D-I-TASSER P58557

D-I-TASSER results for P58557

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

Summary of the Protein

Uniprot ID: P58557
Protein Name: Endoribonuclease YbeY
Gene Name: YBEY

Input Sequence in FASTA format

>P58557 (167 residues)
MSLVIRNLQRVIPIRRAPLRSKIEIVRRILGVQKFDLGIICVDNKNIQHINRIYRDRNVP
TDVLSFPFHEHLKAGEFPQPDFPDDYNLGDIFLGVEYIFHQCKENEDYNDVLTVTATHGL
CHLLGFTHGTEAEWQQMFQKEKAVLDELGRRTGTRLQPLTRGLFGGS

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	P58557-D1	1-95	95		MSLVIRNLQRVIPIRRAPLRSKIEIVRRILGVQKFDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEHLKAGEFPQPDFPDDYNLGDIFLGV
2	P58557-D2	96-167	72		EYIFHQCKENEDYNDVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDELGRRTGTRLQPLTRGLFGGS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.87

(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	1xm5A	0.80	1.83	0.219	0.874	model1_1xm5A.pdb.gz
2	1oz9A	0.77	1.36	0.261	0.826	model1_1oz9A.pdb.gz
3	5zumA	0.59	4.00	0.103	0.862	model1_5zumA.pdb.gz
4	1tviA	0.59	3.31	0.207	0.784	model1_1tviA.pdb.gz
5	6eomA	0.58	4.21	0.093	0.880	model1_6eomA.pdb.gz
6	5yfbA	0.57	4.12	0.103	0.844	model1_5yfbA.pdb.gz
7	4ar1A1	0.56	3.97	0.088	0.802	model1_4ar1A1.pdb.gz
8	3forA	0.56	3.63	0.047	0.766	model1_3forA.pdb.gz
9	3nqxA	0.55	3.65	0.087	0.754	model1_3nqxA.pdb.gz
10	3dbkA	0.55	3.68	0.071	0.754	model1_3dbkA.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:0016787	0.98	hydrolase activity
GO:0016788	0.96	hydrolase activity, acting on ester bonds
GO:0016791	0.87	phosphatase activity
GO:0046872	0.71	metal ion binding
GO:0046914	0.69	transition metal ion binding
GO:0070011	0.67	peptidase activity, acting on L-amino acid peptides
GO:0008270	0.67	zinc ion binding
GO:0008237	0.66	metallopeptidase activity
GO:0004175	0.66	endopeptidase activity
GO:0004222	0.65	metalloendopeptidase 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:0009058	1.00	biosynthetic process
GO:0044699	0.96	single-organism process
GO:0044281	0.95	small molecule metabolic process
GO:0044283	0.94	small molecule biosynthetic process
GO:0071704	0.83	organic substance metabolic process
GO:0044238	0.82	primary metabolic process
GO:0043170	0.78	macromolecule metabolic process
GO:0009987	0.77	cellular process
GO:0019538	0.71	protein metabolic process
GO:0006508	0.68	proteolysis
GO:0044237	0.67	cellular metabolic process
GO:0006807	0.61	nitrogen compound metabolic process
GO:0034641	0.59	cellular nitrogen compound metabolic process
GO:1901360	0.58	organic cyclic compound metabolic process
GO:0044260	0.58	cellular macromolecule metabolic process
GO:0046483	0.57	heterocycle metabolic process
GO:0006725	0.57	cellular aromatic compound metabolic process
GO:0065007	0.56	biological regulation
GO:0006139	0.56	nucleobase-containing compound metabolic process
GO:0090304	0.55	nucleic acid metabolic process
GO:1901576	0.54	organic substance biosynthetic process
GO:0044249	0.54	cellular biosynthetic process
GO:0016070	0.54	RNA metabolic process
GO:0050789	0.53	regulation of biological process
GO:0050794	0.52	regulation of cellular process
GO:0034660	0.51	ncRNA metabolic process
GO:1901564	0.50	organonitrogen compound metabolic process
GO:0006396	0.50	RNA processing

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:0044424	1.00	intracellular part
GO:0043226	0.67	organelle
GO:0043229	0.65	intracellular organelle
GO:0043227	0.65	membrane-bounded organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0044444	0.59	cytoplasmic part
GO:0044446	0.56	intracellular organelle part

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	8tlnE	0.519	3.90	0.039	0.749	3.4.24.27	111,118
2	0.060	1su3B	0.503	3.96	0.132	0.713	3.4.24.7	NA
3	0.060	1zkxB	0.516	4.52	0.101	0.790	3.4.24.69	NA
4	0.060	2dqmA	0.549	3.64	0.069	0.731	3.4.11.2	NA
5	0.060	3ffzA	0.523	4.72	0.103	0.844	3.4.24.69	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	0.22	1xm5A	0.802	1.83	0.219	0.874	1.20	NI	complex1.pdb.gz	118,122,128
2	0.04	3mdjC	0.558	3.41	0.092	0.749	0.54	BES	complex2.pdb.gz	61,62,63,64,65,115,118,119
3	0.02	3b2xA	0.551	3.75	0.092	0.737	0.74	NA	complex3.pdb.gz	146,147,148,149,151
4	0.02	3nn7A	0.561	3.61	0.055	0.760	0.53	BXA	complex4.pdb.gz	63,115,118,119,157
5	0.01	1lncE	0.519	3.68	0.062	0.725	0.57	MN	complex5.pdb.gz	118,119,122,137
6	0.01	1fj3A	0.518	3.91	0.039	0.749	0.52	ACN	complex6.pdb.gz	30,88,120,124
7	0.01	3msaA	0.520	3.90	0.039	0.749	0.51	B3R	complex7.pdb.gz	26,29,120,124

	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.