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COFACTOR result for job id 76335

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>76335 (290 residues)
MTIRKAVIPCAGFGTRFLPFTKSQAKEMLPIIDTPTIEYIVKEAIDSGIKEILIVLNDKK
SEIMNYFSRNIELERFLYNKDKINELEQIKTKYDADIHYIMQDEPLGLGHAISLCKGFIN
NESFAVLLGDDLFKCQTPAIKQLMDLYEEKHSTILGTILIDKKDCKKYGICKTESSNDNV
YKVCSVVEKPDEQNAPSNVAIAGRYILTPEIFNYLDLQLKGETGEIELTDSILRTIKDVD
CYAKVIDGKRYDIGNKLGYLEAFVDFASNRDDTKNEFIKIVKKLNEEETL

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	5i1fA	0.98	0.38	0.381	0.986	Download
2	2pa4B	0.94	1.62	0.353	0.997	Download
3	2ux8G	0.91	1.74	0.358	0.966	Download
4	3jujA	0.89	1.47	0.385	0.931	Download
5	2e3dC	0.88	2.23	0.337	0.952	Download
6	3d8vA	0.77	2.88	0.169	0.876	Download
7	2ggoA	0.76	2.44	0.253	0.838	Download
8	1g3lD	0.76	2.46	0.238	0.838	Download
9	1lvwA	0.75	2.52	0.203	0.841	Download
10	5l6sA	0.75	3.07	0.176	0.872	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:0016779	1.00	nucleotidyltransferase activity
GO:0070569	0.96	uridylyltransferase activity
GO:0003983	0.95	UTP:glucose-1-phosphate uridylyltransferase activity
GO:0043167	0.58	ion binding
GO:0046872	0.55	metal ion 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:

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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:0044238	1.00	primary metabolic process
GO:0009987	1.00	cellular process
GO:0044237	0.99	cellular metabolic process
GO:1901360	0.98	organic cyclic compound metabolic process
GO:0046483	0.98	heterocycle metabolic process
GO:0034641	0.98	cellular nitrogen compound metabolic process
GO:0006725	0.98	cellular aromatic compound metabolic process
GO:1901135	0.97	carbohydrate derivative metabolic process
GO:0006139	0.97	nucleobase-containing compound metabolic process
GO:0009225	0.96	nucleotide-sugar metabolic process
GO:0006011	0.94	UDP-glucose metabolic process
GO:1901576	0.85	organic substance biosynthetic process
GO:0005975	0.85	carbohydrate metabolic process
GO:0043170	0.83	macromolecule metabolic process
GO:0044249	0.81	cellular biosynthetic process
GO:0044699	0.80	single-organism process
GO:0044723	0.78	single-organism carbohydrate metabolic process
GO:0044260	0.74	cellular macromolecule metabolic process
GO:0005976	0.71	polysaccharide metabolic process
GO:0044281	0.69	small molecule metabolic process
GO:0034645	0.68	cellular macromolecule biosynthetic process
GO:0016051	0.68	carbohydrate biosynthetic process
GO:0044763	0.67	single-organism cellular process
GO:0044262	0.64	cellular carbohydrate metabolic process
GO:1901137	0.63	carbohydrate derivative biosynthetic process
GO:0044264	0.63	cellular polysaccharide metabolic process
GO:0000271	0.63	polysaccharide biosynthetic process
GO:0033692	0.62	cellular polysaccharide biosynthetic process
GO:0005996	0.58	monosaccharide metabolic process
GO:0019318	0.56	hexose metabolic 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:0044444	0.90	cytoplasmic part
GO:0005829	0.83	cytosol
GO:0005737	0.65	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	0.649	2e3dC	0.877	2.23	0.337	0.952	2.7.7.9	16
2	0.641	2ux8G	0.914	1.74	0.358	0.966	2.7.7.9	16
3	0.614	2ux8A	0.824	1.51	0.355	0.866	2.7.7.9	16
4	0.559	1lvwA	0.753	2.52	0.203	0.841	2.7.7.24	16
5	0.526	3hl3A	0.739	2.39	0.235	0.810	2.7.7.24	16

	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	0.76	3jukC	0.873	1.19	0.391	0.897	1.49	UPG	Download	9,11,12,26,27,102,105,107,108,111,128,130,131,168,169,188,189,201,202,229
2	0.41	1g0rC	0.757	2.52	0.236	0.838	1.29	THM	Download	9,11,27,102,105,106,107,108,130
3	0.37	3pkpA	0.754	2.50	0.211	0.841	1.21	DTP	Download	9,11,12,13,14,15,16,26,27,102,104,105,129,130

	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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