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COFACTOR result for job id 76432

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

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>76432 (656 residues)
MKTSKNDNLNALRILGVSAINKAKSGHPGIVLGAAGIVYVLFNKIMNFNPKNPEWFNRDR
FILSAGHGSALLYSALHLSGYDLSIDDLKQFRQWDSKTPGHPEKTLTCGVEVTTGPLGQG
VGMGVGMAVAEAHLASVYNKHDFNLIHHYTYVLCGDGDLQEGISQEAISFAGKHKLNKLI
LIHDSNDVQLDSNVVDVQIEDMHKRFKACNWNTIKVSDGEDLNSIYKAIRKAQLSDKPTY
IEVKTIIGLGSTKQGTKDVHGAPLNDDITKVKKYFDWDYDDFIIPDSVYKHWSINAKKGE
IEEEYWNQLKAKYSLKYPELSSYLDNAINKNITFDFSSLLKDIPNNDEATRLSSGKIFEK
IANHEKMLIGGSADLSSSTRIKGADNQFTSLNKTGRNIMYGVREFGMGAINNGIAAHKGL
IPVASGFFVFADYLKPAMRLASIMQLQQLYVFTHDSIAVGEDGPTHQPIEQLSMLRTIPN
HVVLRPADYSETIACYKVALTKLTKTPTSIILTRQNVRQLQHNDVLNQVERGAYIISDQT
DATVSLIASGSEVGLAIDVQKELLNHNIKAKVISMVSTSLFDKQDKEYQNLIINKNTKRI
AIEMGSSAIWYKYVGDDGLVFGIDRFGESAPANSVIKEFGFTKENLTNKILEYLNK

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	5nd5A	0.99	0.83	0.430	0.995	Download
2	2r8oB	0.99	0.87	0.429	0.994	Download
3	1itzA	0.98	0.82	0.439	0.992	Download
4	4c7vA	0.98	0.87	0.467	0.992	Download
5	1ay0A	0.98	0.79	0.444	0.989	Download
6	3rimA	0.98	1.31	0.370	0.997	Download
7	1r9jB	0.98	1.09	0.407	0.989	Download
8	5hgxA	0.98	0.98	0.414	0.989	Download
9	3k95A	0.96	0.93	0.478	0.967	Download
10	2e6kA	0.95	0.90	0.426	0.962	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:0016744	1.00	transferase activity, transferring aldehyde or ketonic groups
GO:0004802	0.99	transketolase activity
GO:0043167	0.57	ion binding
GO:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding
GO:0046872	0.54	metal ion binding
GO:0048037	0.50	cofactor binding

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 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	0.97	cellular process
GO:0008152	0.96	metabolic process
GO:0071704	0.95	organic substance metabolic process
GO:0044237	0.95	cellular metabolic process
GO:0044763	0.89	single-organism cellular process
GO:1901135	0.87	carbohydrate derivative metabolic process
GO:0006796	0.87	phosphate-containing compound metabolic process
GO:0019637	0.86	organophosphate metabolic process
GO:0044710	0.85	single-organism metabolic process
GO:0044238	0.83	primary metabolic process
GO:0019682	0.80	glyceraldehyde-3-phosphate metabolic process
GO:0019693	0.79	ribose phosphate metabolic process
GO:0006807	0.79	nitrogen compound metabolic process
GO:0034641	0.77	cellular nitrogen compound metabolic process
GO:0044281	0.76	small molecule metabolic process
GO:1901360	0.75	organic cyclic compound metabolic process
GO:0046483	0.75	heterocycle metabolic process
GO:0006725	0.75	cellular aromatic compound metabolic process
GO:1901564	0.74	organonitrogen compound metabolic process
GO:0006139	0.70	nucleobase-containing compound metabolic process
GO:0055086	0.62	nucleobase-containing small molecule metabolic process
GO:0051186	0.62	cofactor metabolic process
GO:0009117	0.61	nucleotide metabolic process
GO:0006732	0.61	coenzyme metabolic process
GO:0072524	0.60	pyridine-containing compound metabolic process
GO:0065007	0.58	biological regulation
GO:0006733	0.58	oxidoreduction coenzyme metabolic process
GO:0050789	0.57	regulation of biological process
GO:0046496	0.57	nicotinamide nucleotide metabolic process
GO:0050896	0.55	response to stimulus
GO:0009052	0.53	pentose-phosphate shunt, non-ox.dat.gzive branch
GO:0051156	0.52	glucose 6-phosphate metabolic process
GO:0050794	0.52	regulation of cellular process
GO:0042221	0.52	response to chemical
GO:0006739	0.52	NADP metabolic process
GO:0019222	0.50	regulation of metabolic process
GO:0010035	0.50	response to inorganic substance
GO:0006950	0.50	response to stress

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:0005829	1.00	cytosol
GO:0043226	0.69	organelle
GO:0043229	0.68	intracellular organelle
GO:0043227	0.65	membrane-bounded organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0044446	0.52	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	0.660	1ay0A	0.982	0.79	0.444	0.989	2.2.1.1	404,466
2	0.645	1r9jB	0.978	1.09	0.407	0.989	2.2.1.1	404,466
3	0.557	3l84A	0.927	1.38	0.427	0.945	2.2.1.1	27,67,70,72,91,100,109,115,117
4	0.550	1itzB	0.984	0.82	0.439	0.992	2.2.1.1	25,27,67,92,100,115,117,157,261
5	0.250	1itzA	0.984	0.82	0.439	0.992	2.2.1.1	404,466

	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	0.85	1tkaB	0.982	0.80	0.445	0.989	1.56	N3T	Download	30,67,115,116,117,157,161,186,188,189,190,260

	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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