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COFACTOR result for job id 76559

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

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>76559 (237 residues)
MNYKYKTVLLKLSGEALKGDAEVYDKKCLDNIASQIVHLAKNGLKLAIVIGGGNIWRGKL
GENIGMDAINADYMGMLATVMNGLALESTITKMGYDKIKVYSSLPIKTVTDDYNFKKARI
KMNEGFISIFVGGTGYSYFTTDTNATIRAIEIGADVILMAKNGVKGVYDKDPKQHSDAKF
IKRLTHQEVVDKQLRIMDLTAATLAKDANLKIEVFDMSGDNNIIKVLENKLESTIIE

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	2jjxA	0.97	0.88	0.374	0.992	Download
2	3ek6A	0.95	1.46	0.430	0.992	Download
3	2bneB	0.95	1.44	0.400	0.992	Download
4	1z9dA	0.93	0.94	0.407	0.954	Download
5	4a7wA	0.92	1.18	0.415	0.945	Download
6	2va1B	0.92	1.51	0.367	0.962	Download
7	1ybdA	0.91	1.15	0.390	0.941	Download
8	3nwyA	0.91	1.39	0.385	0.954	Download
9	6gx4B	0.80	2.29	0.220	0.903	Download
10	2rd5B	0.80	2.86	0.176	0.932	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:0016772	0.99	transferase activity, transferring phosphorus-containing groups
GO:0016301	0.98	kinase activity
GO:0009041	0.96	uridylate kinase activity
GO:1901363	0.94	heterocyclic compound binding
GO:0097159	0.94	organic cyclic compound binding
GO:0033862	0.93	UMP kinase activity
GO:0005524	0.92	ATP binding
GO:0042802	0.55	identical protein binding

Download full result of the above consensus prediction.

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(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:0071704	1.00	organic substance metabolic process
GO:0044763	1.00	single-organism cellular process
GO:0044281	1.00	small molecule metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0006807	1.00	nitrogen compound metabolic process
GO:1901566	0.98	organonitrogen compound biosynthetic process
GO:0044249	0.98	cellular biosynthetic process
GO:0006139	0.98	nucleobase-containing compound metabolic process
GO:0055086	0.97	nucleobase-containing small molecule metabolic process
GO:0044711	0.97	single-organism biosynthetic process
GO:0044271	0.96	cellular nitrogen compound biosynthetic process
GO:0009165	0.94	nucleotide biosynthetic process
GO:0046134	0.93	pyrimidine nucleoside biosynthetic process
GO:0009260	0.93	ribonucleotide biosynthetic process
GO:0006221	0.93	pyrimidine nucleotide biosynthetic process
GO:0046940	0.92	nucleoside monophosphate phosphorylation
GO:0044210	0.92	'de novo' CTP biosynthetic process
GO:0016310	0.92	phosphorylation
GO:0006225	0.82	UDP biosynthetic process
GO:0019752	0.54	carboxylic acid metabolic process
GO:0006520	0.53	cellular amino acid metabolic process
GO:0044283	0.52	small molecule 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:0044424	1.00	intracellular part
GO:0005737	0.91	cytoplasm
GO:0044444	0.87	cytoplasmic part
GO:0005829	0.54	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	0.648	2a1fE	0.942	0.90	0.425	0.962	2.7.4.22	13,15,52,75,78,80,134,140,142,198
2	0.628	2bneB	0.946	1.44	0.400	0.992	2.7.4.22	15,53,75,77,80,84,134,140,142,198
3	0.618	3ek6A	0.950	1.46	0.430	0.992	2.7.4.22	12,16,50,52,75,77,79,84,130,134,140,142
4	0.569	1z9dA	0.929	0.94	0.407	0.954	2.7.4.22	12,15,50,52,75,79,84,100,142
5	0.566	2va1B	0.917	1.51	0.367	0.962	2.7.4.22	11,13,53,56,75,79,133,135,140,142,147,198

	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	0.74	2bnfA	0.963	1.02	0.402	0.987	1.52	UTP	Download	11,13,14,51,52,53,56,57,72,75,76,134,136,137,139,140,141
2	0.62	2v4yB	0.946	0.90	0.402	0.966	1.83	GTP	Download	13,14,15,51,52,53,140,141
3	0.27	2v5hD	0.782	2.93	0.158	0.924	0.91	NLG	Download	51,52,53,56,139,142
4	0.06	2j4jE	0.789	2.40	0.255	0.894	1.00	ACP	Download	11,13,14,15,52,53,57,161,162,164,166,168,170,171

	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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