[back]

COFACTOR result for job id 76306

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

User Input

>76306 (275 residues)
MDVTKLILKLDQLSKEHSSASGITSRIILDNIELITNSTISKVAQITYTSPATITRFCQR
HLDISGFSELQTLLRVYLNQQEEQNRLLLQNKDKKISKFEEISKAINATDALIETNQVDK
LVKAIYNTKTVALISYDNSVNHAVTELAEKMNLIGIPPVIINQQDLLDYYTKISDSSWVF
IVISHFAENITTYQSIVQLKKNGSRIGLISMNKPNKYSSVCDYWIKYAVTDADPLQKIKH
SANFSLLYVVQVLFNRILTKDHDRFEKIIKTLKIE

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	4ivnA	0.93	0.43	0.183	0.934	Download
2	2j6hA	0.62	4.39	0.085	0.815	Download
3	4bb9A	0.61	3.88	0.073	0.760	Download
4	4s12A	0.60	3.24	0.095	0.720	Download
5	3w0lB1	0.58	3.19	0.096	0.691	Download
6	1nriA	0.58	3.36	0.134	0.702	Download
7	3etnB	0.57	2.42	0.112	0.633	Download
8	2xhzA	0.56	2.37	0.135	0.615	Download
9	1vivA	0.55	2.98	0.137	0.625	Download
10	1x92B	0.55	2.30	0.095	0.607	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	0.84	transferase activity
GO:0004360	0.79	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
GO:0097367	0.52	carbohydrate derivative 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	0.97	cellular process
GO:0071704	0.95	organic substance metabolic process
GO:0044237	0.95	cellular metabolic process
GO:0044238	0.94	primary metabolic process
GO:0006807	0.94	nitrogen compound metabolic process
GO:1901360	0.93	organic cyclic compound metabolic process
GO:0006725	0.93	cellular aromatic compound metabolic process
GO:0006139	0.92	nucleobase-containing compound metabolic process
GO:1901135	0.87	carbohydrate derivative metabolic process
GO:0019637	0.86	organophosphate metabolic process
GO:0006796	0.86	phosphate-containing compound metabolic process
GO:0006040	0.74	amino sugar metabolic process
GO:0006047	0.73	UDP-N-acetylglucosamine metabolic process
GO:0006002	0.73	fructose 6-phosphate metabolic process
GO:0043170	0.70	macromolecule metabolic process
GO:1901576	0.65	organic substance biosynthetic process
GO:0044249	0.65	cellular biosynthetic process
GO:0044260	0.64	cellular macromolecule metabolic process
GO:0090304	0.62	nucleic acid metabolic process
GO:0034645	0.54	cellular macromolecule biosynthetic process
GO:1901137	0.53	carbohydrate derivative biosynthetic process
GO:0050794	0.52	regulation of cellular process
GO:0044271	0.52	cellular nitrogen compound biosynthetic process
GO:0019222	0.51	regulation of metabolic process
GO:0080090	0.50	regulation of primary metabolic process
GO:0044699	0.50	single-organism process
GO:0034654	0.50	nucleobase-containing compound biosynthetic process
GO:0016070	0.50	RNA metabolic process
GO:0010468	0.50	regulation of gene expression
GO:0009889	0.50	regulation of biosynthetic 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	0.93	cytoplasmic part
GO:0005829	0.90	cytosol
GO:0005737	0.88	cytoplasm

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	0.099	1jeoA	0.536	2.72	0.148	0.604	5.3.1.27	3
2	0.060	2jfdA	0.284	6.29	0.058	0.494	2.3.1.85	NA
3	0.060	3hjbA	0.467	3.96	0.055	0.615	5.3.1.9	NA
4	0.060	3euaF	0.521	3.23	0.105	0.622	3.5.-.-	NA
5	0.060	1ii0B	0.485	5.58	0.053	0.756	3.6.3.16	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	0.04	3etnB	0.584	2.54	0.103	0.654	0.64	CMK	Download	22,23,24,49,50,52,53
2	0.02	2i22B	0.532	2.51	0.114	0.604	0.51	I22	Download	44,52,55
3	0.01	1siwA	0.472	5.00	0.058	0.651	0.47	SF4	Download	184,209,217,220

	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]