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COFACTOR result for job id 76516

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

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>76516 (412 residues)
MNDQFEKIKKQFPLLKKHPNLIYFDNGATTLKPNSVINAQTNYLKNISTNPHSSDYKIGY
QSLEILSNTRELVKNFINANHTSEIIFTSGTTQSINMIAKGLINLINQDDEILITSLEHS
SNLVPWIWLKQKTNAVIKNLELTNDFGIDINKLDQLITPKTKIISFAHISNTTGYINDVK
KIIQKIRSINQNVIIVVDVAQSIAHFKVDVKDWDVDFIAFSAHKMYGPFGVGVLYGKYQL
LDKLEPLNLGGGSSLTISRDFTSYTLKSLPEKLEAGTLNISNIYGFKKAIEFILKIGINN
ICLYETKLKQYTRQQIKANHLENKITFYNLNNDSPLLLFNVNQINAQDISSFLDVKYNIT
SRSGAHCVRRLEDVIHIKSALRISFAIYNTTDEIDKLIDALKNTDKFLDIYF

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	4q75A	0.97	0.89	0.315	0.978	Download
2	5j8qA	0.97	0.70	0.364	0.973	Download
3	6c9eA	0.96	0.79	0.360	0.971	Download
4	1jf9A	0.96	0.89	0.329	0.973	Download
5	4w91A	0.96	0.85	0.328	0.968	Download
6	1t3iA	0.95	1.00	0.321	0.968	Download
7	5b7sA	0.93	1.32	0.317	0.956	Download
8	4lw2A	0.91	1.95	0.332	0.956	Download
9	3caiA	0.88	1.42	0.191	0.915	Download
10	5vprA	0.86	1.17	0.380	0.876	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	0.94	transferase activity
GO:0016782	0.90	transferase activity, transferring sulfur-containing groups
GO:0016783	0.89	sulfurtransferase activity
GO:0043167	0.88	ion binding
GO:0031071	0.88	cysteine desulfurase activity
GO:0048037	0.86	cofactor binding
GO:0030170	0.85	pyridoxal phosphate binding
GO:0016846	0.85	carbon-sulfur lyase activity
GO:0009000	0.80	selenocysteine lyase 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:0044237	1.00	cellular metabolic process
GO:0071704	0.99	organic substance metabolic process
GO:0006807	0.96	nitrogen compound metabolic process
GO:1901564	0.91	organonitrogen compound metabolic process
GO:0044281	0.88	small molecule metabolic process
GO:0044238	0.88	primary metabolic process
GO:0006082	0.86	organic acid metabolic process
GO:1901605	0.81	alpha-amino acid metabolic process
GO:0009069	0.79	serine family amino acid metabolic process
GO:0044249	0.78	cellular biosynthetic process
GO:0043170	0.78	macromolecule metabolic process
GO:0051186	0.76	cofactor metabolic process
GO:0006534	0.75	cysteine metabolic process
GO:0006790	0.71	sulfur compound metabolic process
GO:0071840	0.70	cellular component organization or biogenesis
GO:0051188	0.70	cofactor biosynthetic process
GO:0044260	0.70	cellular macromolecule metabolic process
GO:0016043	0.69	cellular component organization
GO:1901360	0.67	organic cyclic compound metabolic process
GO:0016226	0.67	iron-sulfur cluster assembly
GO:0046483	0.66	heterocycle metabolic process
GO:0043412	0.66	macromolecule modification
GO:0034641	0.66	cellular nitrogen compound metabolic process
GO:0006725	0.61	cellular aromatic compound metabolic process
GO:0019538	0.57	protein metabolic process
GO:0006139	0.55	nucleobase-containing compound metabolic process
GO:0050896	0.54	response to stimulus
GO:0044267	0.54	cellular protein metabolic process
GO:0006464	0.52	cellular protein modification process
GO:1901575	0.51	organic substance catabolic process
GO:0044248	0.50	cellular 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	0.93	cytoplasmic part
GO:0043229	0.85	intracellular organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0005737	0.78	cytoplasm
GO:0005829	0.55	cytosol
GO:0005739	0.55	mitochondrion

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	0.343	1n31A	0.847	2.48	0.198	0.915	4.4.1.-	280
2	0.297	1j04A	0.754	3.17	0.099	0.859	2.6.1.44	198
3	0.292	3ffrA	0.717	3.35	0.151	0.833	2.6.1.52	198
4	0.276	1t3iA	0.954	1.00	0.321	0.968	2.8.1.7	NA
5	0.208	3caiA	0.884	1.42	0.191	0.915	2.6.1.-	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	0.40	1i29A	0.960	0.90	0.329	0.973	1.40	UUU	Download	27,28,91,92,119,171,198,200,221,223,224,382
2	0.28	3a9zB	0.828	2.37	0.241	0.898	0.96	SLP	Download	27,28,119,171,224,382
3	0.07	3lvk0	0.827	2.33	0.247	0.896	1.16	III	Download	23,25,28,29,31,32,37,41,44,45,48,50,55,56,57,58,89,92,93,96,100,120,121,124,128,229,230,247,248,249,250,251,274,276,277,278,279,281,282,360,361

	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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