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COFACTOR result for job id 76495

[Download result.tar.bz2 for all prediction results]

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>76495 (232 residues)
MNIKNFFEKYNIKINNEKLFNEALTHNSYANEHKLKYSYQRLEFLGDAILQMYVSRFLFF
NYSKLSEGELTRLRASTVREETLFRVAKDINLGALVKLGHGEYITKGYEKPSILADVFEA
LTAAIYLDQKEDGLVTWLDQTLFKYIKDSNFINDTKDFKSELQELLQSEKRSDLKYIIEK
EDFFANENKILYTVSVNLNGQKFGVGKGFSKQEAEQNAASDCLSKLKKPTNN

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	1o0wB	0.97	0.50	0.381	0.974	Download
2	5b16A	0.61	2.74	0.199	0.681	Download
3	2a11A	0.60	1.65	0.349	0.642	Download
4	2fflA	0.59	3.58	0.178	0.728	Download
5	3n3wA	0.57	2.01	0.350	0.616	Download
6	3c4bA	0.57	2.37	0.195	0.642	Download
7	1yykA	0.56	2.17	0.180	0.625	Download
8	4ce4h1	0.56	1.99	0.169	0.612	Download
9	4oogC	0.56	2.56	0.145	0.625	Download
10	1vw45	0.55	2.99	0.096	0.647	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	1.00	catalytic activity
GO:1901363	0.99	heterocyclic compound binding
GO:0097159	0.99	organic cyclic compound binding
GO:0004525	0.99	ribonuclease III activity
GO:0003723	0.98	RNA binding
GO:0003725	0.82	double-stranded RNA binding
GO:0043167	0.78	ion binding
GO:0046872	0.76	metal ion binding
GO:0019843	0.53	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:

[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:0016070	1.00	RNA metabolic process
GO:0006396	0.99	RNA processing
GO:0090305	0.89	nucleic acid phosphodiester bond hydrolysis
GO:0090501	0.85	RNA phosphodiester bond hydrolysis
GO:0090502	0.84	RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0030422	0.84	production of siRNA involved in RNA interference
GO:0034660	0.82	ncRNA metabolic process
GO:0034470	0.80	ncRNA processing
GO:1901575	0.71	organic substance catabolic process
GO:0044248	0.70	cellular catabolic process
GO:0044265	0.69	cellular macromolecule catabolic process
GO:0034655	0.69	nucleobase-containing compound catabolic process
GO:0006399	0.66	tRNA metabolic process
GO:0006364	0.65	rRNA processing
GO:0016071	0.64	mRNA metabolic process
GO:0008033	0.64	tRNA processing
GO:0006401	0.63	RNA catabolic process
GO:0016075	0.62	rRNA catabolic process
GO:0006397	0.62	mRNA processing
GO:0031054	0.61	pre-miRNA processing

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:0044424	1.00	intracellular part
GO:0043231	0.97	intracellular membrane-bounded organelle
GO:0005634	0.95	nucleus
GO:0032991	0.88	macromolecular complex
GO:0005737	0.86	cytoplasm
GO:1990904	0.82	ribonucleoprotein complex
GO:0044444	0.78	cytoplasmic part
GO:0030529	0.76	intracellular ribonucleoprotein complex
GO:0016442	0.68	RISC complex
GO:0044446	0.55	intracellular organelle part

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	0.324	1yykA	0.564	2.17	0.180	0.625	3.1.26.3	26,39,43,45,116,126
2	0.060	1r64A	0.398	5.95	0.043	0.703	3.4.21.61	NA
3	0.060	2e1qA	0.339	6.19	0.056	0.612	1.17.3.2 1.17.1.4	NA
4	0.060	3fr8B	0.403	6.03	0.057	0.694	1.1.1.86	NA
5	0.060	3lxuX	0.419	6.09	0.059	0.763	3.4.14.10	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	0.17	2a110	0.601	1.65	0.349	0.642	1.22	III	Download	40,41,42,44,48,49,52,55,56,59,60,62,63,65,67,70,71,74,126,127,131,135
2	0.12	2fflA	0.594	3.58	0.178	0.728	1.66	MN	Download	43,47,116,119
3	0.05	2nugB	0.571	2.00	0.185	0.625	1.12	RQA	Download	43,47,103,106,119

	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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