[back]

COFACTOR result for job id 76384

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

User Input

>76384 (441 residues)
MFKVKFADIGEGLTEGTVAEVLVKVGDVVKEGQSLYFVETDKVNSEIPAPVAGKIAVINI
KAGQEIKVGDVVMEIDEGSGASVASEPKAEAKQEAKVEVVEENASVVGATPVSNDLIVRK
QASTVTKSSTIKATPLARKVAADLNIDLSLVTPTGPNQRILVADIKNYHSSSAQPASQPA
PTPTLVASQPAPAPTPAITPAIKVVEPSAPLSWDEVPMNGVRKATVKAMTKSHTEIAAFT
GMKNTDITETHKMRTELKDHAAASGIKLTYLAFIIKAVAKSLRDMPNINVRGDFANNKIQ
FMHNINIGIAVDTPNGLMVPVIKGADHLSVFEIAIKISELANKAKDGKLTRAEMTEATFT
VSNFGSVGLDYATPIINSPESAILGVGTMSQTPLYINGELQKRFIMPLSMTCDHRIIDGA
DAGRFLIKVQDYLSKPVLLFM

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	1dpbA	0.51	2.00	0.325	0.531	Download
2	1b5sA	0.51	1.79	0.409	0.528	Download
3	4n72A	0.51	1.67	0.336	0.528	Download
4	2ihwA	0.50	1.69	0.383	0.517	Download
5	1sczA	0.49	1.93	0.309	0.515	Download
6	3maeA	0.49	2.04	0.391	0.512	Download
7	3l60A	0.48	1.92	0.307	0.510	Download
8	3rqcA	0.47	1.70	0.373	0.492	Download
9	3b8kA	0.46	3.18	0.260	0.515	Download
10	2xt6A1	0.39	2.24	0.228	0.417	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	0.97	catalytic activity
GO:0016740	0.78	transferase activity
GO:0016747	0.70	transferase activity, transferring acyl groups other than amino-acyl groups
GO:0016417	0.59	S-acyltransferase activity

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	0.97	cellular process
GO:0044699	0.96	single-organism process
GO:0044237	0.94	cellular metabolic process
GO:0071704	0.93	organic substance metabolic process
GO:0044763	0.87	single-organism cellular process
GO:0044281	0.87	small molecule metabolic process
GO:0006082	0.81	organic acid metabolic process
GO:0043436	0.72	oxoacid metabolic process
GO:0044238	0.68	primary metabolic process
GO:0019752	0.62	carboxylic acid metabolic process
GO:0006807	0.62	nitrogen compound metabolic process
GO:1901576	0.60	organic substance biosynthetic process
GO:0044249	0.60	cellular biosynthetic process
GO:1901564	0.54	organonitrogen compound metabolic process
GO:0032787	0.50	monocarboxylic acid 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	0.87	macromolecular complex
GO:1902494	0.82	catalytic complex
GO:1990204	0.81	oxidoreductase complex
GO:0043226	0.78	organelle
GO:0043229	0.77	intracellular organelle
GO:0043227	0.68	membrane-bounded organelle
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0045254	0.64	pyruvate dehydrogenase complex
GO:0005739	0.56	mitochondrion
GO:0044446	0.50	intracellular organelle part

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	0.566	1dpbA	0.511	2.00	0.325	0.531	2.3.1.12	362
2	0.532	1sczA	0.491	1.93	0.309	0.515	2.3.1.61	414
3	0.525	2ihwA	0.498	1.69	0.383	0.517	2.3.1.168	414,362
4	0.508	3l60A	0.484	1.92	0.307	0.510	2.3.1.12	414,362
5	0.138	3b8kA	0.459	3.18	0.260	0.515	2.3.1.12	362

	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:

Click to view	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	1xl8B	0.429	5.90	0.067	0.599	0.47	MPD	Download	16,64,69

	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).

[back]