSYSCSFLLAPEDPIFPIIGSLFLRELI
KEFGTDHIYGADTFNEMQPPSSEPSYLAAATTAVYEAMTAVDTEAVWLLQGWLFQHQPQF
WGPAQIRAVLGAVPRGRLLVLDLFAESQPVYTRTASFQGQPFIWCMLHNFGGNHGLFGAL
EAVNGGPEAARLFPNSTMVGTGMAPEGISQNEVVYSLMAELGWRKDPVPDLAAWVTSFAA
RRYGVSHPDAGAAWRLLLRSVYNCSGEACRGHNRSPLVRRPSLQMNTSIWYNRSDVFEAW
RLLLTSAPSLATSPAFRYDLLDLTRQAVQELVSLYYEEARSAYLSKELASLLRAGGVLAY
ELLPALDEVLASDSRFLLGSWLEQARAAAVSEAEADFYEQNSRYQLTLWGPEGNILDYAN
KQLAGLVANYYTPRWRLFLEALVDSVAQGIPFQQHQFDKNVFQLEQAFVLSKQRYPSQPR
GDTVDLAKKIFLKYYPRWVAGSW

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	P54802-D1	1-164,307-510	368		MEAVAVAAAVGVLLLAGAGGAAGDEAREAAAVRALVARLLGPGPAADFSVSVERALAAKPGLDTYSLGGGGAARVRVRGSTGVAAAAGLHRYLRDFCGCHVAWSGSQLRLPRPLPAVPGELTEATPNRYRYYQNVCTQSYSFVWWDWARWEREIDWMALNGINLHIYGADTFNEMQPPSSEPSYLAAATTAVYEAMTAVDTEAVWLLQGWLFQHQPQFWGPAQIRAVLGAVPRGRLLVLDLFAESQPVYTRTASFQGQPFIWCMLHNFGGNHGLFGALEAVNGGPEAARLFPNSTMVGTGMAPEGISQNEVVYSLMAELGWRKDPVPDLAAWVTSFAARRYGVSHPDAGAAWRLLLRSVYNCSGEACR
2	P54802-D2	165-306	142		ALAWSGQEAIWQRVYLALGLTQAEINEFFTGPAFLAWGRMGNLHTWDGPLPPSWHIKQLYLQHRVLDQMRSFGMTPVLPAFAGHVPEAVTRVFPQVNVTKMGSWGHFNCSYSCSFLLAPEDPIFPIIGSLFLRELIKEFGTD
3	P54802-D3	511-743	233		GHNRSPLVRRPSLQMNTSIWYNRSDVFEAWRLLLTSAPSLATSPAFRYDLLDLTRQAVQELVSLYYEEARSAYLSKELASLLRAGGVLAYELLPALDEVLASDSRFLLGSWLEQARAAAVSEAEADFYEQNSRYQLTLWGPEGNILDYANKQLAGLVANYYTPRWRLFLEALVDSVAQGIPFQQHQFDKNVFQLEQAFVLSKQRYPSQPRGDTVDLAKKIFLKYYPRWVAGSW

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.85

(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	4xwhA	0.97	0.46	1.000	0.968	model1_4xwhA.pdb.gz
2	2vcaA	0.93	1.90	0.276	0.966	model1_2vcaA.pdb.gz
3	6npsA	0.62	4.86	0.071	0.747	model1_6npsA.pdb.gz
4	4c90A	0.62	4.69	0.079	0.732	model1_4c90A.pdb.gz
5	2epoA	0.61	4.93	0.092	0.744	model1_2epoA.pdb.gz
6	2v5dA	0.49	5.32	0.058	0.612	model1_2v5dA.pdb.gz
7	2ylaA	0.35	4.64	0.059	0.417	model1_2ylaA.pdb.gz
8	3n0fA	0.28	7.90	0.059	0.432	model1_3n0fA.pdb.gz
9	2jgqA	0.24	4.27	0.057	0.277	model1_2jgqA.pdb.gz
10	2bwxA	0.22	7.50	0.061	0.324	model1_2bwxA.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:0004561	1.00	alpha-N-acetylglucosaminidase 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:0048856	0.87	anatomical structure development
GO:0044699	0.75	single-organism process
GO:0008152	0.74	metabolic process
GO:0009987	0.72	cellular process
GO:0071704	0.69	organic substance metabolic process
GO:0044763	0.67	single-organism cellular process
GO:0006807	0.61	nitrogen compound metabolic process
GO:1901564	0.58	organonitrogen compound metabolic process
GO:0043170	0.58	macromolecule metabolic process
GO:1901135	0.56	carbohydrate derivative metabolic process
GO:0016043	0.56	cellular component organization
GO:0048869	0.55	cellular developmental process
GO:0044767	0.55	single-organism developmental process
GO:0006996	0.55	organelle organization
GO:1901575	0.54	organic substance catabolic process
GO:0060119	0.54	inner ear receptor cell development
GO:0046548	0.54	retinal rod cell development
GO:0045475	0.54	locomotor rhythm
GO:0042474	0.54	middle ear morphogenesis
GO:0021680	0.54	cerebellar Purkinje cell layer development
GO:0007040	0.54	lysosome organization
GO:1901565	0.53	organonitrogen compound catabolic process
GO:1901136	0.53	carbohydrate derivative catabolic process
GO:0030203	0.52	glycosaminoglycan metabolic process
GO:0009057	0.52	macromolecule catabolic process
GO:0006027	0.51	glycosaminoglycan catabolic 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:0043227	1.00	membrane-bounded organelle
GO:0070062	0.88	extracellular exosome
GO:0044464	0.87	cell part
GO:0044424	0.79	intracellular part
GO:0044444	0.72	cytoplasmic part
GO:0043229	0.65	intracellular organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0005773	0.56	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

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	0.078	2epoA	0.612	4.93	0.092	0.744	3.2.1.52	NA
2	0.060	3bq5A	0.393	6.36	0.050	0.519	2.1.1.14	NA
3	0.060	3ecqB	0.395	7.50	0.034	0.586	3.2.1.97	64
4	0.060	2bfgA	0.371	5.52	0.051	0.471	3.2.1.37	NA
5	0.060	1xc6A	0.378	6.47	0.037	0.510	3.2.1.23	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	2epnA	0.610	4.96	0.087	0.742	0.22	NGT	complex1.pdb.gz	39,77,79,162
2	0.01	1k9eA	0.536	4.86	0.110	0.645	0.10	GCV	complex2.pdb.gz	76,78,89
3	0.01	1k9fA	0.536	4.84	0.108	0.645	0.11	UUU	complex3.pdb.gz	65,88,92,100
4	0.01	1h41A	0.549	5.16	0.094	0.673	0.11	GCV	complex4.pdb.gz	31,32,56
5	0.01	2gk1H	0.462	4.51	0.100	0.542	0.13	NGT	complex5.pdb.gz	77,79,89
6	0.01	2jiwA	0.505	5.52	0.062	0.634	0.12	BEU	complex6.pdb.gz	62,89,158,160
7	0.01	2wcaA	0.505	5.22	0.061	0.625	0.15	NP6	complex7.pdb.gz	39,78,82
8	0.01	2j47A	0.508	5.43	0.060	0.634	0.13	GDV	complex8.pdb.gz	75,95,96

	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.