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COFACTOR result for job id 76677

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>76677 (332 residues)
MNYLLIGGAGYIGSHVAEIINKTDNKVIIYDNLSSGSSDFIEQKSTFIQGDILDFDKLND
VFSSNKIDVVIYLAGLIKVGESVQKPLDYYQTNILGLVNTLKIMQIHNVNYFVFSSSAAV
YGNNSRHNGFFYEDDPKEPCSPYGRTKYFGEEIIKDFAIANPNFHYTFLRYFNVAGASKS
KRIGYLTQNNNKPTHLIPAISYFAFGLTDKFSIFGSDYNTNDGTCIRDYVYVCELAELHL
LTAQKMVKENRNLYYNIGSGKGFSNLEIIKEFERQLGYKLDIDIAQRRSGDPDILVASNT
KLCQELNYEIKTNIKDIVESEIAFRKAHLKNK

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	4lisA	0.98	0.94	0.355	0.994	Download
2	3enkA	0.97	0.84	0.332	0.988	Download
3	1a9yA	0.97	0.94	0.357	0.988	Download
4	2c20A	0.96	0.97	0.368	0.982	Download
5	1ek5A	0.96	1.20	0.357	0.988	Download
6	1gy8C	0.94	1.66	0.372	0.988	Download
7	4twrA	0.94	1.30	0.350	0.967	Download
8	1z45A1	0.93	1.02	0.365	0.949	Download
9	4zrmA	0.88	1.84	0.313	0.925	Download
10	1sb8A	0.88	1.81	0.298	0.931	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:0016857	0.95	racemase and epimerase activity, acting on carbohydrates and derivatives
GO:0003978	0.93	UDP-glucose 4-epimerase activity
GO:0043167	0.69	ion binding
GO:0046872	0.67	metal ion binding
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0042802	0.51	identical protein binding
GO:0036094	0.51	small molecule binding
GO:0000166	0.50	nucleotide 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:0071704	0.96	organic substance metabolic process
GO:0009987	0.94	cellular process
GO:0044238	0.93	primary metabolic process
GO:0044699	0.92	single-organism process
GO:0044237	0.88	cellular metabolic process
GO:0044710	0.83	single-organism metabolic process
GO:0005975	0.83	carbohydrate metabolic process
GO:0044723	0.80	single-organism carbohydrate metabolic process
GO:1901576	0.79	organic substance biosynthetic process
GO:0044281	0.79	small molecule metabolic process
GO:0044249	0.75	cellular biosynthetic process
GO:0043170	0.73	macromolecule metabolic process
GO:0044260	0.68	cellular macromolecule metabolic process
GO:0005996	0.67	monosaccharide metabolic process
GO:1901135	0.66	carbohydrate derivative metabolic process
GO:0044763	0.65	single-organism cellular process
GO:0009059	0.65	macromolecule biosynthetic process
GO:0019318	0.64	hexose metabolic process
GO:0016051	0.64	carbohydrate biosynthetic process
GO:1901137	0.62	carbohydrate derivative biosynthetic process
GO:0034645	0.61	cellular macromolecule biosynthetic process
GO:0005976	0.61	polysaccharide metabolic process
GO:0006012	0.60	galactose metabolic process
GO:0000271	0.60	polysaccharide biosynthetic process
GO:0044262	0.59	cellular carbohydrate metabolic process
GO:1901575	0.57	organic substance catabolic process
GO:0033692	0.57	cellular polysaccharide biosynthetic process
GO:0006807	0.55	nitrogen compound metabolic process
GO:0044282	0.54	small molecule catabolic process
GO:0016052	0.53	carbohydrate catabolic process
GO:0046365	0.51	monosaccharide catabolic process
GO:0019388	0.50	galactose catabolic 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	0.95	cytoplasmic part
GO:0005829	0.84	cytosol
GO:0043226	0.62	organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0005737	0.50	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	0.519	2c20A	0.963	0.97	0.368	0.982	5.1.3.2	11,143,172,174,196,226,229
2	0.482	1eq2D	0.811	2.52	0.183	0.904	5.1.3.20	112
3	0.325	1kewA	0.871	1.91	0.243	0.931	4.2.1.46	12,79,92,142,288
4	0.230	3enkA	0.973	0.84	0.332	0.988	5.1.3.2	NA
5	0.226	1i3kA	0.965	1.06	0.354	0.988	5.1.3.2	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	0.74	1lrjA	0.970	0.96	0.366	0.988	1.50	NAD	Download	7,10,11,12,30,31,32,33,34,35,36,50,51,52,73,74,75,77,92,115,116,143,147,171,172,174,195
2	0.12	2c200	0.963	0.97	0.368	0.982	1.13	III	Download	83,86,87,90,91,95,98,101,102,139,140,141,142,145,152,153,157
3	0.08	1z450	0.930	1.02	0.365	0.949	1.12	III	Download	83,86,87,90,91,95,98,102,142,145,148,152,153
4	0.07	2cnbB	0.935	1.63	0.368	0.982	0.95	UFG	Download	77,79,117,118,143,172,173,195,196,199,225,227
5	0.06	1kew0	0.871	1.91	0.243	0.931	0.93	III	Download	83,86,90,94,95,98,136,137,139,140,141,142,145,148,149,152,153,156,157,159

	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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