D-I-TASSER Q9BQE4

D-I-TASSER results for Q9BQE4

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

Summary of the Protein

Uniprot ID: Q9BQE4
Protein Name: Selenoprotein S
Gene Name: SELENOS

Input Sequence in FASTA format

>Q9BQE4 (189 residues)
MERQEESLSARPALETEGLRFLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQ
RQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWD
SMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGR
RGPSSGGGG

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	Q9BQE4-D1	1-189	189		MERQEESLSARPALETEGLRFLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRRGPSSGGGG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.288

(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	3jc8Na	0.50	4.45	0.086	0.751	model1_3jc8Na.pdb.gz
2	6vq6I	0.49	4.47	0.063	0.704	model1_6vq6I.pdb.gz
3	6thkA	0.49	4.77	0.082	0.762	model1_6thkA.pdb.gz
4	7ko4P	0.49	3.55	0.053	0.656	model1_7ko4P.pdb.gz
5	2dfsA	0.48	3.70	0.049	0.645	model1_2dfsA.pdb.gz
6	2tmaA1	0.47	3.72	0.095	0.656	model1_2tmaA1.pdb.gz
7	3ghgK	0.47	5.20	0.040	0.788	model1_3ghgK.pdb.gz
8	4dl0J	0.47	4.82	0.040	0.720	model1_4dl0J.pdb.gz
9	1m1jE	0.44	4.95	0.082	0.688	model1_1m1jE.pdb.gz
10	2b9cB	0.42	4.50	0.083	0.614	model1_2b9cB.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:1990381	0.99	ubiquitin-specific protease binding
GO:0051117	0.99	ATPase binding
GO:0016209	0.99	antioxidant activity
GO:0004872	0.56	receptor 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:0051649	1.00	establishment of localization in cell
GO:0050794	1.00	regulation of cellular process
GO:0044763	1.00	single-organism cellular process
GO:0008104	1.00	protein localization
GO:2000110	0.99	negative regulation of macrophage apoptotic process
GO:1902236	0.99	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:0080164	0.99	regulation of nitric oxide metabolic process
GO:0071222	0.99	cellular response to lipopolysaccharide
GO:0051775	0.99	response to redox state
GO:0051771	0.99	negative regulation of nitric-oxide synthase biosynthetic process
GO:0045454	0.99	cell redox homeostasis
GO:0034599	0.99	cellular response to oxidative stress
GO:0032720	0.99	negative regulation of tumor necrosis factor production
GO:0032715	0.99	negative regulation of interleukin-6 production
GO:0030970	0.99	retrograde protein transport, ER to cytosol
GO:0030968	0.99	endoplasmic reticulum unfolded protein response
GO:0030433	0.99	ER-associated ubiquitin-dependent protein catabolic process
GO:0006983	0.99	ER overload response
GO:0002865	0.99	negative regulation of acute inflammatory response to antigenic stimulus
GO:0080090	0.58	regulation of primary metabolic process
GO:0031326	0.57	regulation of cellular biosynthetic process
GO:2000112	0.56	regulation of cellular macromolecule biosynthetic process
GO:0032879	0.55	regulation of localization
GO:0031324	0.55	negative regulation of cellular metabolic process
GO:0009719	0.55	response to endogenous stimulus
GO:0046325	0.54	negative regulation of glucose import
GO:0045719	0.54	negative regulation of glycogen biosynthetic process
GO:0032869	0.54	cellular response to insulin stimulus
GO:0009749	0.54	response to glucose
GO:0006111	0.54	regulation of gluconeogenesis

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:0044446	1.00	intracellular organelle part
GO:0044444	1.00	cytoplasmic part
GO:0044430	0.78	cytoskeletal part
GO:0005874	0.77	microtubule
GO:0005881	0.76	cytoplasmic microtubule
GO:0043226	0.64	organelle
GO:0043229	0.62	intracellular organelle
GO:0043227	0.61	membrane-bounded organelle
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0005783	0.51	endoplasmic reticulum

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	1k3iA	0.238	5.81	0.011	0.439	1.1.3.9	NA
2	0.060	2c9aA	0.206	5.63	0.053	0.370	3.1.3.48	NA
3	0.060	1w27A	0.376	5.20	0.039	0.609	4.3.1.24	NA
4	0.060	2ahmE	0.204	4.64	0.017	0.312	2.7.7.48	NA
5	0.060	3b8cB	0.353	5.56	0.050	0.609	3.6.3.6	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	1hvvC	0.280	2.75	0.047	0.339	0.57	TAR	complex1.pdb.gz	155,156,158,159
2	0.01	1w7i0	0.271	4.81	0.047	0.434	0.41	III	complex2.pdb.gz	154,156,158,159,160,168,169
3	0.01	2w6dA	0.432	4.96	0.044	0.709	0.42	GDP	complex3.pdb.gz	163,164,169

	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.