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COFACTOR result for job id 76300

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

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>76300 (199 residues)
MSKVLVLKTTAQADEVSNSVALTNRFLEEYKKFNPDDEIIIVDLNKDEVGTSILTSETFS
TFYQQEVTKKYINLLKSVDKLVIACPMYNFSTPVTLKSFIDHVSVANETFSYKYSKKGDA
IGLITNLKAQILGVQGAPLGWYPWGQHTQYVEGAMRFLGIEFNKTVLLAGVKVAPLLQLT
PEQRVETIIDEVIEAARTF

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	3w78A	0.94	1.02	0.240	0.965	Download
2	1tikA	0.90	1.45	0.274	0.955	Download
3	2hpvA	0.89	1.57	0.273	0.940	Download
4	4c0wA	0.88	1.46	0.245	0.945	Download
5	3kegB	0.88	1.92	0.217	0.950	Download
6	3p0rA	0.88	1.65	0.278	0.940	Download
7	3u7iA	0.88	1.61	0.265	0.930	Download
8	3lcmA	0.81	2.47	0.179	0.920	Download
9	1sg0A	0.79	2.89	0.156	0.935	Download
10	4gi5A	0.78	2.57	0.158	0.925	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:1901363	0.93	heterocyclic compound binding
GO:0097159	0.93	organic cyclic compound binding
GO:0016491	0.93	oxidoreductase activity
GO:0016651	0.91	oxidoreductase activity, acting on NAD(P)H
GO:0048037	0.90	cofactor binding
GO:0000166	0.90	nucleotide binding
GO:0010181	0.89	FMN binding
GO:0016646	0.87	oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
GO:0009055	0.86	electron carrier activity
GO:0016652	0.85	oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor
GO:0008752	0.85	FMN reductase activity
GO:0016655	0.70	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor

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:

[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	0.98	cellular process
GO:0008152	0.98	metabolic process
GO:0044237	0.97	cellular metabolic process
GO:0044699	0.90	single-organism process
GO:0044710	0.88	single-organism metabolic process
GO:0055114	0.87	ox.dat.gzion-reduction process
GO:0044763	0.87	single-organism cellular process
GO:0022900	0.85	electron transport chain
GO:0071704	0.69	organic substance metabolic process
GO:0050896	0.69	response to stimulus
GO:0044238	0.65	primary metabolic process
GO:0006950	0.57	response to stress
GO:0009058	0.55	biosynthetic process
GO:0044249	0.50	cellular biosynthetic process
GO:0006979	0.50	response to ox.dat.gzive stress

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	0.97	cytoplasmic part
GO:0005829	0.95	cytosol
GO:0043226	0.58	organelle
GO:0043227	0.56	membrane-bounded organelle
GO:0005737	0.50	cytoplasm

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	0.134	1qr2A	0.785	2.91	0.156	0.935	1.10.99.2 1.6.99.2	122
2	0.133	2qx9B	0.781	2.91	0.151	0.935	1.10.99.2	104
3	0.108	1d4aA	0.778	2.93	0.146	0.930	1.6.5.2	NA
4	0.093	2yxbA	0.466	3.46	0.099	0.608	5.4.99.2	NA
5	0.070	2rg1B	0.599	2.83	0.114	0.724	1.6.5.2	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	0.40	1t5bA	0.900	1.51	0.293	0.960	1.38	FMN	Download	10,12,17,18,19,86,87,88,89,90,134,135,136,137,139
2	0.18	3r6wB	0.852	1.67	0.221	0.909	0.92	NFZ	Download	104,110,121,157
3	0.16	2bzsA	0.780	2.92	0.156	0.935	0.91	FAD	Download	10,17,18,19,21,86,87,133,141,171,182,185,186
4	0.15	3lcmD	0.804	2.56	0.179	0.920	1.07	NAP	Download	110,112,153,157
5	0.12	3ox1A	0.783	2.92	0.156	0.935	1.00	695	Download	106,110,111,157

	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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