[back]

COFACTOR result for job id 76504

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

User Input

>76504 (224 residues)
MSSNKILDRDLDQLRSLIENMIEETKIQYANSYLVIKEENKLIDAQKVIEHDKIINDMQN
EFTSIALWKISKQKLVAKDLRLAIGGILITREIERIADYSKGISKFFIYYKPNEKHLLMI
SELYELVVEMLDIFSDIFENLKVDKEQQVLSLEEKINTKFRSFYDQLIDDIRQKTTKAEA
EEIAAVLKQMFNLERAGDNLLNVQEIINFIKTSKFIEKTEKINK

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	1sumB	0.96	0.69	0.183	0.973	Download
2	4q25A	0.90	0.95	0.188	0.929	Download
3	1xwmA	0.90	1.27	0.219	0.938	Download
4	2i0mA	0.89	1.25	0.188	0.924	Download
5	1t72A	0.87	1.49	0.163	0.902	Download
6	3l39A	0.76	2.45	0.102	0.875	Download
7	2oltC	0.69	3.05	0.073	0.848	Download
8	2bkpA1	0.40	1.63	0.147	0.420	Download
9	4wrtA	0.36	5.76	0.035	0.612	Download
10	2j9wA	0.31	3.72	0.042	0.411	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:0042803	0.86	protein homodimerization activity
GO:0022857	0.76	transmembrane transporter activity
GO:0022804	0.74	active transmembrane transporter activity
GO:0003824	0.72	catalytic activity
GO:0015075	0.71	ion transmembrane transporter activity
GO:0008509	0.69	anion transmembrane transporter activity
GO:0008324	0.69	cation transmembrane transporter activity
GO:0022853	0.68	active ion transmembrane transporter activity
GO:0015114	0.68	phosphate ion transmembrane transporter activity
GO:0015077	0.68	monovalent inorganic cation transmembrane transporter activity
GO:0015321	0.67	sodium-dependent phosphate transmembrane transporter activity
GO:0005436	0.67	sodium:phosphate symporter activity
GO:0005315	0.67	inorganic phosphate transmembrane transporter 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:0065007	1.00	biological regulation
GO:0009987	0.98	cellular process
GO:0030643	0.95	cellular phosphate ion homeostasis
GO:0031324	0.91	negative regulation of cellular metabolic process
GO:0019220	0.91	regulation of phosphate metabolic process
GO:0045936	0.90	negative regulation of phosphate metabolic process
GO:2000186	0.86	negative regulation of phosphate transmembrane transport
GO:0008152	0.52	metabolic 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:0005737	1.00	cytoplasm
GO:0016020	0.80	membrane
GO:0005886	0.76	plasma membrane
GO:0044444	0.58	cytoplasmic 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	3kb9A	0.450	4.56	0.082	0.643	4.2.3.37	101
2	0.060	1qleC	0.445	4.27	0.055	0.625	1.9.3.1	93
3	0.060	3hq2B	0.555	5.33	0.077	0.875	3.4.24.-	38
4	0.060	1h2rL	0.447	5.18	0.043	0.728	1.12.2.1	97
5	0.060	1wgzA	0.487	5.57	0.033	0.790	3.4.24.66	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	0.05	2i0m0	0.885	1.25	0.188	0.924	0.89	III	Download	52,53,56,59,80,84,87,92,94,95,98,188,195,202,206
2	0.01	2xy9A	0.502	5.77	0.062	0.862	0.61	UUU	Download	100,103,104
3	0.01	3tj5A	0.375	4.58	0.060	0.531	0.45	III	Download	99,102,105,194,198,202,205
4	0.01	3s90A	0.338	5.09	0.034	0.513	0.48	III	Download	102,103,105,106,109,150,164,194,198,201,202,205
5	0.01	1zw2A	0.420	4.28	0.081	0.598	0.47	III	Download	92,96,99,103,107,153,160,194,198
6	0.01	3tj6A	0.350	5.14	0.047	0.536	0.48	III	Download	95,96,106,109,110,157,181,187,191,195,198,199

	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]