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COFACTOR result for job id 76379

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>76379 (190 residues)
MQNLHPLVKEVLFTREQIQNRTKDIAKEIESYYKDKHLKDNSLLVVGLLKGCVPFYTDFC
MVCDLTMEMDFMVVSSYHGSTSSNSAPKINLDLNTDVKDRDILIVEDIIDTGFTLKYVKE
YLLNKGAKSVKILTMLDKPSGRKIDLVADWVCFTIDPCFVIGYGLDYQEKIRNLPYVAVC
DTTKLDDWKW

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	2gebA	0.94	0.58	0.411	0.947	Download
2	3kb8A	0.93	0.80	0.486	0.953	Download
3	1p17B	0.92	1.48	0.339	0.958	Download
4	4pfqA	0.88	1.23	0.416	0.910	Download
5	4rqaA	0.87	1.06	0.421	0.900	Download
6	1fsgA	0.86	2.36	0.266	0.958	Download
7	5eswA	0.86	1.82	0.218	0.937	Download
8	2jbhB	0.86	1.87	0.263	0.932	Download
9	1cjbC	0.86	2.21	0.295	0.953	Download
10	6aqoA	0.86	1.60	0.278	0.916	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:0004422	1.00	hypoxanthine phosphoribosyltransferase activity
GO:0052657	0.96	guanine phosphoribosyltransferase activity
GO:0046872	0.96	metal ion binding
GO:0000287	0.95	magnesium ion binding
GO:0000166	0.95	nucleotide binding
GO:0042802	0.57	identical protein binding
GO:0042803	0.53	protein homodimerization 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:1901137	1.00	carbohydrate derivative biosynthetic process
GO:0043101	1.00	purine-containing compound salvage
GO:0009259	1.00	ribonucleotide metabolic process
GO:0006164	1.00	purine nucleotide biosynthetic process
GO:0032264	0.99	IMP salvage
GO:0046129	0.96	purine ribonucleoside biosynthetic process
GO:0006166	0.95	purine ribonucleoside salvage
GO:0046037	0.94	GMP metabolic process
GO:0046100	0.93	hypoxanthine metabolic process
GO:0006178	0.91	guanine salvage
GO:0006177	0.90	GMP biosynthetic process
GO:0032263	0.89	GMP salvage
GO:0006168	0.89	adenine salvage
GO:0065007	0.60	biological regulation
GO:1901575	0.58	organic substance catabolic process
GO:0050789	0.58	regulation of biological process
GO:0050794	0.57	regulation of cellular process
GO:0044248	0.57	cellular catabolic process
GO:1901292	0.56	nucleoside phosphate catabolic process
GO:0080090	0.56	regulation of primary metabolic process
GO:0051171	0.56	regulation of nitrogen compound metabolic process
GO:0031323	0.56	regulation of cellular metabolic process
GO:0016043	0.56	cellular component organization
GO:0009166	0.55	nucleotide catabolic process
GO:1901565	0.54	organonitrogen compound catabolic process
GO:0065003	0.53	macromolecular complex assembly
GO:0051173	0.53	positive regulation of nitrogen compound metabolic process
GO:0046038	0.53	GMP catabolic process
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0051289	0.52	protein homotetramerization
GO:0050896	0.51	response to stimulus
GO:0045964	0.51	positive regulation of dopamine metabolic process
GO:0043103	0.51	hypoxanthine 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:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0005829	0.97	cytosol
GO:0005737	0.86	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	0.553	3kb8A	0.931	0.80	0.486	0.953	2.4.2.8	77
2	0.504	1grvB	0.843	1.35	0.396	0.879	2.4.2.8	49,51,106,108,114,160,172
3	0.403	1dqnA	0.776	2.74	0.206	0.905	2.4.2.8	77
4	0.243	2igbB	0.748	2.29	0.145	0.858	2.4.2.9	NA
5	0.203	1hgxA	0.827	1.10	0.344	0.858	2.4.2.8	106,107,110

	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	0.73	3h83A	0.930	0.84	0.486	0.953	1.57	SUC	Download	108,160,165,166,167,168
2	0.72	1yfzA	0.921	0.71	0.416	0.937	1.57	IMP	Download	49,50,51,138,159,160,166,172
3	0.68	1i0lA	0.931	1.33	0.339	0.979	1.56	PRP	Download	50,51,106,108,110,111,166,172
4	0.66	1pzmA	0.848	0.94	0.373	0.874	1.47	5GP	Download	107,108,110,111,112,113,114,138,158,159,160,165,166
5	0.49	1tc2A	0.918	1.14	0.359	0.953	1.07	7HP	Download	158,159,160,165,166
6	0.46	1g9sA	0.847	1.27	0.391	0.879	0.85	IMP	Download	106,108,109,110,111,112,113,114,115,138
7	0.38	3ggcB	0.855	2.34	0.290	0.963	0.91	H26	Download	108,110,111,112,114,137,161,162
8	0.35	1cjbB	0.859	2.24	0.295	0.953	0.98	POP	Download	50,51,166,172
9	0.08	1grv0	0.840	1.32	0.393	0.874	1.46	III	Download	19,49,50,53,54,56,57,58,60,61,66,67,68,69,70,71,94,95,163,169,172,173,175

	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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