D-I-TASSER Q11206

D-I-TASSER results for Q11206

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

Summary of the Protein

Uniprot ID: Q11206
Protein Name: CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 4
Gene Name: ST3GAL4

Input Sequence in FASTA format

>Q11206 (333 residues)
MVSKSRWKLLAMLALVLVVMVWYSISREDRYIELFYFPIPEKKEPCLQGEAESKASKLFG
NYSRDQPIFLRLEDYFWVKTPSAYELPYGTKGSEDLLLRVLAITSSSIPKNIQSLRCRRC
VVVGNGHRLRNSSLGDAINKYDVVIRLNNAPVAGYEGDVGSKTTMRLFYPESAHFDPKVE
NNPDTLLVLVAFKAMDFHWIETILSDKKRVRKGFWKQPPLIWDVNPKQIRILNPFFMEIA
ADKLLSLPMQQPRKIKQKPTTGLLAITLALHLCDLVHIAGFGYPDAYNKKQTIHYYEQIT
LKSMAGSGHNVSQEALAIKRMLEMGAIKNLTSF

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	Q11206-D1	1-333	333		MVSKSRWKLLAMLALVLVVMVWYSISREDRYIELFYFPIPEKKEPCLQGEAESKASKLFGNYSRDQPIFLRLEDYFWVKTPSAYELPYGTKGSEDLLLRVLAITSSSIPKNIQSLRCRRCVVVGNGHRLRNSSLGDAINKYDVVIRLNNAPVAGYEGDVGSKTTMRLFYPESAHFDPKVENNPDTLLVLVAFKAMDFHWIETILSDKKRVRKGFWKQPPLIWDVNPKQIRILNPFFMEIAADKLLSLPMQQPRKIKQKPTTGLLAITLALHLCDLVHIAGFGYPDAYNKKQTIHYYEQITLKSMAGSGHNVSQEALAIKRMLEMGAIKNLTSF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6553

(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	6apjA	0.80	1.31	0.245	0.820	model1_6apjA.pdb.gz
2	2wmlA	0.71	2.84	0.263	0.799	model1_2wmlA.pdb.gz
3	5bo6A	0.64	3.57	0.213	0.769	model1_5bo6A.pdb.gz
4	4js1A	0.60	3.39	0.187	0.709	model1_4js1A.pdb.gz
5	2p2vA	0.46	3.84	0.130	0.571	model1_2p2vA.pdb.gz
6	2ycbA	0.45	6.29	0.068	0.745	model1_2ycbA.pdb.gz
7	2xr1A	0.45	6.29	0.063	0.739	model1_2xr1A.pdb.gz
8	5mu5A	0.44	4.33	0.070	0.574	model1_5mu5A.pdb.gz
9	3af5A	0.44	6.30	0.071	0.730	model1_3af5A.pdb.gz
10	1ro7A	0.44	3.83	0.122	0.543	model1_1ro7A.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:0016757	0.99	transferase activity, transferring glycosyl groups
GO:0008373	0.98	sialyltransferase 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:0071704	0.99	organic substance metabolic process
GO:0044699	0.99	single-organism process
GO:0044238	0.99	primary metabolic process
GO:0009987	0.99	cellular process
GO:0044763	0.98	single-organism cellular process
GO:0044710	0.98	single-organism metabolic process
GO:0044237	0.98	cellular metabolic process
GO:0044723	0.97	single-organism carbohydrate metabolic process
GO:0006464	0.97	cellular protein modification process
GO:0009311	0.95	oligosaccharide metabolic process
GO:0006486	0.94	protein glycosylation
GO:0018279	0.91	protein N-linked glycosylation via asparagine
GO:1901135	0.83	carbohydrate derivative metabolic process
GO:0006664	0.82	glycolipid metabolic process
GO:1901564	0.79	organonitrogen compound metabolic process
GO:1901137	0.79	carbohydrate derivative biosynthetic process
GO:0044711	0.79	single-organism biosynthetic process
GO:0006688	0.78	glycosphingolipid biosynthetic process
GO:0001574	0.77	ganglioside biosynthetic 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:0044464	0.90	cell part
GO:0044424	0.88	intracellular part
GO:0044444	0.86	cytoplasmic part
GO:0016020	0.86	membrane
GO:0044446	0.81	intracellular organelle part
GO:0044431	0.79	Golgi apparatus part
GO:0098588	0.75	bounding membrane of organelle
GO:0000139	0.74	Golgi membrane
GO:0043227	0.57	membrane-bounded organelle

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	0.412	2wmlA	0.710	2.84	0.263	0.799	2.4.99.4	124,148,163,172,261,282,294
2	0.060	2gq3A	0.385	6.40	0.037	0.634	2.3.3.9	NA
3	0.060	1ogyA	0.393	6.55	0.056	0.658	1.7.99.4	NA
4	0.060	1oc5A	0.397	5.79	0.056	0.613	3.2.1.91	NA
5	0.060	1y8bA	0.380	5.78	0.033	0.589	2.3.3.9	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:

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
	1	0.62	2wnbA	0.711	2.70	0.261	0.793	1.45	C5P	complex1.pdb.gz	124,125,126,147,148,260,262,281,282,294
	2	0.10	2p2vA	0.460	3.84	0.130	0.571	0.89	CSF	complex2.pdb.gz	124,125,126,147,148,149,169,172,260,261,262,280,281,282,293,294,309

	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.