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COFACTOR result for job id 76526

[Download result.tar.bz2 for all prediction results]

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>76526 (318 residues)
MKKTANKVVLIGAGAVGTSFLYAAINQGIAEHYVLIDAFPQPAEGNALDLSDTLAVIPHS
FSSIKAGTYEDCKDADVVVITAGRPQKPGETRLEMVAGNAEIMKNIATEVKKSGFDGITV
IASNPVDVITHVYQKVTGFDPHKVIGSGTTLDSARLRRLVGQKLNVKPESVQAYVAGEHG
DSSVAIWSQANIMGRPILDYVKCGCLTLEDLDQIQKDTVDMAYKIINLKRATFYGIGACL
TKIVNAVLRDEKSTLMVGAQLNGEYKNKGLYTGVPAIIGSNGWERIIEWDLTKEEQEKFD
KSCETLHKTIDSVKHLFE

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	1ez4B	0.97	1.05	0.472	0.994	Download
2	4plcA	0.97	1.15	0.345	0.994	Download
3	1pzhA	0.97	1.28	0.309	0.997	Download
4	2fnzA	0.96	1.27	0.314	0.991	Download
5	1ldnA	0.96	1.41	0.424	0.987	Download
6	3gvhA	0.96	1.28	0.344	0.987	Download
7	5nfrA	0.95	1.13	0.295	0.981	Download
8	2hjrL	0.95	1.16	0.317	0.981	Download
9	3d4pB	0.94	1.34	0.432	0.975	Download
10	4q3nA	0.94	1.71	0.417	0.981	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:0016614	0.99	oxidoreductase activity, acting on CH-OH group of donors
GO:0016616	0.97	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0004457	0.94	lactate dehydrogenase activity
GO:0004459	0.93	L-lactate dehydrogenase activity
GO:0016615	0.69	malate dehydrogenase activity
GO:0030060	0.58	L-malate dehydrogenase activity
GO:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	organic cyclic compound 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	0.99	organic substance metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0044281	0.98	small molecule metabolic process
GO:0044238	0.98	primary metabolic process
GO:0006082	0.97	organic acid metabolic process
GO:0034641	0.95	cellular nitrogen compound metabolic process
GO:0019752	0.95	carboxylic acid metabolic process
GO:1901564	0.94	organonitrogen compound metabolic process
GO:0006139	0.94	nucleobase-containing compound metabolic process
GO:0032787	0.93	monocarboxylic acid metabolic process
GO:0006796	0.93	phosphate-containing compound metabolic process
GO:1901135	0.92	carbohydrate derivative metabolic process
GO:0009117	0.92	nucleotide metabolic process
GO:0006090	0.92	pyruvate metabolic process
GO:1901575	0.91	organic substance catabolic process
GO:0046496	0.91	nicotinamide nucleotide metabolic process
GO:0046034	0.91	ATP metabolic process
GO:0006091	0.91	generation of precursor metabolites and energy
GO:0005975	0.91	carbohydrate metabolic process
GO:0006096	0.90	glycolytic process
GO:0006099	0.56	tricarboxylic acid cycle

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	0.91	cytoplasmic part
GO:0005737	0.84	cytoplasm
GO:0043226	0.82	organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0043229	0.72	intracellular organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0005829	0.57	cytosol
GO:0016020	0.50	membrane

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	0.475	2j5rA	0.893	1.61	0.324	0.940	1.1.1.37	16,145,148,153,155,178,181,229,232
2	0.472	2v7pA	0.924	1.60	0.362	0.965	1.1.1.27	154,178,180,223,231,235
3	0.325	1ldnA	0.957	1.41	0.424	0.987	1.1.1.27	NA
4	0.311	1ldxA	0.881	2.48	0.260	0.975	1.1.1.27	120,124,128,147,154,182,219,223,236
5	0.266	1ez4B	0.971	1.05	0.472	0.994	1.1.1.27	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	0.90	1ez4B	0.971	1.05	0.472	0.994	1.63	NAD	Download	13,14,15,16,37,38,39,81,82,83,102,122,123,124,126,147,151,179,236
2	0.54	1v6aA	0.919	2.10	0.315	0.984	1.22	TRE	Download	13,14,82,83,85
3	0.07	2frm0	0.944	1.44	0.321	0.981	1.38	III	Download	18,19,22,23,26,27,41,42,44,45,46,48,49,50,52,53,57,58,59,61,154,155,157,167,168,169,224,225,228,229,232,233,234,235,236,238,239,242

	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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