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COFACTOR result for job id 76665

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

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>76665 (287 residues)
MKLVTFASIKDNLATWNKFNGILITILLVVIIVCTISIIYNKKVRNYNIDDKMPGFLVLV
NVFVASVENIVVSILGKKYQKLTPYIMYLFAYIFIGCLLSILGLEAQGTSFTVTLSMGMV
TFIMIYYFGIKYQKLAFFKRFRNPVELFTQFTPLISISFRLFGNLIGGSIILGLLYGLLI
GFQLSWGVNNIEVDGMTRWASYAIWNPELVENGYLKQYEYWWAGLNLFTTPIMPFLHMYF
DLFSGVIQSTVFAMLTLSYWSAQIDDNEKRADLVDQVKEEITNKYQS

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	6fkfa	0.70	1.18	0.223	0.718	Download
2	6b8ha	0.68	3.05	0.208	0.777	Download
3	5t4oK	0.57	2.90	0.114	0.672	Download
4	6f36M	0.57	3.43	0.164	0.672	Download
5	5araW	0.56	3.41	0.149	0.683	Download
6	6o7ua	0.47	4.37	0.092	0.631	Download
7	4a01A	0.45	4.88	0.049	0.641	Download
8	2o8cB	0.45	5.96	0.037	0.718	Download
9	6h5lA	0.45	5.45	0.023	0.679	Download
10	5tsjN	0.45	4.31	0.078	0.603	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	0.96	catalytic activity
GO:0016787	0.92	hydrolase activity
GO:0017111	0.91	nucleoside-triphosphatase activity
GO:0022857	0.84	transmembrane transporter activity
GO:0016887	0.84	ATPase activity
GO:0042623	0.80	ATPase activity, coupled
GO:0019829	0.79	cation-transporting ATPase activity
GO:0015078	0.79	hydrogen ion transmembrane transporter activity
GO:0046933	0.78	proton-transporting ATP synthase activity, rotational mechanism

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:

[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:0044699	1.00	single-organism process
GO:0071704	0.99	organic substance metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0044238	0.98	primary metabolic process
GO:0034641	0.98	cellular nitrogen compound metabolic process
GO:1901564	0.97	organonitrogen compound metabolic process
GO:0044281	0.97	small molecule metabolic process
GO:0006139	0.97	nucleobase-containing compound metabolic process
GO:0009259	0.96	ribonucleotide metabolic process
GO:0009199	0.96	ribonucleoside triphosphate metabolic process
GO:0009161	0.96	ribonucleoside monophosphate metabolic process
GO:0009126	0.96	purine nucleoside monophosphate metabolic process
GO:0006163	0.96	purine nucleotide metabolic process
GO:1901566	0.95	organonitrogen compound biosynthetic process
GO:0098662	0.95	inorganic cation transmembrane transport
GO:0044271	0.95	cellular nitrogen compound biosynthetic process
GO:0015672	0.95	monovalent inorganic cation transport
GO:0015986	0.93	ATP synthesis coupled proton transport
GO:0043170	0.59	macromolecule metabolic process
GO:0044260	0.54	cellular macromolecule 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:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0032991	0.91	macromolecular complex
GO:0044425	0.89	membrane part
GO:0043234	0.85	protein complex
GO:0044446	0.84	intracellular organelle part
GO:0098796	0.75	membrane protein complex
GO:0016020	0.71	membrane
GO:0044429	0.68	mitochondrial part
GO:0043226	0.68	organelle
GO:0098798	0.67	mitochondrial protein complex
GO:0043229	0.67	intracellular organelle
GO:0043227	0.67	membrane-bounded organelle
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0098800	0.65	inner mitochondrial membrane protein complex
GO:0016469	0.58	proton-transporting two-sector ATPase complex
GO:0005753	0.57	mitochondrial proton-transporting ATP synthase complex
GO:0016021	0.51	integral component of 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	0.060	2ewgA	0.386	5.16	0.034	0.565	2.5.1.10	NA
2	0.060	2wghB	0.377	6.52	0.050	0.665	1.17.4.1	NA
3	0.060	1r7aA	0.380	6.19	0.061	0.638	2.4.1.7	NA
4	0.060	2nyfA	0.387	5.60	0.043	0.606	4.3.1.5	NA
5	0.060	1y2mB	0.398	5.68	0.022	0.631	4.3.1.24	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	0.01	1oh8B	0.426	5.68	0.060	0.662	0.46	QNA	Download	114,119,158
2	0.01	1wbbA	0.429	5.71	0.056	0.658	0.45	ADP	Download	79,123,125,126,127,128,260
3	0.01	2j9tA	0.404	5.04	0.027	0.589	0.82	BO3	Download	114,118,157,158,161
4	0.01	3rkoM	0.425	5.70	0.093	0.665	0.42	CA7	Download	156,163,164,167,168
5	0.01	3mmoA	0.402	6.03	0.053	0.658	0.50	NA	Download	114,115,116,160

	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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