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COFACTOR result for job id 76606

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>76606 (129 residues)
MTTDVIADMLTRIRNANQRYLKTVSVPSSKVKLEIARILKEEGFISNFTVEGDVKKTINI
ELKYQGKTRVIQGLKKISKPGLRVYAQANEIPQVLNGLGISIVSTSQGIMTGKKARLANA
GGEVLAFIW

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	2qbfH	0.98	0.61	0.481	1.000	Download
2	5o5jH	0.98	0.80	0.512	1.000	Download
3	5li0h	0.95	1.00	0.566	1.000	Download
4	3rf2A	0.95	0.96	0.457	0.985	Download
5	3bbnH	0.95	1.22	0.419	1.000	Download
6	2zkqh	0.86	1.33	0.303	0.922	Download
7	2xzmH	0.85	1.48	0.289	0.938	Download
8	1i97H1	0.51	1.52	0.479	0.550	Download
9	1seiA2	0.41	1.25	0.571	0.434	Download
10	1i6uA2	0.39	1.31	0.278	0.419	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:0003735	1.00	structural constituent of ribosome
GO:1901363	0.90	heterocyclic compound binding
GO:0097159	0.90	organic cyclic compound binding
GO:0003723	0.89	RNA binding
GO:0019843	0.86	rRNA binding

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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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.97	cellular process
GO:0044237	0.83	cellular metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044238	0.80	primary metabolic process
GO:0006807	0.79	nitrogen compound metabolic process
GO:0034641	0.78	cellular nitrogen compound metabolic process
GO:0043170	0.77	macromolecule metabolic process
GO:0071840	0.72	cellular component organization or biogenesis
GO:1901564	0.71	organonitrogen compound metabolic process
GO:1901576	0.70	organic substance biosynthetic process
GO:0044249	0.70	cellular biosynthetic process
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0044271	0.67	cellular nitrogen compound biosynthetic process
GO:0016043	0.67	cellular component organization
GO:1901566	0.65	organonitrogen compound biosynthetic process
GO:0065007	0.65	biological regulation
GO:0050789	0.65	regulation of biological process
GO:0009059	0.65	macromolecule biosynthetic process
GO:0034645	0.64	cellular macromolecule biosynthetic process
GO:0019538	0.64	protein metabolic process
GO:0044267	0.63	cellular protein metabolic process
GO:0006412	0.61	translation
GO:0050794	0.60	regulation of cellular process
GO:0019222	0.57	regulation of metabolic process
GO:0043933	0.56	macromolecular complex subunit organization
GO:0010468	0.56	regulation of gene expression
GO:0065008	0.55	regulation of biological quality
GO:0065003	0.55	macromolecular complex assembly
GO:0010608	0.55	posttranscriptional regulation of gene expression
GO:0022618	0.54	ribonucleoprotein complex assembly
GO:0043488	0.53	regulation of mRNA stability
GO:2000112	0.52	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.52	regulation of primary metabolic process
GO:0051171	0.52	regulation of nitrogen compound metabolic process
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0000028	0.51	ribosomal small subunit assembly
GO:0006417	0.50	regulation of translation

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:0044444	1.00	cytoplasmic part
GO:0032991	0.96	macromolecular complex
GO:1990904	0.95	ribonucleoprotein complex
GO:0043229	0.93	intracellular organelle
GO:0030529	0.91	intracellular ribonucleoprotein complex
GO:0044446	0.88	intracellular organelle part
GO:0044391	0.82	ribosomal subunit
GO:0043232	0.82	intracellular non-membrane-bounded organelle
GO:0005840	0.81	ribosome
GO:0015935	0.76	small ribosomal subunit
GO:0044445	0.74	cytosolic part
GO:0022627	0.68	cytosolic small ribosomal subunit
GO:0043227	0.65	membrane-bounded organelle
GO:0043231	0.61	intracellular membrane-bounded organelle

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	1mdwA	0.408	4.06	0.041	0.659	3.4.22.53	NA
2	0.060	2z02B	0.455	4.42	0.083	0.752	6.3.2.6	NA
3	0.060	2g8eA	0.439	4.22	0.061	0.682	3.4.22.52	119
4	0.060	1d7fA	0.450	4.79	0.061	0.814	2.4.1.19	NA
5	0.060	1sa3A	0.468	4.48	0.076	0.791	3.1.21.4	108

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1zgl9	0.335	4.68	0.025	0.581	0.40	III	Download	97,99,112
	2	0.01	3l39A	0.476	4.16	0.043	0.721	0.52	PO4	Download	109,121,122,123

	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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