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COFACTOR result for job id QHD43415_1

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>QHD43415_1 (180 residues)
MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGV
LPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK
VLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG

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	2hsxA	0.61	1.37	0.819	0.644	Download
2	3zbdA	0.44	3.35	0.124	0.578	Download
3	5xbcA	0.44	3.24	0.116	0.561	Download
4	4xqkA	0.41	5.03	0.083	0.667	Download
5	3w0lB	0.40	5.82	0.031	0.739	Download
6	4j3pA	0.40	5.83	0.092	0.717	Download
7	5kdvA	0.40	5.80	0.076	0.767	Download
8	5e84A	0.39	5.40	0.052	0.683	Download
9	5zvs21	0.39	5.72	0.084	0.700	Download
10	5kdjB	0.39	5.19	0.076	0.683	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:1990380	1.00	Lys48-specific deubiquitinase activity
GO:0042802	1.00	identical protein binding
GO:0004483	1.00	mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0004482	1.00	mRNA (guanine-N7-)-methyltransferase activity
GO:0004386	1.00	helicase activity
GO:0003968	1.00	RNA-directed 5'-3' RNA polymerase activity
GO:0003727	1.00	single-stranded RNA binding
GO:0003725	1.00	double-stranded RNA binding
GO:0000175	1.00	3'-5'-exoribonuclease activity

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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[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:0044260	1.00	cellular macromolecule metabolic process
GO:0044238	1.00	primary metabolic process
GO:0043412	1.00	macromolecule modification
GO:0039653	1.00	suppression by virus of host transcription
GO:0039604	1.00	suppression by virus of host translation
GO:0039579	1.00	suppression by virus of host ISG15 activity
GO:0006807	1.00	nitrogen compound metabolic process
GO:2000158	0.97	positive regulation of ubiquitin-specific protease activity
GO:0090503	0.97	RNA phosphodiester bond hydrolysis, exonucleolytic
GO:0080009	0.97	mRNA methylation
GO:0039690	0.97	positive stranded viral RNA replication
GO:0039648	0.97	modulation by virus of host protein ubiquitination
GO:0039644	0.97	suppression by virus of host NF-kappaB transcription factor activity
GO:0039548	0.97	suppression by virus of host IRF3 activity
GO:0039519	0.97	modulation by virus of host autophagy
GO:0039502	0.97	suppression by virus of host type I interferon-mediated signaling pathway
GO:0019083	0.97	viral transcription
GO:0006370	0.97	7-methylguanosine mRNA capping
GO:0001172	0.97	transcription, RNA-templated

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:0039714	1.00	cytoplasmic viral factory

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	0.267	2gdtA	0.609	1.37	0.819	0.644	2.7.7.48	16,18,31,39,43,46,49,71,109,119,121,123
2	0.060	1icfA	0.269	5.61	0.108	0.483	3.4.22.15	NA
3	0.060	3lp8A	0.370	5.09	0.053	0.600	6.3.4.13	28,33
4	0.060	3bc3B	0.291	4.81	0.056	0.467	3.4.22.15	98,117
5	0.060	2fhbA	0.359	5.49	0.053	0.639	3.2.1.41	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.

[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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