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COFACTOR result for job id 76683

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>76683 (313 residues)
MEKFTIKDLTDNLKFEIISGQDKLDTEIKSYGINRAGLELADYFKPFKDQSEWRATLMST
KESGYMLQFDEKTKIRKYTQLMKCGIPVLIITNKFKDKTLIKVAKRLNFPLLKSDYPITV
QLVQKIQDIYDIYFSPTSEVHAALMNIFGTGVLIKGKSGIGKSELCLELIKHNHLFVGDD
RIILTNKSNKIIGRVHPILKNLIEIRGIGIFDIVKSNGYQVIMNESPVELVIELVEYKEK
NIDNSDRLGNDWQKTKILGVEIEHIQIPVSAGRSLVNIIESAVAQFKINKSKQFEDVFDV
IHKRTKEFLSSKK

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	1knxE	0.97	0.70	0.304	0.978	Download
2	1ko7A	0.79	2.64	0.310	0.898	Download
3	2qmhB	0.53	2.04	0.309	0.566	Download
4	3tqfA	0.46	2.09	0.333	0.495	Download
5	4xc6A	0.35	6.48	0.048	0.610	Download
6	3sjnA	0.30	5.35	0.054	0.444	Download
7	4lisA	0.28	5.57	0.103	0.399	Download
8	1z45A1	0.27	5.21	0.097	0.383	Download
9	1a9yA	0.27	5.73	0.083	0.406	Download
10	3epjA	0.26	6.13	0.033	0.418	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:0016740	0.91	transferase activity
GO:0016772	0.90	transferase activity, transferring phosphorus-containing groups
GO:0016773	0.89	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.88	kinase activity
GO:0004672	0.83	protein kinase activity
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0016787	0.79	hydrolase activity
GO:0017076	0.78	purine nucleotide binding
GO:0035639	0.77	purine ribonucleoside triphosphate binding
GO:0032555	0.77	purine ribonucleotide binding
GO:0032550	0.77	purine ribonucleoside binding
GO:0030554	0.74	adenyl nucleotide binding
GO:0005524	0.73	ATP binding
GO:0000155	0.73	phosphorelay sensor kinase activity
GO:0004674	0.68	protein serine/threonine kinase activity
GO:0043167	0.56	ion binding
GO:0016788	0.56	hydrolase activity, acting on ester bonds
GO:0016791	0.54	phosphatase activity
GO:0046872	0.53	metal ion binding
GO:0000287	0.50	magnesium ion binding

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:

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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:0009987	0.90	cellular process
GO:0008152	0.87	metabolic process
GO:0044237	0.86	cellular metabolic process
GO:0071704	0.84	organic substance metabolic process
GO:0065007	0.84	biological regulation
GO:0050789	0.84	regulation of biological process
GO:0044238	0.82	primary metabolic process
GO:0050794	0.81	regulation of cellular process
GO:0044699	0.81	single-organism process
GO:0019222	0.81	regulation of metabolic process
GO:0080090	0.80	regulation of primary metabolic process
GO:0043170	0.74	macromolecule metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0006109	0.73	regulation of carbohydrate metabolic process
GO:0000160	0.73	phosphorelay signal transduction system
GO:0043412	0.70	macromolecule modification
GO:0006793	0.68	phosphorus metabolic process
GO:0006796	0.67	phosphate-containing compound metabolic process
GO:0044267	0.65	cellular protein metabolic process
GO:0016310	0.64	phosphorylation
GO:0006464	0.64	cellular protein modification process
GO:0023014	0.63	signal transduction by protein phosphorylation
GO:0051179	0.51	localization
GO:0006810	0.50	transport

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	0.99	cytoplasmic part
GO:0005829	0.98	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	0.060	1b0pA	0.366	6.13	0.043	0.601	1.2.7.1	82
2	0.060	1yq2A	0.412	5.95	0.029	0.655	3.2.1.23	164,280
3	0.060	2vuaA	0.328	6.70	0.039	0.569	3.4.24.69	182
4	0.060	2pffD	0.385	7.07	0.040	0.706	2.3.1.86	NA
5	0.060	3btaA	0.403	6.24	0.066	0.658	3.4.24.69	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	0.19	1ko7B	0.710	3.73	0.305	0.891	1.46	PO4	Download	159,160,161,162,163,164,206
2	0.01	1x6vB	0.413	5.68	0.053	0.639	0.58	ADP	Download	159,161,162,163,164,165,275
3	0.01	3k30A	0.409	6.04	0.051	0.645	0.55	SF4	Download	143,153,154,155,156,157,161,162
4	0.01	1jz2A	0.372	7.42	0.036	0.709	0.57	NA	Download	176,177,194
5	0.01	1djnA	0.413	5.99	0.039	0.649	0.73	SF4	Download	152,177,178,182,184,193,194,225

	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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