D-I-TASSER Q15527

D-I-TASSER results for Q15527

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Summary of the Protein

Uniprot ID: Q15527
Protein Name: Surfeit locus protein 2
Gene Name: SURF2

Input Sequence in FASTA format

>Q15527 (256 residues)
MSELPGDVRAFLREHPSLRLQTDARKVRCILTGHELPCRLPELQVYTRGKKYQRLVRASP
AFDYAEFEPHIVPSTKNPHQLFCKLTLRHINKCPEHVLRHTQGRRYQRALCKYEECQKQG
VEYVPACLVHRRRRREDQMDGDGPRPREAFWEPTSSDEGGAASDDSMTDLYPPELFTRKD
LGSTEDGDGTDDFLTDKEDEKAKPPREKATDESRRETTVYRGLVQKRGKKQLGSLKKKFK
SHHRKPKSFSSCKQPG

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	Q15527-D1	1-62	62		MSELPGDVRAFLREHPSLRLQTDARKVRCILTGHELPCRLPELQVYTRGKKYQRLVRASPAF
2	Q15527-D2	63-256	194		DYAEFEPHIVPSTKNPHQLFCKLTLRHINKCPEHVLRHTQGRRYQRALCKYEECQKQGVEYVPACLVHRRRRREDQMDGDGPRPREAFWEPTSSDEGGAASDDSMTDLYPPELFTRKDLGSTEDGDGTDDFLTDKEDEKAKPPREKATDESRRETTVYRGLVQKRGKKQLGSLKKKFKSHHRKPKSFSSCKQPG

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.71

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2vdcA	0.46	5.89	0.036	0.773	model1_2vdcA.pdb.gz
2	3vsmA	0.46	5.60	0.032	0.750	model1_3vsmA.pdb.gz
3	4rf6A	0.45	5.07	0.021	0.676	model1_4rf6A.pdb.gz
4	1rw9A	0.45	5.70	0.077	0.734	model1_1rw9A.pdb.gz
5	2wdaA	0.45	5.89	0.057	0.746	model1_2wdaA.pdb.gz
6	1n7qA	0.44	5.89	0.051	0.738	model1_1n7qA.pdb.gz
7	1j0nA	0.44	6.25	0.056	0.769	model1_1j0nA.pdb.gz
8	2q1fA	0.44	5.94	0.027	0.734	model1_2q1fA.pdb.gz
9	1hn0A	0.44	6.09	0.026	0.754	model1_1hn0A.pdb.gz
10	7jz6A	0.43	6.25	0.050	0.762	model1_7jz6A.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	0.91	catalytic 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:0008152	0.89	metabolic process
GO:0044238	0.84	primary metabolic process
GO:0071704	0.83	organic substance metabolic process
GO:0009987	0.83	cellular process
GO:0044237	0.75	cellular metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0044699	0.68	single-organism process
GO:0065007	0.63	biological regulation
GO:0050789	0.61	regulation of biological process
GO:0050794	0.60	regulation of cellular process
GO:0019538	0.58	protein metabolic process
GO:0044267	0.57	cellular protein metabolic process
GO:0043412	0.57	macromolecule modification
GO:0048518	0.56	positive regulation of biological process
GO:0006464	0.56	cellular protein modification process
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0048522	0.55	positive regulation of cellular process
GO:0044767	0.54	single-organism developmental process
GO:0051128	0.53	regulation of cellular component organization
GO:0048856	0.53	anatomical structure development
GO:0043687	0.53	post-translational protein modification
GO:0010468	0.53	regulation of gene expression
GO:0045088	0.51	regulation of innate immune response
GO:0031647	0.51	regulation of protein stability
GO:0006508	0.51	proteolysis
GO:1900425	0.50	negative regulation of defense response to bacterium
GO:0060968	0.50	regulation of gene silencing
GO:0045824	0.50	negative regulation of innate immune response
GO:0045751	0.50	negative regulation of Toll signaling pathway
GO:0035220	0.50	wing disc development
GO:0030307	0.50	positive regulation of cell growth
GO:0016579	0.50	protein deubiquitination
GO:0002784	0.50	regulation of antimicrobial peptide production

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:0005886	1.00	plasma membrane
GO:0005730	1.00	nucleolus
GO:0005634	1.00	nucleus

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

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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	2vdcA	0.465	5.89	0.036	0.773	1.4.1.13	NA
2	0.060	1ojnA	0.438	5.98	0.042	0.738	4.2.2.1	NA
3	0.060	2ipyA	0.290	6.11	0.045	0.508	4.2.1.3	NA
4	0.060	1sj2A	0.417	6.21	0.030	0.742	1.11.1.6 1.11.1.7	NA
5	0.060	2x7jA	0.384	6.06	0.058	0.672	2.2.1.9	12

	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

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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	0.01	2bptA	0.401	5.84	0.049	0.676	0.59	III	complex1.pdb.gz	28,31,32,42,46

	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.