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COFACTOR result for job id 76288

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>76288 (266 residues)
MKAKKYYGQNFISDLNLINKIVDVLDQNKDQLIIEIGPGKGALTKELVKRFDKVVVIEID
KDMVEILKTKFNHSNLEIIQADVLEIDLKQLISKYDYKNISIISNTPYYITSEILFKTLQ
ISDLLTKAVFMLQKEVALRICSNKNENNYNNLSIACQFYSQRNFEFVVNKKMFYPIPKVD
SAIISLTFNDIYKKQVNNDKKFIDFVRLLFNNKRKTILNNLNNIIQNKNKALEYLNTLNI
SSNLRPEQLDIDQYIKLFNLIYNSNF

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	1qyrA	0.91	1.17	0.315	0.944	Download
2	3fuxC	0.90	1.37	0.264	0.940	Download
3	3uzuA	0.90	1.80	0.271	0.955	Download
4	6ifsA	0.89	2.34	0.395	1.000	Download
5	4gc5A	0.89	2.23	0.260	0.985	Download
6	3fycA	0.89	1.70	0.343	0.944	Download
7	3tqsA	0.88	1.26	0.325	0.913	Download
8	1zq9A	0.88	1.57	0.283	0.929	Download
9	3ftfA	0.86	1.65	0.320	0.917	Download
10	2h1rB	0.85	1.95	0.280	0.925	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:0000179	1.00	rRNA (adenine-N6,N6-)-dimethyltransferase activity
GO:0052908	0.84	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
GO:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound binding
GO:0003676	0.53	nucleic acid binding
GO:0003723	0.51	RNA 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:0009987	0.99	cellular process
GO:0008152	0.97	metabolic process
GO:0071704	0.96	organic substance metabolic process
GO:0044238	0.96	primary metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0006807	0.96	nitrogen compound metabolic process
GO:0034641	0.94	cellular nitrogen compound metabolic process
GO:0043170	0.93	macromolecule metabolic process
GO:0006139	0.92	nucleobase-containing compound metabolic process
GO:0044260	0.90	cellular macromolecule metabolic process
GO:0090304	0.89	nucleic acid metabolic process
GO:0016070	0.88	RNA metabolic process
GO:0071840	0.73	cellular component organization or biogenesis
GO:0016043	0.72	cellular component organization
GO:0034660	0.69	ncRNA metabolic process
GO:0006396	0.67	RNA processing
GO:0043412	0.66	macromolecule modification
GO:0034470	0.66	ncRNA processing
GO:0009451	0.65	RNA modification
GO:0006364	0.64	rRNA processing
GO:0000154	0.62	rRNA modification
GO:1901576	0.61	organic substance biosynthetic process
GO:0044249	0.61	cellular biosynthetic process
GO:0044271	0.58	cellular nitrogen compound biosynthetic process
GO:0009059	0.56	macromolecule biosynthetic process
GO:0050896	0.52	response to stimulus
GO:0034645	0.52	cellular macromolecule biosynthetic process
GO:0032259	0.51	methylation

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	0.88	cytoplasmic part
GO:0005737	0.78	cytoplasm
GO:0044446	0.70	intracellular organelle part
GO:0044429	0.57	mitochondrial part
GO:0005759	0.51	mitochondrial matrix

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	0.421	3fuxC	0.904	1.37	0.264	0.940	2.1.1.-	37,105
2	0.195	1zq9A	0.878	1.57	0.283	0.929	2.1.1.-	37,105
3	0.113	1qyrA	0.914	1.17	0.315	0.944	2.1.1.-	37,58,105
4	0.111	1yubA	0.635	3.94	0.182	0.827	2.1.1.48	37,58,105
5	0.101	3fycA	0.886	1.70	0.343	0.944	2.1.1.-	37,58,105

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.82	3grrA	0.881	1.66	0.341	0.936	1.50	SAH	Download	9,10,11,12,37,38,39,57,58,59,60,63,81,82,83,105,107
	2	0.58	3gruA	0.880	1.66	0.341	0.936	1.61	AMP	Download	58,59,60,81,82,83,107

	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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