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COFACTOR result for job id 76513

[Download result.tar.bz2 for all prediction results]

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>76513 (132 residues)
MDCLFCKIINQEIPSYKIYENEYVYSFLDVRPVSNGHLLVITKKHFENFSACDDKYLQEV
ILAKKYLVNLLKEKLNPAGFNYLSNEQAISGQTVLHYHEHIMPKYEKDKGFLLKAEIVDI
DELENTFNKIVK

Download query sequence and structure

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	3lb5C	0.96	0.79	0.338	0.985	Download
2	2eo4A	0.90	1.17	0.354	0.947	Download
3	3o0mA	0.88	1.44	0.276	0.962	Download
4	3anoA	0.85	2.21	0.202	0.955	Download
5	3p0tA	0.83	1.98	0.230	0.947	Download
6	3imiA	0.81	1.02	0.333	0.849	Download
7	1emsA	0.81	1.66	0.213	0.901	Download
8	3l7xA	0.81	1.20	0.295	0.849	Download
9	2fitA	0.81	2.01	0.177	0.917	Download
10	1y23B	0.81	1.15	0.356	0.849	Download

(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	0.98	catalytic activity
GO:0016787	0.92	hydrolase activity
GO:0016817	0.61	hydrolase activity, acting on acid anhydrides
GO:0043167	0.56	ion binding
GO:0046872	0.54	metal ion binding
GO:0016462	0.51	pyrophosphatase 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:

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[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:0071704	0.98	organic substance metabolic process
GO:0044237	0.98	cellular metabolic process
GO:0044238	0.97	primary metabolic process
GO:0006807	0.97	nitrogen compound metabolic process
GO:0034641	0.95	cellular nitrogen compound metabolic process
GO:0006139	0.94	nucleobase-containing compound metabolic process
GO:0044281	0.90	small molecule metabolic process
GO:0044763	0.87	single-organism cellular process
GO:0055086	0.86	nucleobase-containing small molecule metabolic process
GO:0019637	0.82	organophosphate metabolic process
GO:0006796	0.82	phosphate-containing compound metabolic process
GO:0009117	0.81	nucleotide metabolic process
GO:1901564	0.78	organonitrogen compound metabolic process
GO:1901575	0.64	organic substance catabolic process
GO:0044248	0.63	cellular catabolic process
GO:0072521	0.61	purine-containing compound metabolic process
GO:0044712	0.60	single-organism catabolic process
GO:0034655	0.60	nucleobase-containing compound catabolic process
GO:0006163	0.58	purine nucleotide metabolic process
GO:0009166	0.54	nucleotide catabolic process
GO:1901135	0.53	carbohydrate derivative metabolic process
GO:0065007	0.52	biological regulation
GO:0050794	0.50	regulation of cellular 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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043227	0.90	membrane-bounded organelle
GO:0044444	0.87	cytoplasmic part
GO:0043229	0.87	intracellular organelle
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0044446	0.63	intracellular organelle part
GO:0005634	0.62	nucleus
GO:0005829	0.60	cytosol
GO:0005737	0.59	cytoplasm
GO:0044428	0.56	nuclear part
GO:0016020	0.56	membrane
GO:0005886	0.53	plasma membrane
GO:0032991	0.51	macromolecular complex

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	0.127	3rhnA	0.712	2.48	0.330	0.826	3.-.-.-	27,29,32,39
2	0.060	2dhtA	0.477	4.01	0.043	0.720	1.1.1.42	NA
3	0.060	2h31A	0.482	3.97	0.042	0.727	4.1.1.21 6.3.2.6	NA
4	0.060	1c8bA	0.507	3.57	0.050	0.705	3.4.24.78	NA
5	0.060	2fitA	0.821	2.00	0.175	0.932	3.6.1.29	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:

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	0.36	3o0mA	0.883	1.44	0.276	0.962	1.03	AMP	Download	4,5,27,28,29,30,31,39,85,91,92,93,94,98,100
	2	0.07	2eo40	0.904	1.17	0.354	0.947	1.18	III	Download	49,50,52,57,58,61,62,65,68,79,80,81,82,83,84,86,88,89,90,104,105,106

	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.

[Download result.tar.bz2 for all prediction results]

Reference:

Chengxin Zhang, Peter L Freddolino, and Yang Zhang. COFACTOR: Improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017)
Ambrish Roy, Jianyi Yang, and Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, 40:W471-W477 (2012).

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