[back]

COFACTOR result for job id 76321

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

User Input

>76321 (318 residues)
MKILAIESSCDEFSISIIDNNKILTNVISSQIKDHQVFGGVVPELAARLHVQNFNWVLKA
ALTEANLSIKDIDYVAYTKSPGLIGSLIVGKLVAETISLYINKPILALDHIQGHIFGASI
ENEFIYPVLAMVVSGGHTQIEIINSANDFQIIGSTRDDAIGECYDKVARVLGLSYPGGPI
LDKLALKGNKDSYLLPVLKDEDNYDFSYSGLKTACINLIHNLNQKNQEINLEDFAASFQY
TATNIVEKKLEKAIKEFKPKTLTVAGGVSANSEIRKIILRLGEKYSIKNTFVPKMSYCTD
NAAMIAKLAYEKILLNNK

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	3zetB	0.99	0.42	0.390	0.991	Download
2	3enoA	0.90	1.74	0.320	0.953	Download
3	2ivoA	0.88	2.08	0.323	0.953	Download
4	3en9A	0.86	2.16	0.306	0.940	Download
5	4k25A	0.81	2.81	0.263	0.934	Download
6	3venA	0.75	3.90	0.140	0.928	Download
7	3vthA	0.74	3.13	0.136	0.880	Download
8	3r6mA	0.48	3.26	0.144	0.566	Download
9	1okjB	0.48	3.83	0.127	0.598	Download
10	2v7yA1	0.39	4.12	0.105	0.513	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	0.98	catalytic activity
GO:0016787	0.93	hydrolase activity
GO:0070011	0.89	peptidase activity, acting on L-amino acid peptides
GO:0004175	0.88	endopeptidase activity
GO:0008237	0.86	metallopeptidase activity
GO:0004222	0.85	metalloendopeptidase activity
GO:0016740	0.82	transferase activity
GO:0043167	0.78	ion binding
GO:0061711	0.77	N(6)-L-threonylcarbamoyladenine synthase
GO:0046872	0.75	metal ion binding
GO:0005506	0.74	iron ion binding
GO:0042802	0.55	identical protein binding
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0000287	0.52	magnesium 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:0044238	1.00	primary metabolic process
GO:0043170	1.00	macromolecule metabolic process
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:0070525	0.98	tRNA threonylcarbamoyladenosine metabolic process
GO:0006400	0.98	tRNA modification
GO:0002949	0.97	tRNA threonylcarbamoyladenosine modification
GO:0019538	0.72	protein metabolic process
GO:0006508	0.70	proteolysis

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:0043234	1.00	protein complex
GO:0000408	0.99	EKC/KEOPS complex
GO:0044444	0.69	cytoplasmic part
GO:0005737	0.62	cytoplasm

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	0.435	2ivpA	0.890	1.86	0.323	0.953	3.4.24.57	81,83,134,136,139,155,176,178,268,300
2	0.090	2ewsA	0.603	3.78	0.129	0.758	2.7.1.33	152,155
3	0.067	3bf3A	0.572	3.44	0.121	0.701	2.7.1.33	80,266
4	0.067	2aa4A	0.579	4.31	0.114	0.770	2.7.1.60	NA
5	0.067	2aa4B	0.578	4.44	0.117	0.777	2.7.1.60	134,136,266,300

	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	0.34	2ivnA	0.890	1.86	0.323	0.953	1.15	ANP	Download	9,10,110,132,134,135,136,161,165,178,179,182,267,268,270,271,295,299,300
2	0.07	3enhA	0.832	2.24	0.317	0.909	1.21	TBR	Download	135,162,165,169
3	0.03	1huxA	0.640	3.64	0.148	0.805	0.55	SF4	Download	45,46,47,85,86

	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]