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COFACTOR result for job id 76417

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>76417 (184 residues)
MIYINDSFDKLEKLNTKKAIITIGNFDGFHIFHQKIINQVINIAKQENLTSIVMSFDKKI
KNNKTHTNLATKKQKLEFINTKLTDLDYFIDIKVDDSLIKTTKDQFIDILLNKLNVIKIV
EGQDFTFGYLSQGNINDLIRVFSKENVIIFKRDNDISSTKIKKLLDENLVDKAQELLGID
LKLK

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	2x0kA	0.96	0.73	0.244	0.978	Download
2	3op1A	0.88	1.78	0.232	0.962	Download
3	1s4mA	0.77	1.85	0.247	0.859	Download
4	1cozA	0.56	2.61	0.216	0.679	Download
5	3do8A	0.50	3.17	0.096	0.625	Download
6	3ha3A	0.45	4.38	0.055	0.685	Download
7	3ie7A1	0.43	4.32	0.046	0.636	Download
8	2yjpA2	0.36	5.15	0.090	0.592	Download
9	1yy7A	0.34	5.45	0.068	0.598	Download
10	2i3oD	0.34	6.38	0.030	0.690	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:0016740	1.00	transferase activity
GO:0016772	0.99	transferase activity, transferring phosphorus-containing groups
GO:0016779	0.89	nucleotidyltransferase activity
GO:0016773	0.87	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.87	kinase activity
GO:0070566	0.86	adenylyltransferase activity
GO:0003919	0.85	FMN adenylyltransferase activity
GO:0008531	0.81	riboflavin kinase activity
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0000166	0.77	nucleotide binding
GO:0005524	0.76	ATP 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	0.99	cellular process
GO:0008152	0.99	metabolic process
GO:0071704	0.98	organic substance metabolic process
GO:0044238	0.98	primary metabolic process
GO:0044237	0.98	cellular metabolic process
GO:0006807	0.97	nitrogen compound metabolic process
GO:1901576	0.96	organic substance biosynthetic process
GO:0034641	0.96	cellular nitrogen compound metabolic process
GO:0044710	0.95	single-organism metabolic process
GO:0006139	0.95	nucleobase-containing compound metabolic process
GO:1901564	0.94	organonitrogen compound metabolic process
GO:0044711	0.94	single-organism biosynthetic process
GO:0044249	0.94	cellular biosynthetic process
GO:0044281	0.93	small molecule metabolic process
GO:0044271	0.93	cellular nitrogen compound biosynthetic process
GO:0019637	0.93	organophosphate metabolic process
GO:0006796	0.93	phosphate-containing compound metabolic process
GO:1901566	0.92	organonitrogen compound biosynthetic process
GO:0090407	0.92	organophosphate biosynthetic process
GO:0055086	0.92	nucleobase-containing small molecule metabolic process
GO:0034654	0.92	nucleobase-containing compound biosynthetic process
GO:0009165	0.91	nucleotide biosynthetic process
GO:0009108	0.91	coenzyme biosynthetic process
GO:0006747	0.86	FAD biosynthetic process
GO:1901135	0.84	carbohydrate derivative metabolic process
GO:1901137	0.83	carbohydrate derivative biosynthetic process
GO:0009259	0.83	ribonucleotide metabolic process
GO:0009260	0.82	ribonucleotide biosynthetic process
GO:0009161	0.78	ribonucleoside monophosphate metabolic process
GO:0046444	0.77	FMN metabolic process
GO:0044283	0.77	small molecule biosynthetic process
GO:0009398	0.76	FMN biosynthetic process
GO:0009231	0.76	riboflavin biosynthetic process
GO:0016310	0.70	phosphorylation
GO:0043170	0.61	macromolecule metabolic process

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:0043231	0.93	intracellular membrane-bounded organelle
GO:0005737	0.89	cytoplasm
GO:0009507	0.78	chloroplast

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	0.200	1n1dC	0.554	2.67	0.208	0.674	2.7.7.39	35,79,124
2	0.072	3f3mA	0.581	3.41	0.142	0.745	2.7.7.3	NA
3	0.071	1o6bA	0.593	3.54	0.155	0.772	2.7.7.3	NA
4	0.067	1vlhB	0.581	3.73	0.161	0.772	2.7.7.3	NA
5	0.067	3k9wA	0.596	3.58	0.145	0.777	2.7.7.3	133

	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	0.39	1t6yA	0.766	1.81	0.248	0.853	1.26	AMP	Download	24,25,26,30,32,33,36,121,122,124,151,152,156

	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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