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COFACTOR result for job id 76348

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>76348 (209 residues)
MTELDINEIEAYNSNKMGWIELITGCMFAGKTEEFIRRLRVLSYAKKRVLAFKPSIDNRY
SVENIISHSGSKLDSYLVHSSDEIKQIIEKENQIQQVDVIGIDEVQFFDEQVVELIEQLA
NQGIIVIVNGLDKDFRCLPFKNVDKLLVTAEFVTKLRARCHLCGNFANRSQRIVNGQPAL
WDSPLILVDGKESYEARCRNCFIAPKKEV

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	2uz3B	0.90	0.74	0.443	0.919	Download
2	2ja1A	0.87	1.74	0.518	0.914	Download
3	1xx6A	0.80	1.45	0.474	0.828	Download
4	2orwB	0.78	1.57	0.339	0.818	Download
5	1w4rA	0.75	1.98	0.353	0.813	Download
6	4uxhA	0.74	2.20	0.353	0.804	Download
7	3e2iA1	0.52	1.21	0.513	0.541	Download
8	3qvoA	0.40	4.92	0.043	0.622	Download
9	3gvpA2	0.36	5.26	0.061	0.593	Download
10	1qzgA	0.26	5.58	0.031	0.435	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:0004797	0.99	thymidine kinase activity
GO:1901363	0.87	heterocyclic compound binding
GO:0097159	0.87	organic cyclic compound binding
GO:0035639	0.85	purine ribonucleoside triphosphate binding
GO:0032559	0.85	adenyl ribonucleotide binding
GO:0005524	0.84	ATP binding
GO:0043167	0.80	ion binding
GO:0046872	0.78	metal ion binding
GO:0008270	0.77	zinc ion binding

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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[0.5,0.6)

[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:1901564	1.00	organonitrogen compound metabolic process
GO:0055086	1.00	nucleobase-containing small molecule metabolic process
GO:0006259	1.00	DNA metabolic process
GO:0046104	0.99	thymidine metabolic process
GO:1901576	0.89	organic substance biosynthetic process
GO:0044249	0.89	cellular biosynthetic process
GO:0044271	0.88	cellular nitrogen compound biosynthetic process
GO:0034654	0.87	nucleobase-containing compound biosynthetic process
GO:0019637	0.87	organophosphate metabolic process
GO:0006796	0.87	phosphate-containing compound metabolic process
GO:1901293	0.86	nucleoside phosphate biosynthetic process
GO:0034645	0.86	cellular macromolecule biosynthetic process
GO:0016310	0.85	phosphorylation
GO:0009124	0.85	nucleoside monophosphate biosynthetic process
GO:0071897	0.84	DNA biosynthetic process
GO:0009157	0.84	deoxyribonucleoside monophosphate biosynthetic 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:0005829	1.00	cytosol
GO:0005737	0.55	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	0.540	2uz3B	0.904	0.74	0.443	0.919	2.7.1.21	27,29,31,59,104,107,131,133,140,156,194
2	0.535	3e2iA	0.727	1.59	0.494	0.766	2.7.1.21	28,30,34,103,105,132,139,154,169
3	0.503	2j9rA	0.794	1.30	0.494	0.818	2.7.1.21	27,34,104,107,131,140,154,169,195
4	0.485	2orwB	0.780	1.57	0.339	0.818	2.7.1.21	27,31,53,104,107,131,140,186
5	0.468	2j87A	0.714	1.45	0.399	0.756	2.7.1.21	27,30,53,103,107,131,135,140,155,170

	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	0.64	2j9rA	0.794	1.30	0.494	0.818	1.61	PO4	Download	26,28,29,30,31,32
2	0.63	2uz3B	0.904	0.74	0.443	0.919	1.50	TTP	Download	27,28,29,30,31,32,57,59,68,104,107,131,134,135,140,170,172,185,186,187,188,189,194
3	0.50	2ja1A	0.874	1.74	0.518	0.914	1.11	MPD	Download	107,131,134,135,140,194
4	0.32	2ja1A	0.874	1.74	0.518	0.914	1.73	TTP	Download	28,30,31,32,33,66,67,68,69,103,104,159,196
5	0.23	2j87A	0.714	1.45	0.399	0.756	1.49	ZN	Download	160,163,198,201

	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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