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COFACTOR result for job id 76578

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

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>76578 (202 residues)
MNSIKFGIFYSKQFNSLLVSFFNKKVTSTQQINNITILKNNDEIIGANIFNVDPNLNLKS
GFCSEDPKAVNYVIQALKNIYEVKQELQFVIGRIIECEPIEGTHLNICQVDIKSEILQII
CGASNARKKVVCVVATLNSWLPNGQQIVQSKIRGVDSFGMLCSYKELNIENDQQGIIELG
SEYNNKIGESFWKEYYAKQDQV

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	3bu2A	0.85	1.07	0.281	0.881	Download
2	4p71A	0.53	1.83	0.244	0.559	Download
3	3pcoB	0.53	1.53	0.250	0.554	Download
4	2iy5B	0.51	2.00	0.212	0.554	Download
5	2rhqB	0.51	1.80	0.255	0.545	Download
6	2e8gA	0.50	3.68	0.112	0.629	Download
7	1ntgA	0.44	3.31	0.193	0.515	Download
8	1e7zA	0.43	2.84	0.173	0.500	Download
9	3ersX	0.42	2.83	0.200	0.490	Download
10	2cwpA	0.41	2.45	0.208	0.465	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	0.95	catalytic activity
GO:0016874	0.87	ligase activity
GO:0004812	0.86	aminoacyl-tRNA ligase activity
GO:0004826	0.75	phenylalanine-tRNA ligase activity
GO:1901363	0.73	heterocyclic compound binding
GO:0097159	0.73	organic cyclic compound binding
GO:0003676	0.72	nucleic acid binding
GO:0003723	0.70	RNA binding
GO:0000049	0.66	tRNA binding
GO:0036094	0.54	small molecule binding
GO:0043167	0.53	ion binding
GO:0035639	0.53	purine ribonucleoside triphosphate binding
GO:0032555	0.53	purine ribonucleotide binding
GO:0030554	0.53	adenyl nucleotide binding
GO:0005524	0.52	ATP binding
GO:0046872	0.50	metal 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:

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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:0016070	1.00	RNA metabolic process
GO:0006520	1.00	cellular amino acid metabolic process
GO:0006418	0.99	tRNA aminoacylation for protein translation
GO:1901576	0.65	organic substance biosynthetic process
GO:0044249	0.65	cellular biosynthetic process
GO:0044271	0.62	cellular nitrogen compound biosynthetic process
GO:1901566	0.60	organonitrogen compound biosynthetic process
GO:0009059	0.59	macromolecule biosynthetic process
GO:0034645	0.58	cellular macromolecule biosynthetic process
GO:0044267	0.57	cellular protein metabolic process
GO:0043043	0.56	peptide biosynthetic process
GO:0006412	0.55	translation

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:0044444	1.00	cytoplasmic part
GO:0005737	1.00	cytoplasm
GO:0032991	0.86	macromolecular complex
GO:0043234	0.80	protein complex
GO:1902494	0.60	catalytic complex
GO:0009328	0.59	phenylalanine-tRNA ligase complex
GO:0005829	0.55	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	0.060	1llwA	0.384	5.70	0.057	0.678	1.4.7.1	NA
2	0.060	1obaA	0.388	5.40	0.052	0.658	3.2.1.17	124
3	0.060	1h09A	0.390	5.36	0.065	0.658	3.2.1.17	NA
4	0.060	2psnC	0.386	5.48	0.032	0.668	4.2.1.11	NA
5	0.060	3b3fA	0.382	5.70	0.031	0.673	2.1.1.125	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	0.03	3ers0	0.416	2.83	0.200	0.490	0.93	III	Download	91,121,122,130,135,148,160,161,162,163,164,174,177,178,179,183,185,189,190,191,192,193
2	0.03	1mkh0	0.404	2.54	0.202	0.460	0.93	III	Download	91,129,132,136,137,148,149,160,162,163,178,179,180,182,185,186,190,191,192
3	0.01	2vdcA	0.408	5.74	0.054	0.733	0.67	F3S	Download	97,98,99,100,101,102,103,122

	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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