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COFACTOR result for job id 76494

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>76494 (129 residues)
MNKNKKILSNNSKISTSPKLFKKDIFFKIAIVHKLDNGFDFKSLTIEGIKEFHNFINEIL
NKKMTISQVENLYMRKTSNPFNNRTVDQQIEIREIHLGKNRQPFRLFGYFNDDNYFVLTK
IDPNHNFHE

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	2kc9A	0.49	2.96	0.047	0.643	Download
2	1wmiA	0.49	2.84	0.071	0.643	Download
3	6i20B	0.48	4.57	0.064	0.837	Download
4	3ue6A	0.48	4.37	0.048	0.814	Download
5	3a3jA1	0.48	3.96	0.031	0.752	Download
6	5zqaA	0.48	3.85	0.052	0.736	Download
7	5k7lA1	0.48	4.57	0.056	0.830	Download
8	5dkkB	0.48	4.37	0.057	0.806	Download
9	4hiaA	0.47	4.49	0.056	0.806	Download
10	3is2A	0.47	4.71	0.066	0.814	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:0016775	0.37	phosphotransferase activity, nitrogenous group as acceptor
GO:0004672	0.37	protein kinase activity

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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:0035556	0.37	intracellular signal transduction

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:0044459	0.67	plasma membrane part
GO:0032991	0.67	macromolecular complex
GO:0016020	0.67	membrane

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	1u60C	0.434	4.79	0.067	0.783	3.5.1.2	NA
2	0.060	1alqA	0.366	4.63	0.082	0.651	3.5.2.6	NA
3	0.060	2ze4A	0.417	5.27	0.049	0.783	3.1.4.4	NA
4	0.060	3a3jA	0.482	3.96	0.031	0.752	3.4.16.4	NA
5	0.060	2wafA	0.443	4.32	0.078	0.760	3.4.-.-	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	0.10	2v0uA	0.470	4.39	0.095	0.783	0.31	FMN	Download	4,56,57,60,105,107,116,117,118,120
2	0.08	3rh8D	0.470	4.59	0.078	0.791	0.28	FAD	Download	8,38,39,40,49,50,52,53,56,104,106,118,120,127
3	0.01	1z6fA	0.465	3.86	0.031	0.729	0.16	BO9	Download	38,39,40,41,108,123,128,129
4	0.01	2pd7B	0.469	4.64	0.076	0.798	0.27	FAD	Download	16,39,40,50,53,54,57
5	0.01	3sh9A	0.453	3.93	0.042	0.729	0.19	PCZ	Download	56,108,109
6	0.01	3kiuy	0.490	2.58	0.084	0.628	0.27	RQA	Download	13,15,31
7	0.01	1i2wA	0.449	3.92	0.031	0.729	0.19	CFX	Download	9,38,107,108
8	0.01	2pdtB	0.471	4.60	0.067	0.798	0.24	FAD	Download	11,49,52,53,56,118
9	0.01	3itbD	0.468	3.98	0.031	0.736	0.16	III	Download	30,31,57,109
10	0.01	3mzdA	0.466	4.08	0.031	0.744	0.15	CXV	Download	38,39,40

	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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