D-I-TASSER O95777

D-I-TASSER results for O95777

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

Summary of the Protein

Uniprot ID: O95777
Protein Name: U6 snRNA-associated Sm-like protein LSm8
Gene Name: LSM8

Input Sequence in FASTA format

>O95777 (96 residues)
MTSALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLY
IVRGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH

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	O95777-D1	1-96	96		MTSALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIVRGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8593

(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	6ppnH	0.93	0.87	0.457	0.979	model1_6ppnH.pdb.gz
2	4m75A	0.76	2.51	0.280	0.896	model1_4m75A.pdb.gz
3	1d3bL	0.72	1.40	0.296	0.781	model1_1d3bL.pdb.gz
4	5mkl11	0.71	2.73	0.215	0.844	model1_5mkl11.pdb.gz
5	5mqfa	0.70	2.30	0.203	0.823	model1_5mqfa.pdb.gz
6	3jcr7	0.69	1.92	0.347	0.781	model1_3jcr7.pdb.gz
7	5uz5K	0.69	1.69	0.302	0.760	model1_5uz5K.pdb.gz
8	4c8qE	0.69	1.95	0.237	0.792	model1_4c8qE.pdb.gz
9	5mqfc	0.68	1.19	0.236	0.750	model1_5mqfc.pdb.gz
10	1jbmA	0.68	1.59	0.301	0.760	model1_1jbmA.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:0003723	0.99	RNA binding

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:0009987	1.00	cellular process
GO:0044238	0.99	primary metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0043170	0.99	macromolecule metabolic process
GO:0016070	0.98	RNA metabolic process
GO:0016071	0.86	mRNA metabolic process
GO:0006396	0.86	RNA processing
GO:0006397	0.71	mRNA processing
GO:0008380	0.69	RNA splicing
GO:0000398	0.67	mRNA splicing, via spliceosome

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:0030529	1.00	intracellular ribonucleoprotein complex
GO:0044446	0.89	intracellular organelle part
GO:0044428	0.87	nuclear part
GO:0097525	0.81	spliceosomal snRNP complex
GO:0097526	0.80	spliceosomal tri-snRNP complex
GO:0043226	0.55	organelle
GO:0046540	0.54	U4/U6 x U5 tri-snRNP complex
GO:0044444	0.54	cytoplasmic part
GO:0005681	0.54	spliceosomal complex
GO:0043229	0.53	intracellular 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	0.060	2ixlC	0.435	4.50	0.037	0.771	5.1.3.13	74
2	0.060	3iaiA	0.470	4.02	0.074	0.740	4.2.1.1	NA
3	0.060	2cghB	0.453	2.30	0.218	0.573	6.3.4.15	NA
4	0.060	3jxfB	0.493	3.45	0.063	0.698	3.1.3.48	NA
5	0.060	1f4rA	0.448	4.27	0.055	0.823	3.2.2.21	59

	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	0.17	1i5lK	0.679	0.93	0.290	0.719	1.32	RQA	complex1.pdb.gz	32,33,35,63,64,65
2	0.05	1b341	0.622	1.47	0.229	0.698	1.31	III	complex2.pdb.gz	21,28,29,30,31,35,36,39,43,55,58,59,60,61,62,63,65
3	0.04	1m8vC	0.656	1.43	0.261	0.719	0.80	RQA	complex3.pdb.gz	2,3,6,29,30
4	0.04	1b340	0.643	1.89	0.215	0.740	1.14	III	complex4.pdb.gz	5,16,18,22,34,64,65,67,68,69,70,71,72,73,74
5	0.03	3resB	0.537	1.27	0.161	0.583	1.38	ADP	complex5.pdb.gz	16,20,22,68,69,71
6	0.03	3rerE	0.540	1.26	0.161	0.583	0.87	RQA	complex6.pdb.gz	29,30,62,64
7	0.03	1y960	0.553	2.17	0.154	0.635	0.87	III	complex7.pdb.gz	3,5,6,9,10,19,21,23,28,29,30,31,32,35,37,59,60,61,62,63,65

	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.