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COFACTOR result for job id 76333

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

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>76333 (414 residues)
MFAYTKNKKKLAKHKPKKNRSFAIVIPAHNESMVVGKLIDSIKAQKYDGVIDIYLVADNC
TDNRKTYNVGIEKGITVLERFHSTLKGGNFAIRHGWRYIRDNNLLDKYDCFCSFDADNLL
DENWVYEVNKTFDFYNDIEVVTTYRNSKNYADNWISSACSIQFLKESDIINKGRATLNHS
SYVNGTGFCITRKIFEQTNWWDFNSLSHDIEFTQWLMLNKIKTGYAPNACFYDEQPIDFK
NSWKQRMRWCVGFKQVWKIYRSEMIKNMFTFKINKIKLWVNFTMIFPAVITLLINLLFWL
ITFGLIISNYIVNYLNSSLVIIEQANNYLRDLIIYCTTTPIVIFGIIFINYLLWGFIIVA
RNKKSIQATSWQKFKSIFTYPFFMLTYIPISFLALFKSTYSTTPVARKAQLVQN

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	4hg6A	0.92	2.22	0.126	0.973	Download
2	4fixA	0.57	5.30	0.082	0.763	Download
3	6e4qA	0.56	5.32	0.094	0.737	Download
4	2d7rA	0.56	5.38	0.101	0.730	Download
5	6iwqA	0.55	5.02	0.083	0.705	Download
6	5nqaA	0.54	4.92	0.092	0.688	Download
7	1xhbA	0.54	5.04	0.082	0.698	Download
8	2ffuA	0.54	5.25	0.106	0.703	Download
9	5tz8A	0.54	4.48	0.076	0.664	Download
10	2z86C1	0.45	2.99	0.143	0.507	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:0016740	0.99	transferase activity
GO:0016757	0.98	transferase activity, transferring glycosyl groups
GO:0016758	0.85	transferase activity, transferring hexosyl groups
GO:0008194	0.62	UDP-glycosyltransferase 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:0071704	0.98	organic substance metabolic process
GO:0009987	0.97	cellular process
GO:0044238	0.95	primary metabolic process
GO:0044237	0.94	cellular metabolic process
GO:1901576	0.93	organic substance biosynthetic process
GO:1901135	0.92	carbohydrate derivative metabolic process
GO:0044699	0.91	single-organism process
GO:0043170	0.91	macromolecule metabolic process
GO:0006807	0.87	nitrogen compound metabolic process
GO:0044249	0.86	cellular biosynthetic process
GO:0044710	0.85	single-organism metabolic process
GO:0044763	0.84	single-organism cellular process
GO:0044260	0.83	cellular macromolecule metabolic process
GO:0005975	0.82	carbohydrate metabolic process
GO:0044711	0.81	single-organism biosynthetic process
GO:1901137	0.78	carbohydrate derivative biosynthetic process
GO:0044723	0.78	single-organism carbohydrate metabolic process
GO:0009059	0.73	macromolecule biosynthetic process
GO:0044281	0.72	small molecule metabolic process
GO:0034641	0.70	cellular nitrogen compound metabolic process
GO:1901564	0.67	organonitrogen compound metabolic process
GO:1901360	0.66	organic cyclic compound metabolic process
GO:0046483	0.66	heterocycle metabolic process
GO:0034645	0.65	cellular macromolecule biosynthetic process
GO:0006139	0.65	nucleobase-containing compound metabolic process
GO:0016051	0.63	carbohydrate biosynthetic process
GO:0044262	0.62	cellular carbohydrate metabolic process
GO:0033692	0.61	cellular polysaccharide biosynthetic process
GO:1901566	0.60	organonitrogen compound biosynthetic process
GO:0055086	0.54	nucleobase-containing small molecule 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:0044464	1.00	cell part
GO:0044424	0.93	intracellular part
GO:0016020	0.87	membrane
GO:0044425	0.86	membrane part
GO:0016021	0.79	integral component of membrane
GO:0044444	0.78	cytoplasmic part
GO:0005886	0.63	plasma membrane
GO:0043226	0.62	organelle
GO:0043229	0.61	intracellular organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0044459	0.56	plasma membrane part
GO:0005887	0.55	integral component of plasma 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	2icyB	0.445	4.81	0.074	0.577	2.7.7.9	NA
2	0.060	2ffvA	0.559	5.39	0.083	0.744	2.4.1.41	NA
3	0.060	3fwwA	0.409	3.95	0.068	0.495	2.3.1.157 2.7.7.23	NA
4	0.060	2rj7A	0.398	3.96	0.092	0.483	2.4.1.37 2.4.1.40	NA
5	0.060	1hm9B	0.415	3.80	0.072	0.498	2.3.1.157 2.7.7.23	28

	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	0.07	3e25A	0.452	3.97	0.095	0.541	0.99	UDP	Download	27,28,29,31,57,87,88,115,116,117,207

	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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