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COFACTOR result for job id 76508

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

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>76508 (387 residues)
MNQNIEKRLFTSESVSEGHPDKICDQISDAILDEVLKQDKNAKVACEVFATTNYLLIGGQ
ISSTAIVDYEQVARDVLKKIGYVDDAYGINANTCKIDIKIESQSPDIAQGVELSNDQIGA
GDQGIMFGYATNESKTYLPLAITIAHELVYNATSQRKKGLFKWARPDMKSQVTIDYTNIN
NPKIDTILMSIQHDPNYNEIEFKKYIKENIMDLVAKEFNLNTDFKVLINPTGRFVIGGPQ
GDTGLTGRKIIADTYGGYSRHGGGAFSGKDSTKVDRSAAYMCRYVAKNLVAAGLADKIEI
QVSYGIGISQPISIFIETFNTHKVDLNTIYKAVYENFDFSVSSMIKNLDLKKPIFFKTSK
YGHFGKKDLPWEKLDKIEVLKEYKKCS

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	1rg9A	0.98	0.60	0.526	0.987	Download
2	5t8sA	0.98	0.69	0.517	0.985	Download
3	5h9uC	0.96	1.55	0.435	0.987	Download
4	4odjA	0.95	0.78	0.496	0.964	Download
5	2p02A	0.95	0.87	0.513	0.966	Download
6	3so4A	0.93	1.59	0.473	0.956	Download
7	4le5A	0.92	1.43	0.406	0.948	Download
8	3rv2A	0.90	1.78	0.477	0.938	Download
9	4gjiA	0.27	6.63	0.034	0.429	Download
10	4kl0A	0.25	7.35	0.046	0.444	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:0004478	1.00	methionine adenosyltransferase activity
GO:1901363	0.90	heterocyclic compound binding
GO:0097159	0.90	organic cyclic compound binding
GO:0000166	0.89	nucleotide binding
GO:0005524	0.88	ATP binding
GO:0042802	0.76	identical protein binding
GO:0043167	0.65	ion binding
GO:0046872	0.61	metal ion binding
GO:0000287	0.59	magnesium ion 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:

[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:0009987	1.00	cellular process
GO:0044237	0.99	cellular metabolic process
GO:0009058	0.97	biosynthetic process
GO:0044249	0.96	cellular biosynthetic process
GO:0006790	0.95	sulfur compound metabolic process
GO:0006556	0.94	S-adenosylmethionine biosynthetic process
GO:0044763	0.93	single-organism cellular process
GO:0044281	0.93	small molecule metabolic process
GO:0071704	0.87	organic substance metabolic process
GO:0044238	0.85	primary metabolic process
GO:0006730	0.85	one-carbon metabolic process
GO:0006807	0.84	nitrogen compound metabolic process
GO:1901564	0.76	organonitrogen compound metabolic process
GO:0034641	0.72	cellular nitrogen compound metabolic process
GO:1901360	0.69	organic cyclic compound metabolic process
GO:0006725	0.69	cellular aromatic compound metabolic process
GO:0046483	0.68	heterocycle metabolic process
GO:0006082	0.68	organic acid metabolic process
GO:0006139	0.67	nucleobase-containing compound metabolic process
GO:0019752	0.65	carboxylic acid metabolic process
GO:0006520	0.64	cellular amino acid metabolic process
GO:0009066	0.60	aspartate family amino acid metabolic process
GO:0050896	0.58	response to stimulus
GO:0006555	0.56	methionine metabolic process
GO:0042221	0.52	response to chemical
GO:0071840	0.51	cellular component organization or biogenesis
GO:0055086	0.50	nucleobase-containing small molecule metabolic process
GO:0016043	0.50	cellular component organization

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:0005829	0.99	cytosol

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	0.638	2obvA	0.964	0.85	0.513	0.977	2.5.1.6	19,169,248,249,269,273,275
2	0.622	3imlA	0.926	1.26	0.511	0.946	2.5.1.6	19,169,248,249,269,273,275
3	0.206	1fugA	0.959	1.46	0.507	0.985	2.5.1.6	19,169,248,249,269,273,275
4	0.206	3imlD	0.788	0.86	0.534	0.798	2.5.1.6	19,169,248,249,269,273,275
5	0.195	2hj2B	0.953	0.87	0.513	0.966	2.5.1.6	13,127,146,245,247,250,257,263,265,269,275,279

	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	0.69	1p7lD	0.980	0.60	0.526	0.987	1.68	SAM	Download	19,20,167,169,231,233,234,242
2	0.66	1o93A	0.908	1.57	0.508	0.941	1.55	ATP	Download	19,20,167,169,249
3	0.66	1o92A	0.908	1.57	0.508	0.941	1.55	MG	Download	20,167,238
4	0.65	1p7lC	0.980	0.60	0.526	0.987	0.92	PPK	Download	19,21,169

	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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