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COFACTOR result for job id 76691

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

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>76691 (344 residues)
MDNKDIYVFGLSASQQLAKEVCHFLGVEQKVVKTTRFADGEILVESIDSVRGKEIYVIQS
TSMPVNENLMELLIAIDAFKRGSAEKINVVIPYYGYARQDRKAKGRQPITAKLVADLLTK
AGADRVIVFDIHSTQTMGFFDMPMDNFHTSQSLANEIVDTIIREKFDPEKCILVSPDYGG
LNRVHKVDSYTANMTNGIAVIGKRRPEPNKAEVEFVLGDIEGRTCFIIDDMIDTGGTIIS
GAKALKANGAKDVYIFACHGLFNGPAKERMTQAIKEGIVKNVVVTNTVEIPQERQFEGLK
IVSVAPLLANMIKESQEHHSLTEVYNKNKDEIQLKIQDFMNHKN

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	5t3oA	0.88	0.64	0.355	0.892	Download
2	2hcrB	0.87	1.31	0.381	0.892	Download
3	1dkrB	0.86	1.24	0.472	0.881	Download
4	2c4kA	0.85	1.14	0.326	0.875	Download
5	4s2uA	0.85	1.52	0.392	0.881	Download
6	5mp7A	0.85	1.21	0.436	0.866	Download
7	3dahC	0.83	1.60	0.403	0.858	Download
8	3lpnA	0.76	1.96	0.260	0.811	Download
9	4twbA	0.76	1.92	0.273	0.808	Download
10	1u9yA	0.74	1.94	0.293	0.794	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	0.99	catalytic activity
GO:0004749	0.97	ribose phosphate diphosphokinase activity
GO:1901363	0.78	heterocyclic compound binding
GO:0097159	0.78	organic cyclic compound binding
GO:0000166	0.73	nucleotide binding
GO:0005524	0.72	ATP binding
GO:0043167	0.66	ion binding
GO:0046872	0.64	metal ion binding
GO:0000287	0.62	magnesium ion binding
GO:0042802	0.56	identical protein binding
GO:0016301	0.53	kinase 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:

[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:0071704	0.97	organic substance metabolic process
GO:0044237	0.97	cellular metabolic process
GO:0044238	0.93	primary metabolic process
GO:0006807	0.92	nitrogen compound metabolic process
GO:1901576	0.89	organic substance biosynthetic process
GO:0034641	0.89	cellular nitrogen compound metabolic process
GO:1901360	0.87	organic cyclic compound metabolic process
GO:0046483	0.87	heterocycle metabolic process
GO:0006725	0.87	cellular aromatic compound metabolic process
GO:1901564	0.86	organonitrogen compound metabolic process
GO:0044699	0.86	single-organism process
GO:0006796	0.86	phosphate-containing compound metabolic process
GO:0006139	0.86	nucleobase-containing compound metabolic process
GO:0019637	0.85	organophosphate metabolic process
GO:0044281	0.84	small molecule metabolic process
GO:1901135	0.83	carbohydrate derivative metabolic process
GO:0090407	0.83	organophosphate biosynthetic process
GO:1901137	0.81	carbohydrate derivative biosynthetic process
GO:0019693	0.81	ribose phosphate metabolic process
GO:0044249	0.80	cellular biosynthetic process
GO:0046390	0.79	ribose phosphate biosynthetic process
GO:0044271	0.78	cellular nitrogen compound biosynthetic process
GO:0055086	0.77	nucleobase-containing small molecule metabolic process
GO:1901362	0.74	organic cyclic compound biosynthetic process
GO:0019438	0.74	aromatic compound biosynthetic process
GO:0018130	0.74	heterocycle biosynthetic process
GO:0034654	0.73	nucleobase-containing compound biosynthetic process
GO:0006753	0.73	nucleoside phosphate metabolic process
GO:1901566	0.71	organonitrogen compound biosynthetic process
GO:0006015	0.71	5-phosphoribose 1-diphosphate biosynthetic process
GO:1901293	0.70	nucleoside phosphate biosynthetic process
GO:0009117	0.66	nucleotide metabolic process
GO:0009165	0.63	nucleotide biosynthetic process
GO:0009116	0.63	nucleoside metabolic process
GO:0072522	0.62	purine-containing compound biosynthetic process
GO:0006163	0.59	purine nucleotide metabolic process
GO:0009156	0.58	ribonucleoside monophosphate biosynthetic process
GO:0006164	0.58	purine nucleotide biosynthetic process
GO:0032502	0.54	developmental process
GO:0016310	0.52	phosphorylation
GO:0006082	0.50	organic acid 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	0.97	intracellular part
GO:0044444	0.80	cytoplasmic part
GO:0032991	0.78	macromolecular complex
GO:1902494	0.72	catalytic complex
GO:0005737	0.68	cytoplasm
GO:0002189	0.66	ribose phosphate diphosphokinase complex
GO:0043226	0.52	organelle
GO:0043227	0.50	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	0.205	1dkrB	0.861	1.24	0.472	0.881	2.7.6.1	NA
2	0.182	1u9yC	0.737	1.95	0.293	0.794	2.7.6.1	NA
3	0.060	2gcgA	0.499	5.14	0.097	0.704	1.1.1.81 1.1.1.79	NA
4	0.060	1gdhA	0.511	4.62	0.077	0.689	1.1.1.29	NA
5	0.060	1gq2A	0.535	5.86	0.068	0.805	1.1.1.40	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	0.04	3mbiA	0.779	1.87	0.259	0.831	0.12	ADP	Download	53,54,83,122
2	0.01	1do8B	0.538	5.71	0.064	0.808	0.14	NAD	Download	8,51,52,53,79,122,123,125
3	0.01	1pjlC	0.533	5.74	0.067	0.799	0.14	NAD	Download	11,12,31,32,74
4	0.01	1gq2A	0.535	5.86	0.068	0.805	0.11	NAP	Download	49,84,122
5	0.01	1dxyA	0.531	4.59	0.074	0.704	0.16	NAD	Download	46,47,48,49,57,120
6	0.01	1pjlA	0.514	5.97	0.066	0.799	0.15	NAD	Download	51,52,53,79,80
7	0.01	1gz3A	0.535	5.89	0.077	0.811	0.17	ATP	Download	77,78,79
8	0.01	2o4cA	0.522	5.09	0.071	0.724	0.11	NAD	Download	17,21,309
9	0.01	1gz4D	0.534	5.81	0.072	0.802	0.16	ATP	Download	70,80,81
10	0.01	1do8A	0.537	5.72	0.064	0.808	0.14	NAD	Download	10,11,58,59,60,123,124,125

	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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