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COFACTOR result for job id 76672

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>76672 (391 residues)
MSFDYFLNNKSLNKINRKLENNIFKTPLPYSLKSKFNYNFIDKISKDRFLSYYTKAFYDD
FLESSVEKKLKTYELALLVMNETKIDLDFLSVLKIFRDIKKGKTPTNYLERLIFNIIYAY
EYIKKPKVLINEENLEMLISILLVGLEYDLDLKTNYYRTPKTKTLISNVLSSQLISKELE
NLLDYLKFLQANNLCTYSQTYLIFSTLVLISPFQKYNLIFATLLSQWISFQYNNSYKLVI
PICHFLKNQNEYMYELENLLNNDFNADKLINLFNIDYLKNINMYNHASCIYKWVKKDKKR
LFIFEDDLSFFVLILILQNTKNLSFNNIKTLLTINKIKLFTDEQIKSTLANLIANQVLQT
TSTSVVKYVLVDKYLEKSKYLVNMKGLYNGL

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	3eqxA	0.87	1.36	0.108	0.898	Download
2	4rglA	0.58	3.31	0.091	0.665	Download
3	3cucB	0.54	2.75	0.131	0.604	Download
4	4u04A	0.53	2.98	0.115	0.593	Download
5	3n3uA	0.47	4.05	0.104	0.568	Download
6	4bepA	0.45	4.39	0.053	0.552	Download
7	4x2cA	0.44	3.08	0.168	0.501	Download
8	3shgA	0.36	2.89	0.068	0.407	Download
9	2g03A	0.35	2.89	0.084	0.386	Download
10	3a9iA	0.27	6.79	0.046	0.430	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:0070566	0.94	adenylyltransferase activity
GO:0070733	0.90	protein adenylyltransferase activity

Download full result of the above consensus prediction.

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(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:

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[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:0044267	0.95	cellular protein metabolic process
GO:0043412	0.95	macromolecule modification
GO:0018117	0.92	protein adenylylation

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:0005886	0.93	plasma membrane
GO:0044424	0.64	intracellular part

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	2e9bA	0.377	7.06	0.030	0.644	3.2.1.41	118,124
2	0.060	3b8eC	0.347	6.75	0.032	0.570	3.6.3.9	NA
3	0.060	1mo7A	0.225	5.84	0.057	0.338	3.6.3.9	NA
4	0.060	1llwA	0.373	7.30	0.062	0.655	1.4.7.1	NA
5	0.060	2fhbA	0.402	7.00	0.061	0.688	3.2.1.41	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	0.01	2nudA	0.403	3.78	0.088	0.483	0.13	III	Download	89,93,135,138,139,142,143,144
2	0.01	1mw0A	0.380	7.08	0.037	0.650	0.21	UUU	Download	103,140,141,145
3	0.01	1ln6A	0.294	6.12	0.050	0.440	0.23	RET	Download	79,80,113,114
4	0.01	2ksbA	0.391	6.11	0.056	0.593	0.15	III	Download	103,114,117
5	0.01	2e8zB	0.382	7.10	0.040	0.652	0.24	GLC	Download	118,140,144,145

	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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