[back]

COFACTOR result for job id 76507

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

User Input

>76507 (257 residues)
MKVLMIGDVYAKPGREMLEKHLKNIVDQNQIDFIVVNGENTTHGKSICKKHYDFYKSLNV
DVITSGNHIFKNAEVLEYIKTTNDLLKPLNMSKHTPGNGNVIVNKNKKKIAVVSLMGQSF
MDAVNNPYDALDEFLKTNTDFDILLVDFHAESTAEKIAFAFNYDGIITAFVGTHTHVMTA
DERLLPNKTAFISDIGMTGVIDSIIGVEVNDVIKRAKTGLPVKFNIATGKCWLNAVIIEI
DDKTNKATSIKRLTIKD

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	4b2oA	0.99	0.47	0.416	1.000	Download
2	1t70A	0.96	0.89	0.377	0.981	Download
3	2z06A	0.95	0.99	0.371	0.977	Download
4	1t71A	0.95	1.42	0.379	0.996	Download
5	2z1aA1	0.73	2.91	0.121	0.868	Download
6	4h1sA1	0.73	2.96	0.121	0.868	Download
7	1oidA1	0.73	2.98	0.148	0.868	Download
8	3gveA	0.72	2.98	0.177	0.856	Download
9	3ivdA	0.71	3.00	0.159	0.856	Download
10	3ztvA1	0.70	3.29	0.126	0.868	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:0042578	1.00	phosphoric ester hydrolase activity
GO:0004113	0.90	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
GO:0043167	0.86	ion binding
GO:0046872	0.85	metal ion binding
GO:0008663	0.64	2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
GO:0016817	0.61	hydrolase activity, acting on acid anhydrides
GO:0008252	0.57	nucleotidase activity
GO:0097159	0.54	organic cyclic compound 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:0044237	0.99	cellular metabolic process
GO:0071704	0.98	organic substance metabolic process
GO:0044238	0.98	primary metabolic process
GO:0034641	0.98	cellular nitrogen compound metabolic process
GO:0006139	0.97	nucleobase-containing compound metabolic process
GO:1901135	0.89	carbohydrate derivative metabolic process
GO:0009225	0.88	nucleotide-sugar metabolic process
GO:0006796	0.70	phosphate-containing compound metabolic process
GO:0044281	0.68	small molecule metabolic process
GO:0016311	0.66	dephosphorylation
GO:0055086	0.60	nucleobase-containing small molecule metabolic process
GO:0019637	0.60	organophosphate metabolic process
GO:0009117	0.59	nucleotide metabolic process
GO:1901575	0.58	organic substance catabolic process
GO:0044248	0.58	cellular catabolic process
GO:0034655	0.57	nucleobase-containing compound catabolic process
GO:1901292	0.56	nucleoside phosphate 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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0005829	0.80	cytosol
GO:0043226	0.55	organelle
GO:0043227	0.54	membrane-bounded organelle

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	0.066	1tqxA	0.515	4.62	0.084	0.728	5.1.3.1	57
2	0.066	2r17B	0.473	3.80	0.182	0.615	3.1.3.3	174
3	0.066	2fliC	0.505	4.51	0.074	0.708	5.1.3.1	NA
4	0.066	3f4wA	0.496	4.50	0.103	0.697	4.1.2.-	89,172
5	0.066	2czfA	0.498	4.53	0.048	0.704	4.1.1.23	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	0.53	2z06B	0.953	0.96	0.371	0.977	1.83	CO	Download	8,173,174,175,176,194,196
2	0.53	2z06D	0.952	0.98	0.371	0.977	1.75	CO	Download	39,67,68,149,174
3	0.50	1t71A	0.950	1.42	0.379	0.996	1.38	FE	Download	8,39,40,176
4	0.26	1t700	0.961	0.89	0.377	0.981	1.42	III	Download	118,120,126,128,129,151,153,154,155,157,158,161,162,175,177,178,179,180,181,183,193,201,202,203,204,205,209,213,216,217,219,254

	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]