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COFACTOR result for job id 76544

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

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>76544 (160 residues)
MSKRLDYLSWQHYFMLIAKASAMRSKDPNTQVGAIVVNELQQIVATGYNGFPRGVSDDEF
PWSKNNEDWLENKYAYVAHAELNAIVSSRSDLSNCDLYVTLFPCNECAKIIIQAGIKRIY
YANDPYHDKKEFIASKKMLDAVNIKYIKLPDIEISLKVKD

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	2w4lE	0.95	0.57	0.481	0.963	Download
2	2hvwA	0.79	2.31	0.299	0.894	Download
3	1vq2A	0.77	2.55	0.295	0.887	Download
4	4p9cA	0.73	2.02	0.293	0.812	Download
5	3zpcA1	0.67	2.55	0.215	0.769	Download
6	2d5nD	0.67	2.44	0.299	0.762	Download
7	1z3aA	0.66	3.19	0.224	0.806	Download
8	2b3jC	0.65	2.87	0.269	0.775	Download
9	2hxvA1	0.65	2.41	0.282	0.744	Download
10	1wwrC	0.65	2.77	0.250	0.769	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:0019239	0.99	deaminase activity
GO:0016787	0.84	hydrolase activity
GO:0016810	0.78	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016814	0.77	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
GO:0043167	0.65	ion binding
GO:0046914	0.63	transition metal ion binding
GO:0008270	0.62	zinc ion binding
GO:0004132	0.60	dCMP deaminase 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)

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[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:1901360	1.00	organic cyclic compound metabolic process
GO:0046483	1.00	heterocycle metabolic process
GO:0044238	1.00	primary metabolic process
GO:0034641	1.00	cellular nitrogen compound metabolic process
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:0043170	0.95	macromolecule metabolic process
GO:0090304	0.94	nucleic acid metabolic process
GO:0016070	0.93	RNA metabolic process
GO:0009451	0.92	RNA modification
GO:1901564	0.78	organonitrogen compound metabolic process
GO:0044281	0.78	small molecule metabolic process
GO:1901576	0.71	organic substance biosynthetic process
GO:0044249	0.71	cellular biosynthetic process
GO:0044271	0.68	cellular nitrogen compound biosynthetic process
GO:1901566	0.67	organonitrogen compound biosynthetic process
GO:0034660	0.65	ncRNA metabolic process
GO:1901362	0.64	organic cyclic compound biosynthetic process
GO:0018130	0.64	heterocycle biosynthetic process
GO:0006399	0.61	tRNA metabolic process
GO:0034470	0.59	ncRNA processing
GO:0055086	0.57	nucleobase-containing small molecule metabolic process
GO:0006400	0.55	tRNA modification
GO:1901135	0.53	carbohydrate derivative metabolic process
GO:0019438	0.52	aromatic compound biosynthetic process
GO:0006796	0.52	phosphate-containing compound metabolic process
GO:0034654	0.51	nucleobase-containing compound biosynthetic process
GO:0019637	0.50	organophosphate 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:0044444	1.00	cytoplasmic part
GO:0005737	1.00	cytoplasm
GO:0005829	0.88	cytosol
GO:0043226	0.61	organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0043229	0.53	intracellular organelle
GO:0043231	0.52	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	0.547	2w4lE	0.950	0.57	0.481	0.963	3.5.4.12	32,82,95,101,105,112,114
2	0.422	1zabA	0.556	2.83	0.152	0.662	3.5.4.5	81
3	0.399	2d30A	0.549	2.36	0.170	0.637	3.5.4.5	81
4	0.398	3dmoA	0.554	2.47	0.218	0.644	3.5.4.5	81
5	0.351	1vq2A	0.765	2.55	0.295	0.887	3.5.4.12	26,46,48,50,82,101,104

	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	0.18	2hvwA	0.793	2.31	0.299	0.894	0.98	DDN	Download	27,29,30,32,49,77,79,80,81,103
2	0.13	1uaqA	0.647	2.59	0.227	0.756	1.01	DUC	Download	32,49,79,80,81,104,107
3	0.12	1wwr0	0.659	2.90	0.260	0.787	0.96	III	Download	76,79,82,86,104,105,106,109,113,114,127,138
4	0.06	2hvwA	0.793	2.31	0.299	0.894	1.37	DCP	Download	24,47,48,50,51,53,54,83
5	0.06	1vq20	0.765	2.55	0.295	0.887	1.05	III	Download	13,16,17,20,21,23,24,42,43,44,45,46
6	0.06	2hvwB	0.787	2.31	0.301	0.887	0.80	DCP	Download	10,41,42

	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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