D-I-TASSER Q9HD40

D-I-TASSER results for Q9HD40

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

Summary of the Protein

Uniprot ID: Q9HD40
Protein Name: O-phosphoseryl-tRNA(Sec) selenium transferase
Gene Name: SEPSECS

Input Sequence in FASTA format

>Q9HD40 (501 residues)
MNRESFAAGERLVSPAYVRQGCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAI
MDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNS
LVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMI
TAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAV
ICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFND
SFIQEISKMYPGRASASPSLDVLITLLSLGSNGYKKLLKERKEMFSYLSNQIKKLSEAYN
ERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFR
GFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRKERSKESDDNYDKTEDVD
IEEMALKLDNVLLDTYQDASS

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	Q9HD40-D1	1-334	334		MNRESFAAGERLVSPAYVRQGCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSLDVLITLLSLGSNGY
2	Q9HD40-D2	335-501	167		KKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRKERSKESDDNYDKTEDVDIEEMALKLDNVLLDTYQDASS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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	3bcbA	0.86	1.30	0.871	0.884	model1_3bcbA.pdb.gz
2	2z67A	0.81	1.73	0.306	0.842	model1_2z67A.pdb.gz
3	4lglA2	0.69	3.69	0.100	0.796	model1_4lglA2.pdb.gz
4	4obuE	0.62	3.11	0.109	0.695	model1_4obuE.pdb.gz
5	4q6rA	0.59	3.35	0.105	0.675	model1_4q6rA.pdb.gz
6	1wyvB	0.59	3.90	0.105	0.685	model1_1wyvB.pdb.gz
7	2c44C	0.58	4.00	0.111	0.695	model1_2c44C.pdb.gz
8	1ibjA	0.57	3.57	0.096	0.655	model1_1ibjA.pdb.gz
9	3hmuA1	0.41	3.78	0.099	0.479	model1_3hmuA1.pdb.gz
10	1v72A1	0.39	3.41	0.124	0.441	model1_1v72A1.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:1901363	0.88	heterocyclic compound binding
GO:0097159	0.88	organic cyclic compound binding
GO:0003723	0.83	RNA binding
GO:0000049	0.82	tRNA binding
GO:0003824	0.61	catalytic activity
GO:0016740	0.50	transferase 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:0001514	1.00	selenocysteine incorporation
GO:0044699	0.77	single-organism process
GO:0044710	0.68	single-organism metabolic process
GO:0044763	0.67	single-organism cellular process
GO:0044281	0.63	small molecule metabolic process
GO:0006807	0.63	nitrogen compound metabolic process
GO:1901564	0.60	organonitrogen compound metabolic process
GO:0006082	0.56	organic acid metabolic process
GO:1901605	0.55	alpha-amino acid metabolic process
GO:0016259	0.54	selenocysteine metabolic 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:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus
GO:0044444	0.77	cytoplasmic part
GO:0005829	0.59	cytosol

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	0.339	1v72A	0.551	3.37	0.114	0.629	4.1.2.26	407
2	0.243	3bcbA	0.863	1.30	0.871	0.884	2.9.1.2	143,145,174,254,281,283,288,290,315,317,321,325
3	0.089	1kkjA	0.611	3.40	0.094	0.697	2.1.2.1	284
4	0.089	2vmzA	0.611	3.40	0.091	0.697	2.1.2.1	254,284
5	0.089	1p3wB	0.602	3.74	0.112	0.703	2.8.1.7	173

	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	0.86	3hl2A	0.857	1.29	0.964	0.878	1.67	PLR	complex1.pdb.gz	143,144,170,174,175,252,254,255,284
2	0.48	3hl2D	0.857	1.30	0.966	0.878	1.79	SEP	complex2.pdb.gz	97,98,99,105,313
3	0.17	3fz7A	0.607	3.69	0.127	0.703	1.28	PO4	complex3.pdb.gz	142,143,144,281,283,284
4	0.02	2vmqA	0.611	3.39	0.094	0.697	0.89	MPD	complex4.pdb.gz	148,152,183,184,311
5	0.02	1ejiA	0.622	3.89	0.085	0.729	0.87	PLG	complex5.pdb.gz	106,312,313

	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.