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COFACTOR result for job id 76600

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>76600 (213 residues)
MNIMLLGAPCCGKGTQAEQLVNKLNFIQVSTGDLMRKEISLNTSLGLKCQEYMNAGKYVP
DQIVNQIVSQFLKNTNDKLIFDGYPRTLEQAKSLEQMLDLYNKKIDYVFYIDINDQILIK
RITNRLVCPLCKASFNLETRKPKQEGLCDFDNTKLVKRSDDSLDKVQIRLQTYKEQTLPL
IDYFKTNSKFIEIKADDLSAEQVFNQIKGELKI

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	3dl0A	0.97	0.89	0.349	0.995	Download
2	3akyA	0.96	1.02	0.321	0.995	Download
3	3tlxA	0.95	1.25	0.349	0.995	Download
4	5g3yA	0.95	1.24	0.398	0.991	Download
5	3be4A	0.94	1.11	0.322	0.977	Download
6	2rgxA	0.92	1.04	0.340	0.953	Download
7	3hprA	0.92	1.41	0.324	0.972	Download
8	1zakA	0.89	1.58	0.322	0.948	Download
9	2cdnA	0.82	1.02	0.369	0.840	Download
10	1qf9A	0.80	1.62	0.250	0.864	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:0019205	1.00	nucleobase-containing compound kinase activity
GO:0016776	1.00	phosphotransferase activity, phosphate group as acceptor
GO:0004017	0.98	adenylate kinase activity
GO:1901363	0.96	heterocyclic compound binding
GO:0097159	0.96	organic cyclic compound binding
GO:0005524	0.95	ATP binding
GO:0043167	0.84	ion binding
GO:0046872	0.83	metal ion binding
GO:0008270	0.82	zinc ion 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:

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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:0071704	1.00	organic substance metabolic process
GO:0044699	1.00	single-organism process
GO:0044238	1.00	primary metabolic process
GO:0034641	1.00	cellular nitrogen compound metabolic process
GO:1901564	0.99	organonitrogen compound metabolic process
GO:1901362	0.99	organic cyclic compound biosynthetic process
GO:0055086	0.99	nucleobase-containing small molecule metabolic process
GO:0044271	0.99	cellular nitrogen compound biosynthetic process
GO:0018130	0.99	heterocycle biosynthetic process
GO:1901566	0.98	organonitrogen compound biosynthetic process
GO:1901293	0.98	nucleoside phosphate biosynthetic process
GO:0009117	0.98	nucleotide metabolic process
GO:1901137	0.97	carbohydrate derivative biosynthetic process
GO:0016310	0.97	phosphorylation
GO:0009259	0.97	ribonucleotide metabolic process
GO:0009165	0.97	nucleotide biosynthetic process
GO:0006163	0.97	purine nucleotide metabolic process
GO:0046128	0.96	purine ribonucleoside metabolic process
GO:0042455	0.96	ribonucleoside biosynthetic process
GO:0009168	0.96	purine ribonucleoside monophosphate biosynthetic process
GO:0009152	0.96	purine ribonucleotide biosynthetic process
GO:0046940	0.95	nucleoside monophosphate phosphorylation
GO:0044209	0.95	AMP salvage
GO:0009132	0.72	nucleoside diphosphate metabolic process
GO:0043170	0.70	macromolecule metabolic process
GO:0044260	0.66	cellular macromolecule metabolic process
GO:0034645	0.64	cellular macromolecule biosynthetic process
GO:0044267	0.62	cellular protein metabolic process
GO:0043603	0.62	cellular amide metabolic process
GO:0006412	0.61	translation
GO:0009185	0.55	ribonucleoside diphosphate metabolic process
GO:0090304	0.54	nucleic acid metabolic process
GO:0015949	0.54	nucleobase-containing small molecule interconversion
GO:0046031	0.53	ADP metabolic process
GO:0016070	0.52	RNA metabolic process
GO:0009188	0.52	ribonucleoside diphosphate biosynthetic process
GO:0009141	0.51	nucleoside triphosphate metabolic process
GO:0006172	0.50	ADP biosynthetic 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:0044424	1.00	intracellular part
GO:0044444	0.94	cytoplasmic part
GO:0043226	0.84	organelle
GO:0043227	0.82	membrane-bounded organelle
GO:0005737	0.82	cytoplasm
GO:0043229	0.77	intracellular organelle
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0044422	0.75	organelle part
GO:0044446	0.74	intracellular organelle part
GO:0032991	0.55	macromolecular complex

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	0.641	1s3gA	0.981	0.68	0.363	0.995	2.7.4.3	13,33,125,158,160,161,164,169
2	0.554	2qajB	0.981	0.67	0.349	0.995	2.7.4.3	12,14,18,30,33,56,59,86,125,158,160
3	0.539	1eckB	0.921	1.35	0.324	0.972	2.7.4.3	7,12,14,28,30,33,53,83,86,125,127,158,161
4	0.443	1dvrA	0.845	2.77	0.300	0.972	2.7.4.3	12,14,31,33,36,83,86,122,125,134,159
5	0.384	2bwjA	0.688	2.63	0.254	0.798	2.7.4.3	7,12,14,18,21,31,83

	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	0.63	3fb4A	0.982	0.65	0.377	0.995	1.53	AP5	Download	9,10,11,12,13,14,15,31,32,35,36,53,57,58,59,64,83,84,86,90,121,122,125,134,135,136,139,158,169,198,200
2	0.46	3ukdA	0.805	1.61	0.250	0.864	1.37	UUU	Download	9,10,13,31,32,35,36,53,57,58,59,83,84,86,90,125,158,160,169
3	0.28	3l0sC	0.701	4.09	0.232	0.892	1.15	TAR	Download	8,9,10,11,12,13,14
4	0.27	2eckA	0.921	1.36	0.324	0.972	1.40	ADP	Download	10,11,12,13,14,15,121,124,125,134,135,136,139,195,197,198,199
5	0.07	1zak0	0.892	1.58	0.322	0.948	1.38	III	Download	54,55,126,129,155,156,157,158,159,162,164,165

	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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