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COFACTOR result for job id 76512

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>76512 (326 residues)
MKKVKDINIEDHLIDTILRIERVIVSTGSSGNNYLILHLADSTGRIEARKWVVSEKDKQL
LKPNTIVLLKDTIVHEYRNILQLKVEDYQVIDEKDLLKYNLNKTDLYITAPLDIKTSYLE
LISLLNSINNQTYKTITLNLIEKYKKEFLTFPAAMSIHHNVTSGLFWHSYTLVKNVLNLK
ENYFYANIDWDLLICGAILHDIGKVIEISDVNGSDYSLEGKLLGHISIGNAEINKLADKL
NLYKDQNNKINKEITLLQHMILASHGKKEFGSPIEPVLIEAVILSALDDLDAKVYKINDE
LSKIEIDNWTQKITSIDNKMFYKHKK

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	6cptA	0.53	5.47	0.098	0.761	Download
2	3tm8A	0.53	5.04	0.102	0.709	Download
3	3ibjA	0.47	4.99	0.092	0.626	Download
4	6mzbB	0.47	4.63	0.075	0.610	Download
5	3g3nA	0.47	4.50	0.078	0.595	Download
6	3ecmA	0.46	4.41	0.100	0.595	Download
7	2r8qA	0.46	5.31	0.100	0.650	Download
8	1t9sA	0.46	4.96	0.096	0.617	Download
9	6ezuA	0.46	4.57	0.075	0.601	Download
10	3v93A	0.46	4.62	0.069	0.598	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	0.91	catalytic activity
GO:0016787	0.74	hydrolase activity
GO:0016788	0.56	hydrolase activity, acting on ester bonds
GO:0042578	0.54	phosphoric ester hydrolase 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:

[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:0009987	0.99	cellular process
GO:0008152	0.98	metabolic process
GO:0006139	0.97	nucleobase-containing compound metabolic process
GO:0043170	0.85	macromolecule metabolic process
GO:0090304	0.84	nucleic acid metabolic process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0016070	0.64	RNA metabolic process
GO:0034660	0.62	ncRNA metabolic process
GO:0006396	0.56	RNA processing
GO:0050896	0.55	response to stimulus
GO:0034470	0.55	ncRNA processing
GO:0065007	0.53	biological regulation
GO:0006364	0.52	rRNA processing
GO:0050794	0.51	regulation of cellular process
GO:0051716	0.50	cellular response to stimulus

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:0044464	1.00	cell part
GO:0044424	0.96	intracellular part
GO:0043226	0.82	organelle
GO:0044446	0.81	intracellular organelle part
GO:0043229	0.81	intracellular organelle
GO:0044428	0.80	nuclear part
GO:0044444	0.58	cytoplasmic part
GO:0005730	0.50	nucleolus

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	2r8qA	0.464	5.31	0.100	0.650	3.1.4.17	262,288
2	0.060	2pulA	0.387	6.54	0.064	0.650	2.7.1.100	NA
3	0.060	3b8cB	0.416	5.99	0.057	0.647	3.6.3.6	167
4	0.060	3ixzA	0.428	6.03	0.066	0.669	3.6.3.10	41
5	0.060	2dqbA	0.388	4.96	0.076	0.506	3.1.5.1	140

	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	0.04	2h42A	0.451	5.36	0.100	0.641	1.24	MG	Download	200,201,226,229,264
2	0.02	1t9rA	0.457	4.87	0.098	0.610	0.72	PO4	Download	172,196,229,260,284
3	0.01	3jwqA	0.463	4.99	0.088	0.617	0.48	VIA	Download	203,222,265
4	0.01	3hqwA	0.451	4.60	0.075	0.583	0.41	PF4	Download	165,217,220,221,224,225,228,231,232
5	0.01	3sieA	0.432	4.79	0.097	0.583	0.40	5BO	Download	195,198,229,232,233,235,236
6	0.01	3qpoA	0.454	4.69	0.075	0.589	0.41	PFR	Download	172,173,193
7	0.01	1tbfA	0.466	5.00	0.092	0.623	0.40	VIA	Download	196,203,228,258
8	0.01	1uduA	0.461	4.76	0.089	0.604	0.45	CIA	Download	225,228,229,232

	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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