[back]

COFACTOR result for job id 76317

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

User Input

>76317 (102 residues)
MADIIKITSKEQFDKEIKEGKVLVDFNATWCGPCKMLAPILHDFAKKVGGVKFLDVDVDL
NRQVAEEFRIMSIPTLITFENGNQVNKHIGFATPDQLKKLID

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	6bkvA	0.95	1.24	0.353	1.000	Download
2	3tcoA	0.95	0.82	0.327	0.990	Download
3	2pukC	0.94	0.74	0.283	0.971	Download
4	6gn9A	0.93	0.82	0.424	0.971	Download
5	4xhmA	0.93	1.21	0.353	0.990	Download
6	2yj7A	0.93	0.85	0.444	0.971	Download
7	2e0qA	0.92	0.83	0.316	0.961	Download
8	2i4aA	0.92	1.06	0.356	0.990	Download
9	1xwaA	0.92	1.17	0.347	0.990	Download
10	6esxA	0.91	0.96	0.253	0.971	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	1.00	catalytic activity
GO:0016667	0.96	oxidoreductase activity, acting on a sulfur group of donors
GO:0015035	0.95	protein disulfide oxidoreductase activity
GO:0016671	0.57	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor

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:0008152	0.98	metabolic process
GO:0065007	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0071704	0.96	organic substance metabolic process
GO:0065008	0.96	regulation of biological quality
GO:0050794	0.96	regulation of cellular process
GO:0044763	0.96	single-organism cellular process
GO:0045454	0.95	cell redox homeostasis
GO:0044710	0.95	single-organism metabolic process
GO:0006950	0.94	response to stress
GO:0033554	0.93	cellular response to stress
GO:0006457	0.93	protein folding
GO:0044281	0.92	small molecule metabolic process
GO:0006662	0.89	glycerol ether metabolic process
GO:0055114	0.86	ox.dat.gzion-reduction process
GO:0044237	0.84	cellular metabolic process
GO:0042221	0.60	response to chemical
GO:0070887	0.57	cellular response to chemical stimulus
GO:0006979	0.57	response to ox.dat.gzive stress
GO:0044238	0.56	primary metabolic process
GO:0034599	0.56	cellular response to ox.dat.gzive stress
GO:0006790	0.56	sulfur compound metabolic process
GO:0000103	0.55	sulfate assimilation
GO:0006807	0.52	nitrogen 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:0044424	1.00	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0043226	0.75	organelle
GO:0043229	0.74	intracellular organelle
GO:0043227	0.74	membrane-bounded organelle
GO:0043231	0.73	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	0.353	1cqgA	0.868	1.28	0.378	0.961	1.8.4.10	35,42,58
2	0.199	1syrA	0.888	1.29	0.374	0.971	1.8.1.8	NA
3	0.191	1uvzA	0.908	1.43	0.324	0.990	1.8.1.8	NA
4	0.188	1nswA	0.905	1.08	0.414	0.971	1.8.1.9	NA
5	0.174	2vm1C	0.894	1.20	0.343	0.971	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	0.10	2pvo2	0.890	1.51	0.277	0.980	1.22	III	Download	28,29,30,31,32,33,36,58,73
2	0.08	1x9m1	0.899	1.08	0.394	0.971	1.40	III	Download	30,31,32,33,36,58,62,65,66,71,72,73,88,89,90,91,92,96,99,100
3	0.07	2o8v2	0.893	1.48	0.376	0.980	0.90	III	Download	31,32,33,35,72,73,74,89,90
4	0.06	1oaz2	0.806	2.00	0.309	0.951	0.91	III	Download	71,72,73,90
5	0.05	1i5gA	0.689	3.16	0.218	0.931	1.28	TS5	Download	30,31,33,71,72,73

	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).

[back]