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COFACTOR result for job id 76681

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>76681 (310 residues)
MKNLTNEIYDVIIIGSGPAGLTSAIYTARAGLKTVIYEQSAPGGKLIKTDLIENYPGFET
IQGPDLASKMYLQALSLNASVEFVGVNSIFKNADDIFEISLANGETKKAYAVILATGTQE
NKLGIKGEDELYGKGVSYCAVCDGAFYKNKPVAVVGGGYSAVQEAMYLSQLVDKVYLIVR
RDVFRADANKVAKLKAQPNVEFLLKSQVKEIHGTEKVESLTITTPNGEKKLEVSAIFPYI
GSTPLIDSVKHLCIENEKGYIPTNDKMQTEIKGLFVAGDVRDVPLRQIAIACGDGAIAGQ
MAVEYVQEIK

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	2q7vA	0.98	0.74	0.414	0.990	Download
2	2a87A	0.96	1.17	0.373	0.981	Download
3	1vdcA	0.95	1.18	0.372	0.981	Download
4	4jnqA	0.95	1.38	0.358	0.990	Download
5	3d8xA	0.95	1.21	0.366	0.977	Download
6	3f8pD	0.94	1.67	0.384	0.984	Download
7	3ishA	0.93	1.34	0.402	0.971	Download
8	1hyuA	0.93	1.84	0.333	0.997	Download
9	4gcmA	0.93	1.28	0.446	0.955	Download
10	5m5jA	0.93	1.63	0.364	0.974	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:0016491	1.00	oxidoreductase activity
GO:0016668	0.98	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0004791	0.97	thioredoxin-disulfide reductase activity
GO:1901363	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0043167	0.53	ion binding
GO:0000166	0.53	nucleotide binding
GO:0050662	0.50	coenzyme binding
GO:0043169	0.50	cation binding

Download full result of the above consensus prediction.

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(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:0009987	1.00	cellular process
GO:0044237	0.99	cellular metabolic process
GO:0044699	0.98	single-organism process
GO:0044710	0.95	single-organism metabolic process
GO:0072593	0.94	reactive oxygen species metabolic process
GO:0055114	0.94	ox.dat.gzion-reduction process
GO:0019430	0.93	removal of superoxide radicals
GO:0044763	0.85	single-organism cellular process
GO:0065007	0.83	biological regulation
GO:0050794	0.82	regulation of cellular process
GO:0042592	0.80	homeostatic process
GO:0045454	0.79	cell redox homeostasis
GO:0071704	0.75	organic substance metabolic process
GO:0050896	0.70	response to stimulus
GO:0044238	0.67	primary metabolic process
GO:0006950	0.66	response to stress
GO:0006807	0.66	nitrogen compound metabolic process
GO:0034641	0.58	cellular nitrogen compound metabolic process
GO:1901360	0.50	organic cyclic compound 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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0043229	0.63	intracellular organelle
GO:0005737	0.63	cytoplasm
GO:0043227	0.62	membrane-bounded organelle
GO:0005829	0.61	cytosol
GO:0043231	0.60	intracellular membrane-bounded 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	0.471	3d8xB	0.946	1.22	0.366	0.977	1.8.1.9	18,22,52,70,117,141,143,279,282,286,293
2	0.277	2q7vA	0.978	0.74	0.414	0.990	1.8.1.9	NA
3	0.235	3d8xA	0.946	1.21	0.366	0.977	1.8.1.9	NA
4	0.229	1vdcA	0.951	1.19	0.372	0.981	1.8.1.9	NA
5	0.109	1f6mA	0.733	3.51	0.252	0.868	1.8.1.9	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	0.85	2q7vA	0.978	0.74	0.414	0.990	1.57	FAD	Download	15,17,18,19,37,38,39,44,45,46,49,54,84,85,86,115,116,117,142,248,278,279,286,287,288,291
2	0.56	3d8xA	0.946	1.21	0.366	0.977	0.96	NAP	Download	15,17,19,39,40,116
3	0.08	2a87A	0.959	1.17	0.373	0.981	0.93	NAP	Download	121,123,158,159,160,207,240,241,260,283,286

	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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