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COFACTOR result for job id 76667

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>76667 (207 residues)
MAFTEIKHPLIIDKLTRMRKTETSSKDFRENLNEIAQLMVYEIFRDLKLEPVEITTPVAK
TTGYTINQPVVLVPILRAGIGMLDGIQKLIPTARIAHVGLYRDEETLEIHQYFAKTTKDI
DKSYVIVVDPMLATGGSACKAIDIVKQWGAKEVKFVCLVAVEPGIKRLQEQHPDVEIYAA
SKDEKLNEKGYIVPGLGDAGDRIFGTK

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	1o5oA	0.98	0.71	0.512	1.000	Download
2	2ehjA	0.98	0.79	0.493	1.000	Download
3	2e55A	0.96	0.94	0.385	0.990	Download
4	1v9sB	0.94	0.85	0.485	0.966	Download
5	5e38A	0.93	1.38	0.422	0.986	Download
6	3dmpA	0.91	1.80	0.443	0.981	Download
7	1vstA	0.90	1.86	0.333	0.986	Download
8	1bd3D	0.88	2.33	0.338	1.000	Download
9	1qcdA	0.65	3.56	0.128	0.812	Download
10	2dy0A	0.63	3.13	0.153	0.758	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:0016740	1.00	transferase activity
GO:0016772	0.97	transferase activity, transferring phosphorus-containing groups
GO:0004849	0.96	uridine kinase activity
GO:0043167	0.88	ion binding
GO:1901363	0.87	heterocyclic compound binding
GO:0097159	0.87	organic cyclic compound binding
GO:0046872	0.87	metal ion binding
GO:0016763	0.87	transferase activity, transferring pentosyl groups
GO:0035639	0.86	purine ribonucleoside triphosphate binding
GO:0032555	0.86	purine ribonucleotide binding
GO:0004845	0.86	uracil phosphoribosyltransferase activity
GO:0000287	0.86	magnesium ion binding
GO:0005525	0.85	GTP 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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Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044281	1.00	small molecule metabolic process
GO:0008655	1.00	pyrimidine-containing compound salvage
GO:0043097	0.99	pyrimidine nucleoside salvage
GO:0006206	0.99	pyrimidine nucleobase metabolic process
GO:0019637	0.89	organophosphate metabolic process
GO:0006796	0.89	phosphate-containing compound metabolic process
GO:0019693	0.88	ribose phosphate metabolic process
GO:0009165	0.88	nucleotide biosynthetic process
GO:0009260	0.87	ribonucleotide biosynthetic process
GO:0009156	0.87	ribonucleoside monophosphate biosynthetic process
GO:0009119	0.86	ribonucleoside metabolic process
GO:0006221	0.86	pyrimidine nucleotide biosynthetic process
GO:0044206	0.85	UMP salvage
GO:0006223	0.85	uracil salvage

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:0005829	0.99	cytosol

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	0.690	2e55A	0.964	0.94	0.385	0.990	2.4.2.9	102,106,198
2	0.660	1i5eB	0.927	1.81	0.551	1.000	2.4.2.9	76,78,80,100,129,131,133,136,192,197,199
3	0.626	1v9sB	0.977	0.86	0.488	1.000	2.4.2.9	101,102,133,198
4	0.609	1o5oD	0.974	0.93	0.512	1.000	2.4.2.9	76,78,101,129,132,134,192,197,199,202
5	0.574	2e55D	0.961	0.99	0.385	0.990	2.4.2.9	76,78,99,129,131,133,191,197

	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	0.84	1i5eA	0.927	1.81	0.551	1.000	1.64	U5P	Download	129,131,133,134,135,136,137,190,191,192,197,198,199
2	0.71	3g6wD	0.912	1.71	0.333	0.986	1.49	PRP	Download	76,77,78,101,102,129,132,133,134,135,136,137
3	0.71	1jlsB	0.885	2.29	0.338	1.000	1.53	URA	Download	131,190,191,192,197,198,199
4	0.54	1bd3C	0.884	2.28	0.338	1.000	1.48	PO4	Download	102,133,134,135,136,137
5	0.18	1qk5B	0.586	3.59	0.150	0.758	0.82	UUU	Download	77,78,99,101,130,131,133,134,135,137,161,200,201
6	0.17	1qk5A	0.582	3.64	0.151	0.754	1.00	POP	Download	77,78,99,101,201,205

	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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