COFACTOR result for job id QHD43422

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User Input

>protein (121 residues)
MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIEL
CVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDF
I

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	3knyA	0.54	4.07	0.042	0.876	Download
2	5k8gA	0.53	3.84	0.105	0.835	Download
3	2h6oA	0.53	3.79	0.048	0.851	Download
4	6k4zA	0.52	3.70	0.057	0.802	Download
5	6h3iF	0.52	4.23	0.047	0.851	Download
6	1vw1A	0.52	3.94	0.079	0.810	Download
7	2gjjA	0.52	4.24	0.037	0.835	Download
8	1jp5A	0.52	3.99	0.046	0.810	Download
9	7k5xM	0.52	4.09	0.047	0.818	Download
10	3wbdA	0.52	3.94	0.055	0.818	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:0003779	0.07	actin binding

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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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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0030042	0.07	actin filament depolymerization
GO:0019058	0.07	viral life cycle

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)

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[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044423	0.50	virion part
GO:0019031	0.25	viral envelope
GO:0019028	0.25	viral capsid
GO:0019012	0.25	virion
GO:0016021	0.25	integral component of membrane
GO:0015629	0.25	actin cytoskeleton
GO:0005622	0.25	intracellular

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	2e1qA	0.352	5.57	0.050	0.793	1.17.3.2 1.17.1.4	NA
2	0.060	2aeyA	0.462	5.09	0.068	0.893	3.2.1.80	NA
3	0.060	2ac1A	0.470	4.81	0.079	0.901	3.2.1.26	NA
4	0.060	1rjcA	0.439	3.83	0.079	0.711	3.2.1.17	8
5	0.060	2ckjA	0.412	4.61	0.017	0.711	1.17.1.4 1.17.3.2	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	0.20	1f3dJ	0.425	3.80	0.071	0.686	0.64	TPM	Download	8,49,54,56
2	0.01	1indH	0.471	4.02	0.065	0.752	0.66	EOT	Download	6,11,50,51
3	0.01	1kc5L	0.396	4.24	0.057	0.686	0.61	III	Download	8,49,50
4	0.01	1kn4L	0.429	3.93	0.047	0.694	0.67	PDE	Download	8,48,53,55,57
5	0.01	1m7dA	0.432	3.85	0.058	0.694	0.67	UUU	Download	6,49,51,56
6	0.01	1qygH	0.477	4.04	0.043	0.752	0.70	BCG	Download	8,49,51,55

	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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