D-I-TASSER Q5QJU3

D-I-TASSER results for Q5QJU3

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

Summary of the Protein

Uniprot ID: Q5QJU3
Protein Name: Alkaline ceramidase 2
Gene Name: ACER2

Input Sequence in FASTA format

>Q5QJU3 (275 residues)
MGAPHWWDQLQAGSSEVDWCEDNYTIVPAIAEFYNTISNVLFFILPPICMCLFRQYATCF
NSGIYLIWTLLVVVGIGSVYFHATLSFLGQMLDELAVLWVLMCALAMWFPRRYLPKIFRN
DRGRFKVVVSVLSAVTTCLAFVKPAINNISLMTLGVPCTALLIAELKRCDNMRVFKLGLF
SGLWWTLALFCWISDRAFCELLSSFNFPYLHCMWHILICLAAYLGCVCFAYFDAASEIPE
QGPVIKFWPNEKWAFIGVPYVSLLCANKKSSVKIT

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	Q5QJU3-D1	1-275	275		MGAPHWWDQLQAGSSEVDWCEDNYTIVPAIAEFYNTISNVLFFILPPICMCLFRQYATCFNSGIYLIWTLLVVVGIGSVYFHATLSFLGQMLDELAVLWVLMCALAMWFPRRYLPKIFRNDRGRFKVVVSVLSAVTTCLAFVKPAINNISLMTLGVPCTALLIAELKRCDNMRVFKLGLFSGLWWTLALFCWISDRAFCELLSSFNFPYLHCMWHILICLAAYLGCVCFAYFDAASEIPEQGPVIKFWPNEKWAFIGVPYVSLLCANKKSSVKIT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7625

(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	6krzA	0.77	2.63	0.112	0.855	model1_6krzA.pdb.gz
2	4xtlA	0.65	3.61	0.066	0.826	model1_4xtlA.pdb.gz
3	5b2nA	0.65	3.54	0.071	0.811	model1_5b2nA.pdb.gz
4	6nwdA	0.62	3.52	0.070	0.782	model1_6nwdA.pdb.gz
5	2z73A	0.62	5.01	0.077	0.902	model1_2z73A.pdb.gz
6	4zwjA	0.61	4.53	0.066	0.855	model1_4zwjA.pdb.gz
7	5wb1A	0.61	4.53	0.086	0.847	model1_5wb1A.pdb.gz
8	3ddlA	0.61	3.72	0.088	0.785	model1_3ddlA.pdb.gz
9	1u19A	0.61	4.56	0.084	0.851	model1_1u19A.pdb.gz
10	2ks9A	0.60	4.95	0.051	0.873	model1_2ks9A.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:0017040	1.00	ceramidase activity
GO:0004553	0.83	hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0071633	0.68	dihydroceramidase 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:0006665	1.00	sphingolipid metabolic process
GO:0034641	0.95	cellular nitrogen compound metabolic process
GO:0030148	0.91	sphingolipid biosynthetic process
GO:0044271	0.86	cellular nitrogen compound biosynthetic process
GO:0044281	0.83	small molecule metabolic process
GO:0065007	0.78	biological regulation
GO:0006670	0.78	sphingosine metabolic process
GO:0050789	0.77	regulation of biological process
GO:0044283	0.77	small molecule biosynthetic process
GO:0046512	0.76	sphingosine biosynthetic process
GO:0050896	0.66	response to stimulus
GO:0080090	0.64	regulation of primary metabolic process
GO:0050794	0.60	regulation of cellular process
GO:0042221	0.60	response to chemical
GO:0048522	0.56	positive regulation of cellular process
GO:0008284	0.54	positive regulation of cell proliferation

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:0044444	1.00	cytoplasmic part
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0044446	0.81	intracellular organelle part
GO:0044425	0.77	membrane part
GO:0016020	0.67	membrane
GO:0016021	0.64	integral component of membrane
GO:0044431	0.63	Golgi apparatus part
GO:0030173	0.60	integral component of Golgi 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	3bhgA	0.415	4.66	0.031	0.593	4.3.2.2	NA
2	0.060	1h2aL	0.423	5.23	0.029	0.629	1.12.2.1	212
3	0.060	2o6yA	0.491	5.12	0.038	0.727	4.3.1.-	NA
4	0.060	1qleA	0.556	5.47	0.059	0.866	1.9.3.1	NA
5	0.060	1y2mB	0.431	5.74	0.073	0.698	4.3.1.24	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	0.09	3abwD	0.597	3.79	0.093	0.764	1.08	22B	complex1.pdb.gz	42,70,74,79
2	0.07	3abwA	0.597	3.73	0.088	0.760	0.94	AZI	complex2.pdb.gz	75,78,93,97
3	0.06	1brrB	0.597	3.39	0.069	0.742	0.90	ARC	complex3.pdb.gz	74,77,93,97,98
4	0.05	2zzlA	0.590	3.25	0.060	0.724	0.93	SOG	complex4.pdb.gz	41,42,43,75,78
5	0.03	3qbgB	0.597	3.80	0.083	0.764	1.00	22B	complex5.pdb.gz	36,40,76,79
6	0.03	3qbgA	0.597	3.81	0.083	0.764	0.94	22B	complex6.pdb.gz	69,73,77,92,96
7	0.02	2at9A	0.564	3.54	0.067	0.709	1.08	2DP	complex7.pdb.gz	39,76,79,80,83
8	0.02	1jv6A	0.560	3.30	0.058	0.695	1.03	LI1	complex8.pdb.gz	76,79,80,84,85
9	0.02	1jv6A	0.560	3.30	0.058	0.695	0.88	LI1	complex9.pdb.gz	69,72,76,92,95

	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.