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COFACTOR result for job id 76381

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>76381 (326 residues)
MIKKIGILTSGGDAPGMNNAIAGVVKTAASKGIEVYGINDGYKGLVNGWFEKLNVEKTLD
ILSRGGTYLGSARLPEFKELEVRQKAVANLKKAGIEALVVIGGDGSYMGAQKLTEMGINC
IGLPGTIDNDISSTDYTIGFHTALNTIVEAVDRIRDTMQSHNRADVVEIMGNGCGDLVTY
TAVATGAEIFSPAEDLLTIEQMGQKAKQFRLLGKKSLIILVSEKSYGISAEEIAEKIQKI
SGYETKATVLGHIQRGGRPTAMDRYIAFTAGMFAVEKLAEGKGGLFIGLENNKLVARDID
STLNMKKEDKKPFINYLREINGYFSK

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	1mtoA	0.97	0.55	0.502	0.979	Download
2	1pfkA	0.97	0.74	0.520	0.979	Download
3	1zxxA	0.96	0.81	0.439	0.979	Download
4	3o8lA	0.96	1.47	0.371	1.000	Download
5	3o8oB	0.95	1.62	0.362	1.000	Download
6	3o8oA	0.95	1.49	0.373	0.994	Download
7	3opyB	0.95	1.63	0.357	0.997	Download
8	3opyA2	0.94	1.77	0.373	0.991	Download
9	5xoeA	0.94	1.27	0.465	0.969	Download
10	2f48B	0.91	2.12	0.231	0.997	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:0016772	1.00	transferase activity, transferring phosphorus-containing groups
GO:0008443	0.99	phosphofructokinase activity
GO:0003872	0.98	6-phosphofructokinase activity
GO:1901363	0.93	heterocyclic compound binding
GO:0097159	0.93	organic cyclic compound binding
GO:0005524	0.91	ATP binding
GO:0042802	0.71	identical protein binding
GO:0070095	0.70	fructose-6-phosphate binding
GO:0030246	0.70	carbohydrate binding
GO:0048029	0.69	monosaccharide binding
GO:0016208	0.66	AMP binding
GO:0043167	0.54	ion binding
GO:0046872	0.52	metal ion 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:

[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:0044237	1.00	cellular metabolic process
GO:1901135	0.99	carbohydrate derivative metabolic process
GO:0044699	0.99	single-organism process
GO:0044238	0.99	primary metabolic process
GO:0019637	0.99	organophosphate metabolic process
GO:0006796	0.99	phosphate-containing compound metabolic process
GO:1901360	0.98	organic cyclic compound metabolic process
GO:0046483	0.98	heterocycle metabolic process
GO:0044281	0.98	small molecule metabolic process
GO:0034641	0.98	cellular nitrogen compound metabolic process
GO:0016310	0.98	phosphorylation
GO:0006725	0.98	cellular aromatic compound metabolic process
GO:0005975	0.98	carbohydrate metabolic process
GO:1901564	0.97	organonitrogen compound metabolic process
GO:0055086	0.97	nucleobase-containing small molecule metabolic process
GO:0044724	0.97	single-organism carbohydrate catabolic process
GO:0019752	0.97	carboxylic acid metabolic process
GO:0006096	0.96	glycolytic process
GO:0006002	0.91	fructose 6-phosphate metabolic process
GO:0044262	0.80	cellular carbohydrate metabolic process
GO:0046835	0.78	carbohydrate phosphorylation
GO:0005996	0.76	monosaccharide metabolic process
GO:0006006	0.75	glucose metabolic process
GO:0044282	0.74	small molecule catabolic process
GO:0061615	0.73	glycolytic process through fructose-6-phosphate
GO:0030388	0.73	fructose 1,6-bisphosphate metabolic process
GO:0006007	0.73	glucose catabolic process
GO:0061621	0.71	canonical glycolysis
GO:0016043	0.65	cellular component organization
GO:0065003	0.60	macromolecular complex assembly
GO:0051259	0.59	protein oligomerization
GO:0044248	0.56	cellular catabolic process
GO:0051289	0.53	protein homotetramerization
GO:0044275	0.50	cellular carbohydrate catabolic 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	0.98	cytoplasmic part
GO:0005829	0.80	cytosol
GO:0032991	0.68	macromolecular complex
GO:1902494	0.62	catalytic complex
GO:0044445	0.61	cytosolic part
GO:0061695	0.60	transferase complex, transferring phosphorus-containing groups
GO:0043226	0.59	organelle
GO:0005945	0.59	6-phosphofructokinase complex
GO:0043227	0.58	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	0.709	1pfkA	0.967	0.74	0.520	0.979	2.7.1.11	12,73,126,128
2	0.616	1zxxA	0.965	0.81	0.439	0.979	2.7.1.11	12,73,126,128
3	0.602	5pfkA	0.973	0.52	0.495	0.979	2.7.1.11	12,67,103,126,128,130,145,170,176,251,255,260
4	0.542	1mtoA	0.972	0.55	0.502	0.979	2.7.1.11	12,126,128
5	0.085	2f48B	0.914	2.12	0.231	0.997	2.7.1.90	12,73,126,128

	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	0.62	1pfkA	0.967	0.74	0.520	0.979	1.73	FBP	Download	12,73,126,128,170,171,172,223,252,255
2	0.48	3k2qA	0.881	2.15	0.216	0.960	1.36	NA	Download	11,12,73,125
3	0.34	1pfkB	0.966	0.76	0.520	0.979	1.84	ADP	Download	10,42,73,74,75,77,78,103,104,105,106,108,109
4	0.19	2f48B	0.914	2.12	0.231	0.997	1.42	AF3	Download	10,73,103,104,105,125
5	0.15	3o8lB	0.929	1.77	0.277	0.982	1.09	PO4	Download	126,128,130
6	0.06	1kzh0	0.917	2.09	0.234	0.997	0.81	III	Download	13,61,64,65,66,67,68,72,153,154,156,157,159,160,161,162,231,250,252,253,255,256,257,258

	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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