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COFACTOR result for job id 76478

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>76478 (183 residues)
MKKIALYLNPGFEEIEAVTACDVLKRAGILVDMVSTIDSLEVKGAHNIVIKANKLWKELN
INYYDGMVLPGGSGVTSLFDNQTLIDNILEFNKQNKLIASICAAPQVIGQTKLLDNKTIT
HYPNCNFYLDKANVVLDKPFVVDNNFITGASAGSSMLFSLAIVEYLLGKEKKEEIYKNLV
IFG

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	4e08A	0.99	0.52	0.333	1.000	Download
2	3b38A	0.98	0.74	0.286	0.995	Download
3	5sy4A	0.96	1.05	0.308	0.995	Download
4	4k2hA	0.95	1.10	0.308	0.995	Download
5	4xllA	0.95	1.15	0.293	0.989	Download
6	3ot1A	0.92	1.35	0.277	0.967	Download
7	4gdhA	0.92	1.49	0.318	0.978	Download
8	3nooA	0.88	1.91	0.194	0.984	Download
9	3uk7A	0.87	2.39	0.228	0.984	Download
10	3fseB1	0.85	2.43	0.254	0.956	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:0019172	0.98	glyoxalase III activity
GO:0003713	0.72	transcription coactivator activity
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	organic cyclic compound 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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[0.8,0.9)

[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:0044763	0.99	single-organism cellular process
GO:0044281	0.99	small molecule metabolic process
GO:0044248	0.98	cellular catabolic process
GO:0019752	0.98	carboxylic acid metabolic process
GO:0019243	0.97	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione
GO:0044238	0.89	primary metabolic process
GO:0050896	0.85	response to stimulus
GO:0043170	0.84	macromolecule metabolic process
GO:0033554	0.83	cellular response to stress
GO:0006807	0.83	nitrogen compound metabolic process
GO:0065007	0.82	biological regulation
GO:0050789	0.81	regulation of biological process
GO:0050794	0.80	regulation of cellular process
GO:0034641	0.80	cellular nitrogen compound metabolic process
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0031323	0.78	regulation of cellular metabolic process
GO:2000112	0.77	regulation of cellular macromolecule biosynthetic process
GO:1901564	0.77	organonitrogen compound metabolic process
GO:0080090	0.77	regulation of primary metabolic process
GO:0051171	0.77	regulation of nitrogen compound metabolic process
GO:0010468	0.77	regulation of gene expression
GO:0042221	0.76	response to chemical
GO:0019538	0.76	protein metabolic process
GO:0006355	0.76	regulation of transcription, DNA-templated
GO:1901701	0.75	cellular response to oxygen-containing compound
GO:0044267	0.75	cellular protein metabolic process
GO:0006357	0.73	regulation of transcription from RNA polymerase II promoter
GO:1901576	0.72	organic substance biosynthetic process
GO:0044249	0.72	cellular biosynthetic process
GO:1901360	0.70	organic cyclic compound metabolic process
GO:0046483	0.70	heterocycle metabolic process
GO:0043412	0.70	macromolecule modification
GO:0006725	0.70	cellular aromatic compound metabolic process
GO:0044271	0.69	cellular nitrogen compound biosynthetic process
GO:1901566	0.68	organonitrogen compound biosynthetic process
GO:0006464	0.68	cellular protein modification process
GO:0006139	0.68	nucleobase-containing compound metabolic process
GO:0006517	0.67	protein deglycosylation
GO:0010035	0.65	response to inorganic substance
GO:0006979	0.65	response to ox.dat.gzive stress
GO:0070301	0.64	cellular response to hydrogen peroxide
GO:0090304	0.62	nucleic acid metabolic process
GO:1901362	0.58	organic cyclic compound biosynthetic process
GO:0019438	0.58	aromatic compound biosynthetic process
GO:0018130	0.58	heterocycle biosynthetic process
GO:0044283	0.57	small molecule biosynthetic process
GO:0072527	0.53	pyrimidine-containing compound metabolic process
GO:0032501	0.53	multicellular organismal process
GO:0007610	0.53	behavior
GO:0072528	0.52	pyrimidine-containing compound biosynthetic process
GO:0008344	0.52	adult locomotory behavior
GO:0006790	0.52	sulfur compound metabolic process
GO:0009228	0.51	thiamine biosynthetic process
GO:0006259	0.51	DNA metabolic process
GO:0006281	0.50	DNA repair

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:0005829	1.00	cytosol
GO:0043231	0.97	intracellular membrane-bounded organelle
GO:0005634	0.96	nucleus
GO:0005739	0.95	mitochondrion

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	0.067	2issD	0.588	3.43	0.157	0.760	2.6.-.-	18
2	0.066	1cb7A	0.487	4.03	0.102	0.678	5.4.99.1	22
3	0.066	2ywdA	0.582	3.46	0.142	0.754	2.6.-.-	NA
4	0.066	2ywxA	0.510	3.88	0.115	0.694	4.1.1.21	NA
5	0.066	1qzuC	0.526	3.61	0.099	0.700	4.1.1.36	36

	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	0.14	2ab00	0.961	1.05	0.308	0.995	1.37	III	Download	13,14,15,18,19,21,22,25,26,46,48,49,50,51,122,123,139,150,152,153,154,156,178,179,180,181
2	0.04	1rw70	0.785	2.32	0.218	0.902	0.64	III	Download	116,118,139,140,141,142,143
3	0.02	1rk2A	0.619	4.59	0.114	0.923	0.70	MG	Download	11,74,77
4	0.02	1rka0	0.619	4.62	0.114	0.923	0.41	III	Download	27,28,29,30,33,97,98,99,100,101,102

	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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