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COFACTOR result for job id 76327

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

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>76327 (303 residues)
MITNETKPILLIDGYHLLHKGYYGTLKRTIVSKNKDGIVINAIYSFVANILKFVQSDRYH
SVIVAFDFDENCWRKELYSEYKAKRKPTPIDLVPQLQIARDFLTSANISWYEKYNYEGDD
VIGSICRIANKLGYDVCILTNDKDIYQLVNNKTSIITNISKKEKTKIIKPQQVYEHFLCQ
PNQVADIKAILGDQSDNIKGVKYIKRKQAENLINKYENVENILAHINELNEPLKTIISEN
KQLIIDNKKITKILTNVKLGRINFKPTKITYYGLIRFLKEQEMYAFIKPIRRYLDRTNKN
LKK

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	6c33A	0.94	0.67	0.247	0.951	Download
2	4wa8A	0.72	3.28	0.160	0.868	Download
3	1ut5B	0.72	2.19	0.218	0.795	Download
4	5t9jA	0.72	3.54	0.097	0.888	Download
5	2ihnA	0.72	3.23	0.144	0.855	Download
6	3zd8A	0.72	1.93	0.186	0.779	Download
7	1a76A	0.71	3.80	0.161	0.881	Download
8	1rxwA	0.69	3.59	0.165	0.848	Download
9	1bgxT	0.68	3.61	0.225	0.848	Download
10	1a65A	0.35	6.68	0.037	0.624	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	1.00	catalytic activity
GO:0016787	0.99	hydrolase activity
GO:0004518	0.98	nuclease activity
GO:0016779	0.95	nucleotidyltransferase activity
GO:0004527	0.94	exonuclease activity
GO:0003887	0.94	DNA-directed DNA polymerase activity
GO:0008409	0.92	5'-3' exonuclease activity
GO:0004536	0.65	deoxyribonuclease activity
GO:0004519	0.65	endonuclease activity
GO:0048256	0.64	flap endonuclease activity
GO:0016893	0.63	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
GO:0017108	0.62	5'-flap endonuclease activity
GO:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound binding
GO:0043167	0.52	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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0034641	1.00	cellular nitrogen compound metabolic process
GO:0006259	0.99	DNA metabolic process
GO:1901576	0.97	organic substance biosynthetic process
GO:0044249	0.97	cellular biosynthetic process
GO:0034645	0.96	cellular macromolecule biosynthetic process
GO:0006260	0.93	DNA replication
GO:0006261	0.86	DNA-dependent DNA replication
GO:0050896	0.83	response to stimulus
GO:0033554	0.82	cellular response to stress
GO:0006974	0.81	cellular response to DNA damage stimulus
GO:0006281	0.80	DNA repair
GO:0044271	0.56	cellular nitrogen compound biosynthetic process
GO:1901362	0.54	organic cyclic compound biosynthetic process
GO:0019438	0.54	aromatic compound biosynthetic process
GO:0018130	0.54	heterocycle biosynthetic process
GO:0034654	0.53	nucleobase-containing compound biosynthetic 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:0005634	1.00	nucleus
GO:0005737	0.94	cytoplasm
GO:0044444	0.66	cytoplasmic part
GO:0032991	0.51	macromolecular complex

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	0.492	1exnB	0.725	2.18	0.218	0.795	3.1.11.3	82
2	0.132	1xo1A	0.679	2.17	0.220	0.746	3.1.11.3	NA
3	0.101	1rxvA	0.700	3.57	0.174	0.858	3.1.-.-	67,197
4	0.093	2ihnA	0.723	3.23	0.144	0.855	3.1.26.4	82
5	0.086	1mc8A	0.693	4.03	0.116	0.884	3.1.-.-	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	0.29	1tauA	0.738	3.00	0.254	0.871	1.58	ZN	Download	13,16,119,142
2	0.12	3qebZ	0.624	3.84	0.120	0.776	1.03	MN	Download	119,142,144
3	0.12	1ul1X	0.682	3.88	0.114	0.855	0.84	MG	Download	13,67,117,119
4	0.03	2ihnA	0.723	3.23	0.144	0.855	0.81	QNA	Download	16,19,20,23,69,90,93,97,141,143,161,195

	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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