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COFACTOR result for job id 76406

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>76406 (138 residues)
MKVKVNNLEQTYKIAKKIKKIIQNQKIPFYILLKGDLGAGKTTFTKALLEQFNIKDNITS
PSFVIMNQYFIDDLKINHMDAYRLNNDSEIEMYLDEFLDGLNIIEWYENLDLDLNAINKL
IIEIKIIDENQRLFFIGE

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	1htwA	0.94	1.04	0.257	0.986	Download
2	6fpeE	0.88	1.47	0.293	0.964	Download
3	5mvrA	0.82	1.40	0.341	0.891	Download
4	2c9oA	0.67	3.48	0.131	0.927	Download
5	4wvyA	0.66	3.48	0.147	0.920	Download
6	5e7pA	0.66	3.81	0.148	0.949	Download
7	4wvyB	0.66	3.55	0.132	0.920	Download
8	3eihA	0.65	3.97	0.168	0.949	Download
9	6b5cA	0.65	3.97	0.124	0.949	Download
10	3cmuA	0.65	3.75	0.096	0.913	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	0.96	catalytic activity
GO:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0016787	0.81	hydrolase activity
GO:0000166	0.79	nucleotide binding
GO:0032559	0.78	adenyl ribonucleotide binding
GO:0032550	0.78	purine ribonucleoside binding
GO:0017111	0.74	nucleoside-triphosphatase activity
GO:0016887	0.72	ATPase activity
GO:0035639	0.59	purine ribonucleoside triphosphate binding
GO:0005524	0.58	ATP binding
GO:0043167	0.51	ion binding
GO:0042802	0.51	identical protein 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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[0.5,0.6)

[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	0.98	cellular process
GO:0008152	0.97	metabolic process
GO:0071704	0.96	organic substance metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0044238	0.95	primary metabolic process
GO:0006807	0.95	nitrogen compound metabolic process
GO:0034641	0.93	cellular nitrogen compound metabolic process
GO:0006139	0.92	nucleobase-containing compound metabolic process
GO:0043170	0.91	macromolecule metabolic process
GO:0090304	0.89	nucleic acid metabolic process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0034660	0.88	ncRNA metabolic process
GO:0043412	0.87	macromolecule modification
GO:0034470	0.87	ncRNA processing
GO:0006399	0.87	tRNA metabolic process
GO:0002949	0.86	tRNA threonylcarbamoyladenosine modification

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	0.99	intracellular part
GO:0032991	0.83	macromolecular complex
GO:0044446	0.82	intracellular organelle part
GO:0044427	0.79	chromosomal part
GO:0043234	0.78	protein complex
GO:1902494	0.69	catalytic complex
GO:1904949	0.67	ATPase complex
GO:0044428	0.58	nuclear part
GO:1990234	0.57	transferase complex
GO:0097255	0.56	R2TP complex
GO:0035267	0.56	NuA4 histone acetyltransferase complex
GO:0031011	0.56	Ino80 complex
GO:0044444	0.55	cytoplasmic part
GO:0043229	0.55	intracellular organelle
GO:0043227	0.54	membrane-bounded organelle
GO:0043231	0.53	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	1gojA	0.589	4.05	0.107	0.870	3.6.4.4	NA
2	0.060	2qe7A	0.611	3.59	0.104	0.870	3.6.1.34	NA
3	0.060	3b9pA	0.627	3.88	0.117	0.913	3.6.4.3	40,42
4	0.060	1g8pA	0.609	3.94	0.144	0.906	6.6.1.1	NA
5	0.060	3g61A	0.579	3.86	0.066	0.855	3.6.3.44	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	0.29	1htwA	0.941	1.04	0.257	0.986	0.86	ADP	Download	38,39,40,41,42,43,105,130,132
2	0.21	1ofhC	0.639	3.64	0.162	0.899	1.24	PO4	Download	36,37,38,41
3	0.07	1htwA	0.941	1.04	0.257	0.986	1.28	NA	Download	32,33,34,104,105,106,107

	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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