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COFACTOR result for job id 76387

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>76387 (393 residues)
MILVINSGSSSIKFKLFDTSKTIEPILDGLAERIGIDGFLKFEHNNQKYKFEDTLPDHEH
AIQLILNKLLELKIISNIDEINGVGFRVVHGGEISHSSIITDEILSKIQDSVKLAPLHNP
AAIIAIKAVKKLMPNTNMVACFDTAFHQTMPEVNYLYTVPYKWYEEFGVRKYGFHGISYE
YIVNKSSEILNKKKENLNLIVCHLGNGASISCIKDGKSYDTSMGLTPLAGLMMGTRSGDI
DVSICEYIAKQTNTDIFTITQTLNKQSGLLGLSQVSADMRDVLEQYDKNDKKAVIAVEKY
VQIVADFIVKYANYLDSIDAVVFTAGIGENADVIRDLICKKVKLLDLQIDQDKNQAKYSD
YKLISSEESKIPVYAIRTNEEKMICLDTLNLIK

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	1tuuA	0.98	0.94	0.427	0.995	Download
2	2iirA	0.94	1.85	0.452	0.998	Download
3	2e1yA	0.92	1.90	0.408	0.980	Download
4	4ijnA	0.92	1.38	0.373	0.949	Download
5	6ioyA	0.92	2.23	0.375	0.998	Download
6	4h0pA	0.91	2.24	0.329	0.982	Download
7	3p4iA	0.90	1.79	0.355	0.954	Download
8	3khyA	0.88	1.97	0.435	0.942	Download
9	4h0oA	0.88	2.26	0.341	0.954	Download
10	1sazA	0.71	3.10	0.191	0.822	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:0016774	1.00	phosphotransferase activity, carboxyl group as acceptor
GO:0016301	1.00	kinase activity
GO:0008776	0.98	acetate kinase activity
GO:0046872	0.95	metal ion binding
GO:0005524	0.94	ATP binding
GO:0000287	0.93	magnesium ion binding
GO:0008980	0.70	propionate kinase activity

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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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044710	1.00	single-organism metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0071704	0.99	organic substance metabolic process
GO:0044763	0.99	single-organism cellular process
GO:0044281	0.98	small molecule metabolic process
GO:0006082	0.97	organic acid metabolic process
GO:1901576	0.96	organic substance biosynthetic process
GO:0044249	0.96	cellular biosynthetic process
GO:0006796	0.94	phosphate-containing compound metabolic process
GO:0016310	0.93	phosphorylation
GO:0009108	0.93	coenzyme biosynthetic process
GO:0006085	0.92	acetyl-CoA biosynthetic process
GO:0044238	0.70	primary metabolic process
GO:0006091	0.62	generation of precursor metabolites and energy
GO:0019752	0.60	carboxylic acid metabolic process
GO:0055114	0.59	ox.dat.gzion-reduction process
GO:0015980	0.58	energy derivation by ox.dat.gzion of organic compounds
GO:0006113	0.57	fermentation
GO:0006807	0.56	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:0016020	1.00	membrane
GO:0005829	1.00	cytosol
GO:0005737	0.52	cytoplasm
GO:0005622	0.51	intracellular

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	0.653	1tuuA	0.978	0.94	0.427	0.995	2.7.2.1	9,87,143,207,236
2	0.622	1x3mA	0.922	1.87	0.408	0.980	2.7.2.15 2.7.2.-	9,87,143,207,236
3	0.580	2e20A	0.924	1.83	0.408	0.980	2.7.2.15	6,8,87,114,116,118,174,203,206,227,236,380
4	0.197	2iirA	0.939	1.85	0.452	0.998	2.7.2.1	9,87,143,207,236
5	0.125	2iirJ	0.941	1.83	0.452	0.998	2.7.2.1	6,8,87,89,115,118,174,203,206,227,236,380

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.54	2e20A	0.924	1.83	0.408	0.980	1.37	B4P	Download	6,87,89,174,175,203,205,206,207,227,278,279,280,326,327,330
	2	0.04	1hkbB	0.566	4.81	0.097	0.743	0.50	G6P	Download	6,205,206,324,325,326,380

	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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