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COFACTOR result for job id 76439

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>76439 (205 residues)
MKIAIFGTVGAGKSTISAEISKKLGYEIFKEPVEENPYFEQYYKDLKKTVFKMQIYMLTA
RSKQLKQAKNLENIIFDRTLLEDPIFMKVNYDLNNVDQTDYNTYIDFYNNVVLENLKIPE
NKLSFDIVIYLRVSTKTAISRIKKRGRSEELLIGEEYWETLNKNYEEFYKQNVYDFPFFV
VDAELDVKTQIELIMNKLNSMKNPN

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	2jasC	0.94	0.40	0.995	0.946	Download
2	2ocpA	0.87	2.13	0.229	0.981	Download
3	1p60A	0.86	2.12	0.259	0.981	Download
4	5xtcw	0.83	2.51	0.192	0.966	Download
5	1p7cB	0.81	2.50	0.145	0.942	Download
6	1p6xA	0.79	2.48	0.167	0.927	Download
7	1zm7B	0.78	2.03	0.257	0.873	Download
8	1osnA1	0.67	2.44	0.161	0.785	Download
9	1z83A	0.67	3.09	0.148	0.824	Download
10	2cdnA	0.65	3.36	0.182	0.829	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:0016740	0.99	transferase activity
GO:0019205	0.98	nucleobase-containing compound kinase activity
GO:0005524	0.92	ATP binding
GO:0019206	0.84	nucleoside kinase activity
GO:0016776	0.80	phosphotransferase activity, phosphate group as acceptor
GO:0009041	0.79	uridylate kinase activity
GO:0004798	0.79	thymidylate kinase activity
GO:0019136	0.71	deoxynucleoside kinase activity
GO:0004138	0.58	deoxyguanosine kinase activity

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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:0044281	0.98	small molecule metabolic process
GO:0055086	0.97	nucleobase-containing small molecule metabolic process
GO:1901576	0.96	organic substance biosynthetic process
GO:1901564	0.96	organonitrogen compound metabolic process
GO:0044249	0.96	cellular biosynthetic process
GO:1901135	0.95	carbohydrate derivative metabolic process
GO:0034654	0.94	nucleobase-containing compound biosynthetic process
GO:0072527	0.93	pyrimidine-containing compound metabolic process
GO:1901566	0.92	organonitrogen compound biosynthetic process
GO:1901137	0.92	carbohydrate derivative biosynthetic process
GO:0044711	0.91	single-organism biosynthetic process
GO:0009117	0.90	nucleotide metabolic process
GO:0072528	0.89	pyrimidine-containing compound biosynthetic process
GO:0090407	0.85	organophosphate biosynthetic process
GO:0009262	0.84	deoxyribonucleotide metabolic process
GO:0009165	0.84	nucleotide biosynthetic process
GO:0009141	0.83	nucleoside triphosphate metabolic process
GO:0006220	0.83	pyrimidine nucleotide metabolic process
GO:0009394	0.81	2'-deoxyribonucleotide metabolic process
GO:0009263	0.81	deoxyribonucleotide biosynthetic process
GO:0009200	0.81	deoxyribonucleoside triphosphate metabolic process
GO:0009142	0.80	nucleoside triphosphate biosynthetic process
GO:0009132	0.80	nucleoside diphosphate metabolic process
GO:0006221	0.80	pyrimidine nucleotide biosynthetic process
GO:0006235	0.79	dTTP biosynthetic process
GO:0006233	0.79	dTDP biosynthetic process
GO:0006227	0.79	dUDP biosynthetic process
GO:0009123	0.73	nucleoside monophosphate metabolic process
GO:0046940	0.71	nucleoside monophosphate phosphorylation
GO:0009124	0.58	nucleoside monophosphate biosynthetic process
GO:0009157	0.56	deoxyribonucleoside monophosphate biosynthetic process
GO:0009116	0.52	nucleoside 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:0005737	1.00	cytoplasm
GO:0044444	0.95	cytoplasmic part
GO:0005829	0.89	cytosol
GO:0043227	0.74	membrane-bounded organelle
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0005634	0.59	nucleus

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	0.553	1jagA	0.868	2.13	0.229	0.981	2.7.1.113	31,78
2	0.548	1p60A	0.863	2.12	0.259	0.981	2.7.1.74	31,78
3	0.343	3hjnA	0.724	2.56	0.180	0.839	2.7.4.9	14,32
4	0.279	2cdnA	0.649	3.36	0.182	0.829	2.7.4.3	13,145,147
5	0.251	2grjG	0.588	2.98	0.158	0.712	2.7.1.24	10,12,14,161,181,183

	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	0.87	2jatA	0.901	1.14	0.989	0.927	1.79	POP	Download	8,10,11,12,13,14,15,145
2	0.55	2jasB	0.931	0.59	1.000	0.942	1.83	DTP	Download	9,10,11,12,13,14,31,39,42,43,53,61,77,78,83,86,150
3	0.52	2jatB	0.913	1.11	0.995	0.937	1.09	DCM	Download	9,13,33,78,83,86
4	0.30	1p5zB	0.861	2.15	0.259	0.981	1.38	ADP	Download	10,11,12,13,14,15,77,141,144,145,182,184,186,187
5	0.15	2jaq0	0.890	1.25	0.995	0.922	1.09	III	Download	37,38,51,52,55,59,63

	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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