[back]

COFACTOR result for job id 76599

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

User Input

>76599 (251 residues)
MITIKNQEQIQKMKIAGQVLAKGLNLLKSMIKPGVNCLDLDKAFEEFIKQNGCESNFKNY
QGFPKTICISINDQLIHGIPKNRILQNGDIVSIDAGCMYQKWHADSAFTMVCGIANDKKN
DILIRVTEKALDLAIAELKPGIRVGTIGSIIQNYVESHNFSVPRDYTGHGIGLALHEDPY
IPNYGIPNTGVRLQENMVICIEPMVQMGTYKTKLADDNWTVYSADHSMTAHFEHTILITK
DGCEVLTKEER

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	3tb5A	0.99	0.58	0.388	0.996	Download
2	4matA	0.97	1.25	0.396	0.996	Download
3	3s6bA	0.97	1.33	0.363	1.000	Download
4	3mr1A	0.97	0.75	0.429	0.984	Download
5	2b3lA	0.97	1.27	0.348	0.996	Download
6	1o0xA	0.97	0.92	0.452	0.988	Download
7	4fo7A	0.96	1.11	0.388	0.996	Download
8	4fukA	0.96	0.90	0.308	0.984	Download
9	3iu7A	0.96	1.16	0.351	0.988	Download
10	3tavA	0.95	1.30	0.361	0.992	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:0016787	1.00	hydrolase activity
GO:0008238	0.99	exopeptidase activity
GO:0008235	0.97	metalloexopeptidase activity
GO:0004177	0.97	aminopeptidase activity
GO:0070006	0.94	metalloaminopeptidase activity
GO:0043167	0.60	ion binding
GO:0046914	0.58	transition metal ion binding
GO:0005506	0.51	iron ion 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	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0019538	0.99	protein metabolic process
GO:0044267	0.97	cellular protein metabolic process
GO:0006508	0.97	proteolysis
GO:0006464	0.95	cellular protein modification process
GO:0070084	0.92	protein initiator methionine removal
GO:0006807	0.71	nitrogen compound metabolic process
GO:0034641	0.65	cellular nitrogen compound metabolic process
GO:1901564	0.60	organonitrogen compound metabolic process
GO:0009058	0.51	biosynthetic process
GO:1901576	0.50	organic substance biosynthetic process
GO:0044249	0.50	cellular 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	0.95	cytoplasmic part
GO:0043226	0.84	organelle
GO:0043229	0.81	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005737	0.73	cytoplasm
GO:0044446	0.61	intracellular organelle part
GO:0032991	0.54	macromolecular complex
GO:0005829	0.50	cytosol

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	0.495	1pv9B	0.735	1.83	0.313	0.789	3.4.13.9	176,202
2	0.403	2dfiA	0.868	1.78	0.273	0.920	3.4.11.18	202
3	0.394	2b3lA	0.968	1.27	0.348	0.996	3.4.11.18	202
4	0.346	1r58A	0.862	2.03	0.244	0.936	3.4.11.18	202
5	0.277	1wn1A	0.805	2.07	0.240	0.880	3.4.-.-	39

	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	0.75	2gg0A	0.966	1.22	0.398	0.992	1.52	U11	Download	57,60,68,77,94,96,105,166,167,169,175,176,202,233
2	0.75	3mr1A	0.969	0.75	0.429	0.984	1.58	MN	Download	105,169,200,202,233
3	0.61	2gg5A	0.966	1.32	0.396	0.996	1.19	U19	Download	60,63,68,94,105,169,175,176,202,219
4	0.56	2g6pA	0.970	1.25	0.348	0.996	1.27	CO	Download	94,96,105,107,233
5	0.51	1qxwA	0.939	1.52	0.331	0.988	0.96	M1C	Download	76,77,94,105,166,169,202,204,233
6	0.37	2nq6A	0.969	1.26	0.348	0.996	1.04	HM4	Download	57,60,61,63,68,77,167,176,219
7	0.06	1xgs0	0.867	1.50	0.284	0.912	1.24	III	Download	77,143,152,156,164,165,166,176,179,180,184,185,186,190,211,214,221

	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]